Re: [Paraview] Confirming that pvserver runs with OSMesa + OpenSWR driver on cpu only compute nodes

[Burlen Loring]

Hi Fabrizio,

in the shell where you launch your pvserver you could set the following 
environment variables:


   export LIBGL_ALWAYS_SOFTWARE=1 GALLIUM_DRIVER=swr

this is bash syntax, your shell may be different. When I do that I see 
"SWR detected AVX" print in that shell when the connection to paraview 
client is made.


Burlen

On 12/21/2017 08:02 AM, Fabrizio Bisetti wrote:

Hello there:

I've successfully built and installed the following OSMesa rendering stack 
(from source) for use on CPU only compute nodes of a small cluster

I've then built Paraview 5.4.0 (from source). The pvserver runs on a compute 
node and we connect to it from a remote Paraview client via forward connection 
with SSH tunneling.

I am having trouble confirming which driver the pvserver uses for rendering. My 
understanding is that OSMesa gets compiled with various cpu-based driver 
options, i.e. soft pipe (classic OSMesa), llvmpipe, and swr.

I would like to ensure that swr (OpenSWR) is being used.

Note that one complicating factor is that the CPU-based compute nodes do not 
have any X installed and I've compiled only OSMesa (see below). Thus, I cannot 
compile the GLUT based utility glinfo or gears, which could possibly tell me 
how the rendering is done.

Finally, while it seems that one can invoke paraview with a switch 
--mesa-swr-avx2, I am not sure that can be done with pvserver.

Also, even then, how would I confirm this is which driver is being used?

Thank you for any help/pointers.

Fabrizio




**HARDWARE**

Each compute node features two (x2) Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz 
for a total of 28 cores. The compute nodes do not have a GPU.

**SOFTWARE STACK**

Everything is compiled with gcc version 4.8.5 20150623 (Red Hat 4.8.5-11) (GCC) 
on a Linux 3.10.0-514.el7.x86_64 (Centos 7).

Here is the cpu-based rendering stack

1) LLVM 5.0.0

cmake3 -G "Unix Makefiles"  \
-DCMAKE_BUILD_TYPE=Release \
-DLLVM_TARGETS_TO_BUILD=X86 \
-DLLVM_INSTALL_UTILS=TRUE \
-DLLVM_ENABLE_RTTI=TRUE \
-DBUILD_SHARED_LIBS=TRUE \
-DCMAKE_INSTALL_PREFIX=$INSTALLDIR \
../llvm-5.0.0.src

2) Mesa3D 17.3.0

Note that the compute nodes do not have any X servers (X11) nor any other 
OpenGL implementation (e.g. repo based from a yum install)

./configure \
 --disable-xvmc \
 --disable-glx \
 --disable-dri \
 --with-dri-drivers= \
 --with-gallium-drivers=swrast,swr \
 --enable-texture-float \
 --disable-egl \
 --disable-gbm \
 --with-platforms= \
 --enable-gallium-osmesa \
 --enable-llvm \
 --prefix=$INSTALLDIR

3) GLU 9.0.0

SITE_MESA_LIB=/path/to/mesa/install/above

PKG_CONFIG_PATH="$SITE_MESA_LIB/pkgconfig" \
OSMESA_LIBS="-L$SITE_MESA_LIB -lOSMesa" \
 ./configure --prefix=$INSTALLDIR \
 --enable-osmesa \
 --enable-shared

4) ParaView 5.4.0

I've configured the basic ParaView build as recommended.
I am using OpenMPI 2.1.0 compiled with the system gcc.

The additional OSMesa options are as below:

VTK_USE_X=OFF
VTK_USE_OFFSCREEN:BOOL=ON

OPENGL_INCLUDE_DIR=/path/to/mesa/install/above/include
OPENGL_gl_LIBRARY:FILEPATH=/path/to/mesa/install/above/lib/libOSMesa.so
OPENGL_glu_LIBRARY:FILEPATH=/path/to/glu/install/above/lib/libGLU.so

VTK_OPENGL_HAS_OSMESA:BOOL=ON
OSMESA_INCLUDE_DIR:PATH=/path/to/mesa/install/above/include
OSMESA_LIBRARY:FILEPATH=/path/to/mesa/install/above/lib/libOSMesa.so

Note that I've set everything to point to the OSMesa install directory.
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Re: [Paraview] gpu_shader4 extension is not supported

[Burlen Loring]

Sweet!

On 05/23/2017 12:51 AM, Patrick Begou wrote:
Thanks a lot Burlen, all is running fine now with this setup for mesa 
on the front-end.
With Paraview, I had to add some parameters for ffmpeg-3.3 libraries 
that were not automaticaly loaded and set LD_LIBRARY_PATH to load llvm 
is a separate directory from mesa but all runs fine now:
export 
LD_LIBRARY_PATH=/share/apps/mesa/17.0.6-x11-swr/lib/:$LD_LIBRARY_PATH

export LD_LIBRARY_PATH=/share/apps/llvm/4.0.0/lib:$LD_LIBRARY_PATH

and for cmake:
cmake 
   -DPARAVIEW_ENABLE_FFMPEG=ON \
   -DFFMPEG_ROOT=/share/apps/ffmpeg-3.3-GCC485 \
-DCMAKE_EXE_LINKER_FLAGS="-Wl,-rpath-link=/share/apps/ffmpeg-3.3-GCC485/lib:/share/apps/llvm/4.0.0/lib:/share/apps/mesa/17.0.6-x11-swr/lib 
-L/share/apps/ffmpeg-3.3-GCC485/lib -lswresample -lavutil -lavformat 
-lavcodec -lswscale -lavdevice -lavfilter" \

   -DVTK_FFMPEG_AVCODECID=ON \
...

Burlen Loring wrote:
- one build for the front end with GUI: it has no GPU but a 
windowing system (this is the blocking point at this time) 
OK. to accomplish this, first do a Mesa build configured as 
follows(glx+software rendering)


../mesa-17.0.6/configure --enable-texture-float --enable-glx
--disable-dri --disable-egl --disable-gles1 --disable-gles2
--disable-gbm --disable-driglx-direct --disable-xvmc
--with-gallium-drivers=swrast,swr
--prefix=/work/apps/mesa/17.0.6-x11-swr

make sure ParaView can find it, and configure ParaView as follows

export
LD_LIBRARY_PATH=/work/apps/mesa/17.0.6-x11-swr/lib/:$LD_LIBRARY_PATH
cmake -DOPENGL_INCLUDE_DIR=/work/apps/mesa/17.0.6-x11-swr/include
-DOPENGL_gl_LIBRARY=/work/apps/mesa/17.0.6-x11-swr/lib/libGL.so
~/work/ParaView/

when you run ParaView the "help/about" dialog should report VMWare 
Mesa 17.0.6 Gallium on llvmpipe.


On 05/16/2017 11:18 PM, Patrick Begou wrote:

Yes Burlen,  this is exactly what I try to do:
- one build for the nodes whitout GUI as they have no windowing 
system nor GPU (I build this using the wiki documentation)
- one build for the front end with GUI: it has no GPU but a 
windowing system (this is the blocking point at this time)
- one build on the users workstations where a GPU and a windowing 
system are available (this is working too thanks to the wiki 
documentation)


On the front-end I have a system libGL but too old for Paraview 5 
and it is requested by other commercial softwares. This is why I try 
to build a new mesa from sources for Paraview. I use the module 
environment then to set the LD_LIBRARY_PATH and PATH order to reach 
the right libraries and, as strace show, it seams to work fine. So I 
suppose it is a mesa configuration mistake in my build.


May be should I post on the Mesa forum ?

Patrick


Burlen Loring wrote:
that's the point. this allows you to run without the windowing 
system or GPU on the cluster. Most cluster have neither. If you 
wanted to provide the GUI then I would suggest you have two 
installs of both ParaView and Mesa. One based on OSMesa, the other 
based on some X11 enabled OpenGL. Alternatively you could install 
only the OSMesa capable pvserver as suggested in previous email and 
direct your users to the ParaView GUI enabled binaries that Kitware 
provides on their web site. The latter is what I have been doing.


As an aside, it gets messy when you have two libGL in the same 
build. One need to be very careful about library dependencies. It 
is possible to do this if one is very careful during link time. 
However as far as I know this has not been supported for quite a 
long time in VTK/ParaView, and I think it would require some 
reorganization of VTK OpernGL classes.


Burlen

On 05/16/2017 08:38 AM, Patrick Begou wrote:

Burlen Loring wrote:
../mesa-17.0.2/configure --enable-texture-float --disable-glx 
--disable-dri --disable-egl --disable-gles1 --disable-gles2 
--disable-gbm --disable-driglx-direct --disable-xvmc 
--enable-gallium-osmesa --with-gallium-drivers=swrast,swr 
--prefix=/usr/common/software/ParaView/mesa/17.0.2/


Hi Burlen,

this Mesa setup does not provide libGL requested to build paraview 
with GUI enabled :-(
It is OK for the cluster nodes but not for the frontend where I 
need this GUI even with no GPU installed.


Patrick












--
===
|  Equipe M.O.S.T. |  |
|  Patrick BEGOU   |mailto:patrick.be...@grenoble-inp.fr  |
|  LEGI|  |
|  BP 53 X | Tel 04 76 82 51 35   |
|  38041 GRENOBLE CEDEX| Fax 04 76 82 52 71   |
===


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Re: [Paraview] gpu_shader4 extension is not supported

[Burlen Loring]

- one build for the front end with GUI: it has no GPU but a windowing 
system (this is the blocking point at this time) 
OK. to accomplish this, first do a Mesa build configured as 
follows(glx+software rendering)


   ../mesa-17.0.6/configure --enable-texture-float --enable-glx
   --disable-dri --disable-egl --disable-gles1 --disable-gles2
   --disable-gbm --disable-driglx-direct --disable-xvmc
   --with-gallium-drivers=swrast,swr
   --prefix=/work/apps/mesa/17.0.6-x11-swr

make sure ParaView can find it, and configure ParaView as follows

   export
   LD_LIBRARY_PATH=/work/apps/mesa/17.0.6-x11-swr/lib/:$LD_LIBRARY_PATH
   cmake -DOPENGL_INCLUDE_DIR=/work/apps/mesa/17.0.6-x11-swr/include
   -DOPENGL_gl_LIBRARY=/work/apps/mesa/17.0.6-x11-swr/lib/libGL.so
   ~/work/ParaView/

when you run ParaView the "help/about" dialog should report VMWare Mesa 
17.0.6 Gallium on llvmpipe.


On 05/16/2017 11:18 PM, Patrick Begou wrote:

Yes Burlen,  this is exactly what I try to do:
- one build for the nodes whitout GUI as they have no windowing system 
nor GPU (I build this using the wiki documentation)
- one build for the front end with GUI: it has no GPU but a windowing 
system (this is the blocking point at this time)
- one build on the users workstations where a GPU and a windowing 
system are available (this is working too thanks to the wiki 
documentation)


On the front-end I have a system libGL but too old for Paraview 5 and 
it is requested by other commercial softwares. This is why I try to 
build a new mesa from sources for Paraview. I use the module 
environment then to set the LD_LIBRARY_PATH and PATH order to reach 
the right libraries and, as strace show, it seams to work fine. So I 
suppose it is a mesa configuration mistake in my build.


May be should I post on the Mesa forum ?

Patrick


Burlen Loring wrote:
that's the point. this allows you to run without the windowing system 
or GPU on the cluster. Most cluster have neither. If you wanted to 
provide the GUI then I would suggest you have two installs of both 
ParaView and Mesa. One based on OSMesa, the other based on some X11 
enabled OpenGL. Alternatively you could install only the OSMesa 
capable pvserver as suggested in previous email and direct your users 
to the ParaView GUI enabled binaries that Kitware provides on their 
web site. The latter is what I have been doing.


As an aside, it gets messy when you have two libGL in the same build. 
One need to be very careful about library dependencies. It is 
possible to do this if one is very careful during link time. However 
as far as I know this has not been supported for quite a long time in 
VTK/ParaView, and I think it would require some reorganization of VTK 
OpernGL classes.


Burlen

On 05/16/2017 08:38 AM, Patrick Begou wrote:

Burlen Loring wrote:
../mesa-17.0.2/configure --enable-texture-float --disable-glx 
--disable-dri --disable-egl --disable-gles1 --disable-gles2 
--disable-gbm --disable-driglx-direct --disable-xvmc 
--enable-gallium-osmesa --with-gallium-drivers=swrast,swr 
--prefix=/usr/common/software/ParaView/mesa/17.0.2/


Hi Burlen,

this Mesa setup does not provide libGL requested to build paraview 
with GUI enabled :-(
It is OK for the cluster nodes but not for the frontend where I need 
this GUI even with no GPU installed.


Patrick









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Re: [Paraview] gpu_shader4 extension is not supported

[Burlen Loring]

that's the point. this allows you to run without the windowing system or 
GPU on the cluster. Most cluster have neither. If you wanted to provide 
the GUI then I would suggest you have two installs of both ParaView and 
Mesa. One based on OSMesa, the other based on some X11 enabled OpenGL. 
Alternatively you could install only the OSMesa capable pvserver as 
suggested in previous email and direct your users to the ParaView GUI 
enabled binaries that Kitware provides on their web site. The latter is 
what I have been doing.


As an aside, it gets messy when you have two libGL in the same build. 
One need to be very careful about library dependencies. It is possible 
to do this if one is very careful during link time. However as far as I 
know this has not been supported for quite a long time in VTK/ParaView, 
and I think it would require some reorganization of VTK OpernGL classes.


Burlen

On 05/16/2017 08:38 AM, Patrick Begou wrote:

Burlen Loring wrote:
../mesa-17.0.2/configure --enable-texture-float --disable-glx 
--disable-dri --disable-egl --disable-gles1 --disable-gles2 
--disable-gbm --disable-driglx-direct --disable-xvmc 
--enable-gallium-osmesa --with-gallium-drivers=swrast,swr 
--prefix=/usr/common/software/ParaView/mesa/17.0.2/


Hi Burlen,

this Mesa setup does not provide libGL requested to build paraview 
with GUI enabled :-(
It is OK for the cluster nodes but not for the frontend where I need 
this GUI even with no GPU installed.


Patrick



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Re: [Paraview] gpu_shader4 extension is not supported

[Burlen Loring]

Hi Patrick,

Your output shows you enabled some gpu specific drivers, and GLX. I 
think that is going to screw things up for you. Best to disable all of 
them but the ones you specifically need and to explicitly disable glx.


Here is how I configured OSMesa for a Cray

   ../mesa-17.0.2/configure --enable-texture-float --disable-glx
   --disable-dri --disable-egl --disable-gles1 --disable-gles2
   --disable-gbm --disable-driglx-direct --disable-xvmc
   --enable-gallium-osmesa --with-gallium-drivers=swrast,swr
   --prefix=/usr/common/software/ParaView/mesa/17.0.2/

And here is how ParaView is configured on the same system. When building 
ParaView with OSMesa the ParaView GUI should be disabled to prevent 
window system dependencies(X11, Qt etc). Note that there are a number of 
options in play to configure for OSMesa. I've highlighted them in blue 
below. This info is also on the Wiki.


   #!/bin/bash

   LIB_EXT=so
   PY_LIB_EXT=so
   GLU_LIB_EXT=so
   MESA_LIB_EXT=so

   COMP_FLAGS="-fPIC -Ofast -march=native -mtune=native"
   CCOMP=`which gcc`
   CXXCOMP=`which g++`
   FTNCOMP=`which gfortran`

   export XTPE_LINK_TYPE=dynamic

   PYTHON=/usr/common/software/ParaView/python/2.7.12
   GLU=/usr/common/software/ParaView/glu/9.0.0/
   BOOST=/usr/common/software/ParaView/boost/1.63.0/
   MESA=/usr/common/software/ParaView/mesa/17.0.2/

   RCA=/opt/cray/rca/2.1.6_g2c60fbf-2.265/lib64
   ALPS=/opt/cray/alps/6.3.4-2.21/lib64
   XPMEM=/opt/cray/xpmem/2.1.1_gf9c9084-2.38/lib64
   DMAPP=/opt/cray/dmapp/7.1.1-39.37/lib64
   PMI=/opt/cray/pe/pmi/5.0.10-1..11050.0.0.ari/lib64
   UGNI=/opt/cray/ugni/6.0.15-2.2/lib64
   UDREG=/opt/cray/udreg/2.3.2-7.54/lib64
   MPT=/opt/cray/pe/mpt/7.4.4/gni/mpich-gnu/5.1/lib

   cmake \
-DCMAKE_C_COMPILER=$CCOMP \
-DCMAKE_CXX_COMPILER=$CXXCOMP \
-DCMAKE_Fortran_COMPILER=$FTNCOMP \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_CXX_FLAGS=$COMP_FLAGS \
-DCMAKE_C_FLAGS=$COMP_FLAGS \
-DBUILD_SHARED_LIBS=OFF \
-DPARAVIEW_ENABLE_PYTHON=ON \
-DPYTHON_EXECUTABLE=$PYTHON/bin/python \
-DPYTHON_INCLUDE_DIR=$PYTHON/include/python2.7 \
-DPYTHON_LIBRARY=$PYTHON/lib/libpython2.7.$PY_LIB_EXT \
-DPYTHON_UTIL_LIBRARY=/usr/lib64/libutil.$PY_LIB_EXT \
-DPARAVIEW_FREEZE_PYTHON=OFF \
-DBUILD_TESTING=OFF \
   *-DPARAVIEW_BUILD_QT_GUI=OFF \**
   **-DCMAKE_X_LIBS="" \**
   **-DX11_LIBRARIES="" \**
   **-DVTK_USE_X=OFF \**
   **-DVTK_OPENGL_HAS_OSMESA=ON \**
   **-DOSMESA_INCLUDE_DIR=$MESA/include \**
   **-DOSMESA_LIBRARY="$MESA/lib/libOSMesa.$MESA_LIB_EXT;" \**
   **-DOPENGL_INCLUDE_DIR=$MESA/include \**
   **-DOPENGL_gl_LIBRARY=$MESA/lib/libOSMesa.$MESA_LIB_EXT \**
   **-DOPENGL_glu_LIBRARY=$GLU/lib/libGLU.$GLU_LIB_EXT \**
   **-DOPENGL_xmesa_INCLUDE_DIR=$MESA/include \*
-DPARAVIEW_USE_MPI=ON \
-DMPI_CXX_LIBRARIES="" \
   
-DMPI_C_LIBRARIES="-Wl,--start-group;$MPT/libmpich.$LIB_EXT;$PMI/libpmi.$LIB_EXT;$DMAPP/libdmapp.$LIB_EXT;$MPT/libmpichcxx.$LIB_EXT;$UGNI/libugni.$LIB_EXT;$ALPS/libalpslli.$LIB_EXT;$ALPS/libalpsutil.$LIB_EXT;$RCA/librca.$LIB_EXT;$XPMEM/libxpmem.$LIB_EXT;-Wl,--end-group;"
   \
-DMPI_INCLUDE_PATH=$MPT/../include \
-DMPIEXEC=`which srun` \
-DMPI_CXX_LIBRARIES="" \
-DPARAVIEW_USE_VISITBRIDGE=ON \
-DBoost_INCLUDE_DIR=$BOOST/include \
-DVISIT_BUILD_READER_CGNS=OFF \
-DVISIT_BUILD_READER_Silo=OFF \
-DVTK_USE_SYSTEM_HDF5=OFF \
-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON \
    $*



On 05/15/2017 02:24 AM, Patrick Begou wrote:

Hi Chuck, Hi Burlen

Thanks for your reply.

I've attached the setup of my mesa installation. I have more options 
enabled in my config than in yours.  May be too much as this frontend 
has no GPU available.


I'll try a setup with -DVTK_USE_X=OFF as Burlen suggest, but is it 
possible to build paraview GUI with this option ? It is not clear for me.


Patrick

prefix:  /share/apps/paraview-5.3.0
exec_prefix: ${prefix}
libdir:  ${exec_prefix}/lib
includedir:  ${prefix}/include

OpenGL:  yes (ES1: yes ES2: yes)

OSMesa:  libOSMesa (Gallium)

DRI platform:drm
DRI drivers: i915 i965 nouveau r200 radeon swrast
DRI driver dir:  ${libdir}/dri
GLX: DRI-based

EGL: yes
EGL platforms:   x11 drm
EGL drivers: builtin:egl_dri2 builtin:egl_dri3
GBM: yes

Vulkan drivers:  no

llvm:yes
llvm-config: /share/apps/paraview-5.3.0/bin/llvm-config
llvm-version:4.0.0

Gallium drivers: r300 r600 svga swrast
Gallium st:  mesa xvmc

HUD extra stats: no
HUD lmsensors:   no

Shared libs: yes
Static libs: 

Re: [Paraview] gpu_shader4 extension is not supported

[Burlen Loring]

Hi Patrick,

OSMesa (and friends such as OpenSWR) do not need to make use of GLX. In 
fact I think it should be disabled completely for that case in both Mesa 
and ParaView builds. For eg, when you configure ParaView you'd specify 
-DVTK_USE_X=OFF. At least this is how it was in the past. I haven't been 
following developments lately. The wiki 
<http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D> has specifics.


Burlen

On 05/12/2017 07:25 AM, Patrick Begou wrote:

Hi,

I'm still trying to build paraview 5.3 with Qt4.8. As paraview 
superbuild was failing on my desktop (centos 6.9, Nvidia GPU), I build 
paraview by hand and it is running now with and without pvserver 
connection

.
The problem went back with building same paraview version on the 
cluster frontend: CentOS 6.7, no GPU. The compilation is successfull 
but launching paraview I get some errors with OpenGL:


ERROR: In 
/kareline/data/begou/PARAVIEW5/paraview/VTK/Rendering/OpenGL2/vtkOpenGLRenderWindow.cxx, 
line 825
vtkXOpenGLRenderWindow (0x2280fb0): GL version 2.1 with the 
gpu_shader4 extension is not supported by your graphics driver but is 
required for the new OpenGL rendering backend. Please update your 
OpenGL driver. If you are using Mesa please make sure you have version 
10.6.5 or later and make sure your driver in Mesa supports OpenGL 3.2.


ERROR: In 
/kareline/data/begou/PARAVIEW5/paraview/VTK/Rendering/OpenGL2/vtkXOpenGLRenderWindow.cxx, 
line 812

vtkXOpenGLRenderWindow (0x2280fb0): failed to create offscreen window

ERROR: In 
/kareline/data/begou/PARAVIEW5/paraview/VTK/Rendering/OpenGL2/vtkOpenGLRenderWindow.cxx, 
line 813

vtkXOpenGLRenderWindow (0x2280fb0): GLEW could not be initialized.

I've built and installed mesa from mesa-17.0.4.tar.gz using:
./configure \
PKG_CONFIG_PATH=/share/apps/paraview-5.3.0/lib/pkgconfig \
--prefix=/share/apps/paraview-5.3.0 \
--disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm \
--with-llvm-prefix=/share/apps/paraview-5.3.0

With several requested libraries:
libxshmfence-1.2.tar.gz
libxcb-1.12.tar.gz
libXau-1.0.8.tar.gz
pthread-stubs-0.3.tar.gz
xcb-proto-1.12.tar.gz
libdrm-2.4.70.tar.gz
llvm-4.0.0.src.tar.xz
all under /share/apps/paraview-5.3.0/

I've checked with strace that paraview was loading libGL in 
/share/apps/paraview-5.3.0/lib and not the system one, requested by 
other application (frontend is in production and I cannont break these 
libraries used by other softwares).



I must confess I'm not familiar at all with these libraries and 
environments, mesa or osmesa, GPU or not GPU, of screen rendering... 
all documentation deeping in obscure details while I'm searching to 
understand these concepts.
it is clear for me that on the nodes (without GPU) I will use OSMesa 
and no GUI, but on the frontend where I need GUI ???


Thanks for your advices and sorry if this is a very basic lack of 
understanding from myself.


Patrick


Paraview cmake is:
ccmake -DBUILD_SHARED_LIBS=ON \
   -DPARAVIEW_USE_MPI=ON \
   -DCMAKE_BUILD_TYPE=Release \
   -DPARAVIEW_BUILD_QT_GUI=ON \
   -DPARAVIEW_QT_VERSION=4 \
-DQT_QMAKE_EXECUTABLE=/share/apps/paraview-5.3.0/qt4.8.6/bin/qmake \
   -DPARAVIEW_ENABLE_FFMPEG=ON \
   -DPARAVIEW_ENABLE_PYTHON=ON \
-DPYTHON_INCLUDE_DIR=/share/apps/python279/include/python2.7 \
-DPYTHON_LIBRARY=/share/apps/python279/lib/libpython2.7.so \
-DPYTHON_LIBRARY_DEBUG=/share/apps/python279/lib/libpython2.7.so \
   -DCMAKE_INSTALL_PREFIX=/share/apps/paraview-5.3.0 \
   -DCMAKE_VERBOSE_MAKEFILE=ON \
   -DCMAKE_CXX_COMPILER=/share/apps/GCC485/bin/g++ \
   -DCMAKE_C_COMPILER=/share/apps/GCC485/bin/gcc \
-DCMAKE_Fortran_COMPILER=/share/apps/GCC485/bin/gfortran \
   -DFFMPEG_ROOT=/share/apps/paraview-5.3.0 \
-DOPENGL_INCLUDE_DIR=/share/apps/paraview-5.3.0/include \
-DOPENGL_gl_LIBRARY=/share/apps/paraview-5.3.0/lib/libGL.so \
 ../paraview


--
===
|  Equipe M.O.S.T. |  |
|  Patrick BEGOU   |mailto:patrick.be...@grenoble-inp.fr  |
|  LEGI|  |
|  BP 53 X | Tel 04 76 82 51 35   |
|  38041 GRENOBLE CEDEX| Fax 04 76 82 52 71   |
===


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Re: [Paraview] problem freezing python

[Burlen Loring]

Hi Ben,

Right you are, should be : and not ' '. Seems as though the issues are 
all related to recent OS upgrades on our side. I reinstalled Python and 
the build completes without error and I see all the output of the 
freezing process.


One issue I'm still having is that import math fails. Other modules like 
numpy import it, and as a result fail to import as well. See below. I'm 
hesitant to install with freezing because of this. math seems to be an 
essential module, without which it would be difficult to do any on the 
fly calculations such as camera positioning etc. Do you have any plans 
to fix this?


swowner@cori01:/usr/common/software/ParaView/builds/ParaView-5.3.0> 
./bin/pvpython

Python 2.7.12 (default, Apr 24 2017, 13:19:37)
[GCC 6.3.0 20161221 (Cray Inc.)] on linux2
>>> import math
Traceback (most recent call last):
  File "", line 1, in 
ImportError: No module named math

On 04/24/2017 06:52 AM, Ben Boeckel wrote:

On Fri, Apr 21, 2017 at 12:10:36 -0700, Burlen Loring wrote:

That file lives in: lib/python2.7/config/config.c.in

OK, it looks like the freeze_paraview.py file can't find it. Could you
debug around line 250 to see what it is actually doing?


-set(ENV{PYTHONPATH} "${PACKAGE_ROOT}")
+set(ENV{PYTHONPATH} "${PACKAGE_ROOT} $ENV{PYTHONPATH}")

I don't see how this is valid (unless breaking the first entry in
`PYTHONPATH` is the goal); it should be separated by a colon.


"/usr/common/software/ParaView/python/2.7.12/lib/python2.7/struct.py",

What Python is this? Where did it come from?


line 1, in 
  from _struct import *
ImportError: No module named _struct

Can you import it in the interpreter living in the above directory?

--Ben


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Re: [Paraview] problem freezing python

[Burlen Loring]

On 04/21/2017 10:19 AM, Ben Boeckel wrote:

On Thu, Apr 20, 2017 at 14:44:47 -0700, Burlen Loring wrote:

[100%] Freezing Python and ParaView Python packages and modules
Removing
/usr/common/software/ParaView/builds/ParaView-5.3.0/Utilities/PythonInitializer/FrozenPython
Error: could not find python lib directory
Use
``/usr/common/software/ParaView/builds/ParaView/ThirdParty/FreezePython/freeze/freeze_paraview.py
-h'' for help
CMake Error at
/usr/common/software/ParaView/builds/ParaView/ThirdParty/FreezePython/vtkFreezePython.cmake:64
(message):
freeze_paraview failed (2)

Looking at the code, it seems that there is not a `config.c.in` in your
`lib/python2.x` directory. It seems that it only searches `lib`. Are you
on a platform which uses `/usr/lib64`, `/usr/lib/x86_64-linux-gnu`, or
similar? Can you find a `config.c.in` near your Python installation?

--Ben

That file lives in: lib/python2.7/config/config.c.in

On this system Python (and all software) is installed on a high 
performance file system that is mounted read only on the compute system. 
We have to set certain environment vars to get Python to run from this 
location, but PV's cmake code overwrites at least one of them.


I made the following change

diff --git a/ThirdParty/FreezePython/vtkFreezePython.cmake 
b/ThirdParty/FreezePython/vtkFreezePython.cmake

index a94a5d7..405f87b 100644
--- a/ThirdParty/FreezePython/vtkFreezePython.cmake
+++ b/ThirdParty/FreezePython/vtkFreezePython.cmake
@@ -33,7 +33,7 @@ endif()
 message("Removing ${OUTPUT_DIRECTORY}")
 file(REMOVE_RECURSE "${OUTPUT_DIRECTORY}")
 file(MAKE_DIRECTORY "${OUTPUT_DIRECTORY}")
-set(ENV{PYTHONPATH} "${PACKAGE_ROOT}")
+set(ENV{PYTHONPATH} "${PACKAGE_ROOT} $ENV{PYTHONPATH}")
 execute_process(
 COMMAND ${PYTHON_EXECUTABLE}
"${CMAKE_CURRENT_LIST_DIR}/freeze/freeze_paraview.py"
lines 1-13/13 (END)

the change got me further but still there are some issues

[100%] Freezing Python and ParaView Python packages and modules
Removing 
/usr/common/software/ParaView/builds/ParaView-5.3.0/Utilities/PythonInitializer/FrozenPython

Traceback (most recent call last):
  File 
"/usr/common/software/ParaView/builds/ParaView/ThirdParty/FreezePython/freeze/freeze_paraview.py", 
line 100, in 

import modulefinder
  File 
"/usr/common/software/ParaView/python/2.7.12/lib/python2.7/modulefinder.py", 
line 10, in 

import struct
  File 
"/usr/common/software/ParaView/python/2.7.12/lib/python2.7/struct.py", 
line 1, in 

from _struct import *
ImportError: No module named _struct
CMake Error at 
/usr/common/software/ParaView/builds/ParaView/ThirdParty/FreezePython/vtkFreezePython.cmake:64 
(message):

  freeze_paraview failed (1)


Utilities/PythonInitializer/CMakeFiles/vtkUtilitiesPythonInitializer.dir/build.make:61: 
recipe for target 
'Utilities/PythonInitializer/FrozenPython/vtkFrozenParaViewPython.h' failed
make[2]: *** 
[Utilities/PythonInitializer/FrozenPython/vtkFrozenParaViewPython.h] Error 1
CMakeFiles/Makefile2:51795: recipe for target 
'Utilities/PythonInitializer/CMakeFiles/vtkUtilitiesPythonInitializer.dir/all' 
failed
make[1]: *** 
[Utilities/PythonInitializer/CMakeFiles/vtkUtilitiesPythonInitializer.dir/all] 
Error 2

Makefile:149: recipe for target 'all' failed
make: *** [all] Error 2

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Re: [Paraview] Program received signal SIGFPE, Arithmetic exception.

[Burlen Loring]

OK, good to know. would any one be willing to give a quick review?

https://gitlab.kitware.com/paraview/paraview/merge_requests/1476

On 03/20/2017 12:16 PM, Ben Boeckel wrote:

On Mon, Mar 20, 2017 at 11:31:28 -0700, Burlen Loring wrote:

I had to apply to clang-format manually. it's up there now. changes were
minimal so I squashed them into the patch.

The fixes would have had to had been squashed in anyways; the robot
checks each commit individually.


System has yet to acknowledge and re check. I assume it will
eventually.

The new robot is silent on successful checks, so if it's silent, you're
(likely) good.


Try as I may the clang-format script you guys are using doesn't work for
me.  here are the errors:
Fedora 24:

 smic:~/work/ParaView$Utilities/Scripts/clang-format.bash --amend
 YAML:4:24: error: invalid boolean
 AlignAfterOpenBracket: DontAlign
 ^
 Error reading /home/bloring/work/ParaView/.clang-format: Invalid
 argument

Maybe this is due to clang-format --version == 3.7? not sure but I won't
have time to re-install clang on this system, so I also tried on a newer
system.

Yeah, I think it requires 3.8. There is a new `Do: reformat` command
coming soon (this week ideally) to do the reformatting of your branch
for you since not everyone has a suitable clang-format just laying
around.

--Ben


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Re: [Paraview] Program received signal SIGFPE, Arithmetic exception.

[Burlen Loring]

Hi Cory,

I had to apply to clang-format manually. it's up there now. changes were 
minimal so I squashed them into the patch. System has yet to acknowledge 
and re check. I assume it will eventually.


Try as I may the clang-format script you guys are using doesn't work for 
me.  here are the errors:

Fedora 24:

   smic:~/work/ParaView$Utilities/Scripts/clang-format.bash --amend
   YAML:4:24: error: invalid boolean
   AlignAfterOpenBracket: DontAlign
   ^
   Error reading /home/bloring/work/ParaView/.clang-format: Invalid
   argument

Maybe this is due to clang-format --version == 3.7? not sure but I won't 
have time to re-install clang on this system, so I also tried on a newer 
system.


OSX Sierra:

   pipin:~/ParaView/ParaView$./Utilities/Scripts/clang-format.bash --amend
   sed: 1: "/: format\.clang-format ...": bad flag in substitute
   command: '}'
   xargs: illegal option -- d
   usage: xargs [-0opt] [-E eofstr] [-I replstr [-R replacements]] [-J
   replstr]
 [-L number] [-n number [-x]] [-P maxprocs] [-s size]
 [utility [argument ...]]

clang-format --version==4.0. what ended up working on the OSX system was

   clang-format -style="{BasedOnStyle: Mozilla, AlignAfterOpenBracket:
   DontAlign, AlignOperands: false, AlwaysBreakAfterReturnType: None,
   AlwaysBreakAfterDefinitionReturnType: None, BreakBeforeBraces:
   Allman, ColumnLimit: 100, Standard: Cpp03}" -i
   Qt/Components/pqPresetToPixmap.cxx

where style arguments were extracted from .clang-format in top level 
ParaView dir.


Burlen

On 03/17/2017 12:50 PM, Cory Quammen wrote:

Burlen,

Thanks for the patch.

With regards to clang-format, we recently enabled automatic style
enforcement checks. This way to fix is to install clang-format, run
`git clang-format` in your ParaView source directory, amend your
commit, then force push it with `git gitlab-push -f`.

- Cory

On Fri, Mar 17, 2017 at 3:36 PM, Burlen Loring <burlen.lor...@gmail.com> wrote:

fyi, https://gitlab.kitware.com/paraview/paraview/merge_requests/1476

it complains about clang-format, but it seems that the source file was not
formatted in that way to begin with.


On 03/17/2017 12:11 PM, Burlen Loring wrote:

Thank you guys. I poked around this morning and found the following:

The "BlueObeliskElements" is the only cmap in the default presets that
triggers the issue. It has more values than can be displayed on a single
line, and this is what triggers the FPE in the logic.

Enforcing a minimum swatch size(terminology from the code) prevents the
FPE and seems to produce the desired result of displaying all of the cmap
values in one line, although they are quite small.

a moment ago I pushed a patch onto gitlab demonstrating. Perhaps it or
something like it could be back ported to the 5.3.0 branch?

On 03/17/2017 07:09 AM, Cory Quammen wrote:

Burlen,

I've created an issue for your report. It sure looks like a bug.

https://gitlab.kitware.com/paraview/paraview/issues/17305

Ufuk,

That fix turns out to already be in v5.3.0:

commit 90e710d5792116e640d25caa8ff455ae4e65d718
Author: Sergey Sindeev <ssind...@yandex.ru>
Date:   Sun Dec 18 13:21:27 2016 +0100

  fix a compilation crash when using the latest ICC compiler

diff --git a/Qt/Components/pqPresetToPixmap.cxx
b/Qt/Components/pqPresetToPixmap.cxx
index 13f6b2e..b80fb80 100644
--- a/Qt/Components/pqPresetToPixmap.cxx
+++ b/Qt/Components/pqPresetToPixmap.cxx
@@ -254,15 +254,12 @@ QPixmap
pqPresetToPixmap::renderIndexedColorTransferFunction(
   // Now determine best value for Nh in [Nh/2,Nh-1]
   double bestQ = vtkMath::Inf();
   int best = -1;
-for (int i = Nh / 2; i < Nh; ++i)
+double ar = Nv * wmp / static_cast(hmp * Nh);
+double q = (ar >= 1.0) ? ar : 1. / ar;
+if (q < bestQ)
   {
-  double ar = Nv * wmp / static_cast(hmp * Nh);
-  double q = (ar >= 1.0) ? ar : 1. / ar;
-  if (q < bestQ)
-  {
-bestQ = q;
-best = i;
-  }
+  bestQ = q;
+  best = Nh-1;
   }
   Nh = best;
 }

Thanks to you and Sergey for pursuing this Intel compiler issue and
ParaView issue!

- Cory

On Fri, Mar 17, 2017 at 3:18 AM, <u.utku.turunco...@be.itu.edu.tr> wrote:

Hi Burlen,

Your issue could be related with following,

https://software.intel.com/en-us/forums/intel-c-compiler/topic/702934

I opened a bug report in Intel form and they found a bug in that
particular source file (pqPresetToPixmap.cxx). So, if you apply the fix
you might solve the problem but i am not sure.

I hope it helps,
Regards,

--ufuk



I tried out ParaView 5.3.0 today, and I encountered the above crash.

steps to reproduce: load data (sphere source will work), set color by
var, open color map dialog, change to categorical, open choose presets
dialog, scroll down, when you get near the bottom you will get the
crash.

Program received signal SIGFP

Re: [Paraview] Program received signal SIGFPE, Arithmetic exception.

[Burlen Loring]

fyi, https://gitlab.kitware.com/paraview/paraview/merge_requests/1476

it complains about clang-format, but it seems that the source file was 
not formatted in that way to begin with.


On 03/17/2017 12:11 PM, Burlen Loring wrote:

Thank you guys. I poked around this morning and found the following:

The "BlueObeliskElements" is the only cmap in the default presets that 
triggers the issue. It has more values than can be displayed on a 
single line, and this is what triggers the FPE in the logic.


Enforcing a minimum swatch size(terminology from the code) prevents 
the FPE and seems to produce the desired result of displaying all of 
the cmap values in one line, although they are quite small.


a moment ago I pushed a patch onto gitlab demonstrating. Perhaps it or 
something like it could be back ported to the 5.3.0 branch?


On 03/17/2017 07:09 AM, Cory Quammen wrote:

Burlen,

I've created an issue for your report. It sure looks like a bug.

https://gitlab.kitware.com/paraview/paraview/issues/17305

Ufuk,

That fix turns out to already be in v5.3.0:

commit 90e710d5792116e640d25caa8ff455ae4e65d718
Author: Sergey Sindeev <ssind...@yandex.ru>
Date:   Sun Dec 18 13:21:27 2016 +0100

 fix a compilation crash when using the latest ICC compiler

diff --git a/Qt/Components/pqPresetToPixmap.cxx
b/Qt/Components/pqPresetToPixmap.cxx
index 13f6b2e..b80fb80 100644
--- a/Qt/Components/pqPresetToPixmap.cxx
+++ b/Qt/Components/pqPresetToPixmap.cxx
@@ -254,15 +254,12 @@ QPixmap
pqPresetToPixmap::renderIndexedColorTransferFunction(
  // Now determine best value for Nh in [Nh/2,Nh-1]
  double bestQ = vtkMath::Inf();
  int best = -1;
-for (int i = Nh / 2; i < Nh; ++i)
+double ar = Nv * wmp / static_cast(hmp * Nh);
+double q = (ar >= 1.0) ? ar : 1. / ar;
+if (q < bestQ)
  {
-  double ar = Nv * wmp / static_cast(hmp * Nh);
-  double q = (ar >= 1.0) ? ar : 1. / ar;
-  if (q < bestQ)
-  {
-bestQ = q;
-best = i;
-  }
+  bestQ = q;
+  best = Nh-1;
  }
  Nh = best;
}

Thanks to you and Sergey for pursuing this Intel compiler issue and
ParaView issue!

- Cory

On Fri, Mar 17, 2017 at 3:18 AM, <u.utku.turunco...@be.itu.edu.tr> 
wrote:

Hi Burlen,

Your issue could be related with following,

https://software.intel.com/en-us/forums/intel-c-compiler/topic/702934

I opened a bug report in Intel form and they found a bug in that
particular source file (pqPresetToPixmap.cxx). So, if you apply the fix
you might solve the problem but i am not sure.

I hope it helps,
Regards,

--ufuk



I tried out ParaView 5.3.0 today, and I encountered the above crash.

steps to reproduce: load data (sphere source will work), set color by
var, open color map dialog, change to categorical, open choose presets
dialog, scroll down, when you get near the bottom you will get the 
crash.


Program received signal SIGFPE, Arithmetic exception.
0x7660a833 in
pqPresetToPixmap::renderIndexedColorTransferFunction (this=0x5e22560,
stc=0x647f460, size=...) at
/home/bloring/work/ParaView/Qt/Components/pqPresetToPixmap.cxx:273
273  Nh = wmp / (ss + PQ_SWATCH_PAD);
(gdb) p ss
$5 = -2

of course PQ_SWATCH_PAD == 2
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Re: [Paraview] Program received signal SIGFPE, Arithmetic exception.

[Burlen Loring]

Thank you guys. I poked around this morning and found the following:

The "BlueObeliskElements" is the only cmap in the default presets that 
triggers the issue. It has more values than can be displayed on a single 
line, and this is what triggers the FPE in the logic.


Enforcing a minimum swatch size(terminology from the code) prevents the 
FPE and seems to produce the desired result of displaying all of the 
cmap values in one line, although they are quite small.


a moment ago I pushed a patch onto gitlab demonstrating. Perhaps it or 
something like it could be back ported to the 5.3.0 branch?


On 03/17/2017 07:09 AM, Cory Quammen wrote:

Burlen,

I've created an issue for your report. It sure looks like a bug.

https://gitlab.kitware.com/paraview/paraview/issues/17305

Ufuk,

That fix turns out to already be in v5.3.0:

commit 90e710d5792116e640d25caa8ff455ae4e65d718
Author: Sergey Sindeev <ssind...@yandex.ru>
Date:   Sun Dec 18 13:21:27 2016 +0100

 fix a compilation crash when using the latest ICC compiler

diff --git a/Qt/Components/pqPresetToPixmap.cxx
b/Qt/Components/pqPresetToPixmap.cxx
index 13f6b2e..b80fb80 100644
--- a/Qt/Components/pqPresetToPixmap.cxx
+++ b/Qt/Components/pqPresetToPixmap.cxx
@@ -254,15 +254,12 @@ QPixmap
pqPresetToPixmap::renderIndexedColorTransferFunction(
  // Now determine best value for Nh in [Nh/2,Nh-1]
  double bestQ = vtkMath::Inf();
  int best = -1;
-for (int i = Nh / 2; i < Nh; ++i)
+double ar = Nv * wmp / static_cast(hmp * Nh);
+double q = (ar >= 1.0) ? ar : 1. / ar;
+if (q < bestQ)
  {
-  double ar = Nv * wmp / static_cast(hmp * Nh);
-  double q = (ar >= 1.0) ? ar : 1. / ar;
-  if (q < bestQ)
-  {
-bestQ = q;
-best = i;
-  }
+  bestQ = q;
+  best = Nh-1;
  }
  Nh = best;
}

Thanks to you and Sergey for pursuing this Intel compiler issue and
ParaView issue!

- Cory

On Fri, Mar 17, 2017 at 3:18 AM,  <u.utku.turunco...@be.itu.edu.tr> wrote:

Hi Burlen,

Your issue could be related with following,

https://software.intel.com/en-us/forums/intel-c-compiler/topic/702934

I opened a bug report in Intel form and they found a bug in that
particular source file (pqPresetToPixmap.cxx). So, if you apply the fix
you might solve the problem but i am not sure.

I hope it helps,
Regards,

--ufuk



I tried out ParaView 5.3.0 today, and I encountered the above crash.

steps to reproduce: load data (sphere source will work), set color by
var, open color map dialog, change to categorical, open choose presets
dialog, scroll down, when you get near the bottom you will get the crash.

Program received signal SIGFPE, Arithmetic exception.
0x7660a833 in
pqPresetToPixmap::renderIndexedColorTransferFunction (this=0x5e22560,
stc=0x647f460, size=...) at
/home/bloring/work/ParaView/Qt/Components/pqPresetToPixmap.cxx:273
273  Nh = wmp / (ss + PQ_SWATCH_PAD);
(gdb) p ss
$5 = -2

of course PQ_SWATCH_PAD == 2
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Re: [Paraview] Program received signal SIGFPE, Arithmetic exception.

[Burlen Loring]

not sure if it matters, but I had been trying to load a color map that 
was saved from ParaView 5.1.0. attached.


On 03/16/2017 04:50 PM, Burlen Loring wrote:

I tried out ParaView 5.3.0 today, and I encountered the above crash.

steps to reproduce: load data (sphere source will work), set color by 
var, open color map dialog, change to categorical, open choose presets 
dialog, scroll down, when you get near the bottom you will get the crash.


Program received signal SIGFPE, Arithmetic exception.
0x7660a833 in 
pqPresetToPixmap::renderIndexedColorTransferFunction (this=0x5e22560, 
stc=0x647f460, size=...) at 
/home/bloring/work/ParaView/Qt/Components/pqPresetToPixmap.cxx:273

273  Nh = wmp / (ss + PQ_SWATCH_PAD);
(gdb) p ss
$5 = -2

of course PQ_SWATCH_PAD == 2




red_cmap.json
Description: application/json
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[Paraview] Program received signal SIGFPE, Arithmetic exception.

[Burlen Loring]

I tried out ParaView 5.3.0 today, and I encountered the above crash.

steps to reproduce: load data (sphere source will work), set color by 
var, open color map dialog, change to categorical, open choose presets 
dialog, scroll down, when you get near the bottom you will get the crash.


Program received signal SIGFPE, Arithmetic exception.
0x7660a833 in 
pqPresetToPixmap::renderIndexedColorTransferFunction (this=0x5e22560, 
stc=0x647f460, size=...) at 
/home/bloring/work/ParaView/Qt/Components/pqPresetToPixmap.cxx:273

273  Nh = wmp / (ss + PQ_SWATCH_PAD);
(gdb) p ss
$5 = -2

of course PQ_SWATCH_PAD == 2
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Re: [Paraview] plugins with 5.2

[Burlen Loring]

sure, although I hope this isn't asking too much, as the build has a few 
dependencies, I think for this only NetCDF is needed.


here is the repo
https://github.com/LBL-EESA/TECA
plugin is in the ParaView dir.

On 01/03/2017 01:35 PM, Utkarsh Ayachit wrote:

Burlen,

Happy new year to you too!

Hmm, that's odd. Can you share the plugin code with me? Let's see if I
can reproduce the issue.

Utkarsh

On Tue, Jan 3, 2017 at 2:13 PM, Burlen Loring <blor...@lbl.gov> wrote:

Hi Utkarsh, Happy new year!

I have a couple of questions about the new way.

Shouldn't this be automatically added by ADD_PARAVIEW_PLUGIN macro like the
rest of the PV related link dependencies?
Should you really need to link Qt to all plugins?

My plugin is a number of simple server side only classes, for ex a reader.
It has no need of Qt. I'd rather not have Qt as a dependency of my project.

Burlen


On 12/22/2016 12:17 PM, Utkarsh Ayachit wrote:

Burlen,

See Qt dependencies changes documented here:
http://www.paraview.org/ParaView3/Doc/Nightly/www/cxx-doc/MajorAPIChanges.html

include(ParaViewQt) # generally not needed, since auto-included
pv_find_package_qt(qt_targets
   QT4_COMPONENTS QtGui
   QT5_COMPONENTS Widgets)

pv_qt_wrap_cpp(moc_files ${headers})
pv_qt_wrap_ui(ui_files ${uis})

...
target_link_libraries(${target} LINK_PRIVATE ${qt_targets})


Utkarsh

On Wed, Dec 21, 2016 at 1:25 PM, Burlen Loring <burlen.lor...@gmail.com>
wrote:

After upgrading to 5.2 my plugin is not compiling. When I configure the
plugin I see a few pages of the following:

CMake Warning (dev) at io/CMakeLists.txt:54 (add_library):
   Policy CMP0028 is not set: Double colon in target name means ALIAS or
   IMPORTED target.  Run "cmake --help-policy CMP0028" for policy details.
   Use the cmake_policy command to set the policy and suppress this
warning.

   Target "teca_io" links to target "Qt4::QtCore" but the target was not
   found.  Perhaps a find_package() call is missing for an IMPORTED target,
or
   an ALIAS target is missing?
This warning is for project developers.  Use -Wno-dev to suppress it.

then linker errors

[ 32%] Linking CXX shared library ../lib/libteca_io.so
/bin/ld: cannot find -lQt4::QtCore
/bin/ld: cannot find -lQt4::QtGui
collect2: error: ld returned 1 exit status
io/CMakeFiles/teca_io.dir/build.make:402: recipe for target
'lib/libteca_io.so' failed
make[2]: *** [lib/libteca_io.so] Error 1
CMakeFiles/Makefile2:196: recipe for target
'io/CMakeFiles/teca_io.dir/all' failed
make[1]: *** [io/CMakeFiles/teca_io.dir/all] Error 2
Makefile:127: recipe for target 'all' failed
make: *** [all] Error 2

It's not a library so I set  the policy to new,  and the cmake configure
errors out. Any idea what's missing?


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[Paraview] plugins with 5.2

[Burlen Loring]

After upgrading to 5.2 my plugin is not compiling. When I configure the 
plugin I see a few pages of the following:


   CMake Warning (dev) at io/CMakeLists.txt:54 (add_library):
  Policy CMP0028 is not set: Double colon in target name means ALIAS or
  IMPORTED target.  Run "cmake --help-policy CMP0028" for policy
   details.
  Use the cmake_policy command to set the policy and suppress this
   warning.

  Target "teca_io" links to target "Qt4::QtCore" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED
   target, or
  an ALIAS target is missing?
   This warning is for project developers.  Use -Wno-dev to suppress it.

then linker errors

   [ 32%] Linking CXX shared library ../lib/libteca_io.so
   /bin/ld: cannot find -lQt4::QtCore
   /bin/ld: cannot find -lQt4::QtGui
   collect2: error: ld returned 1 exit status
   io/CMakeFiles/teca_io.dir/build.make:402: recipe for target
   'lib/libteca_io.so' failed
   make[2]: *** [lib/libteca_io.so] Error 1
   CMakeFiles/Makefile2:196: recipe for target
   'io/CMakeFiles/teca_io.dir/all' failed
   make[1]: *** [io/CMakeFiles/teca_io.dir/all] Error 2
   Makefile:127: recipe for target 'all' failed
   make: *** [all] Error 2

It's not a library so I set  the policy to new,  and the cmake configure 
errors out. Any idea what's missing?


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Re: [Paraview] RAW (binary) file import issues

[Burlen Loring]

File sizes and linear offsets use a type MPI_Offset, which according 
to the specification should be large enough to hold the size of any 
file supported by the file system.


hmm, that may be but there are places in MPI I/O that limit to size of 
signed int, here is cut direct from the mpi 3 standard:


   int MPI_File_read_all(MPI_File fh, void *buf, int count,
   MPI_Datatype datatype, MPI_Status *status)

the count argument is a signed int, so one can't read more than INT_MAX 
in one go, and here is the VTK code where that is used


291   // Figure out how many bytes to read.
292   vtkIdType length = this->GetDataScalarTypeSize();
293   length *= this->NumberOfScalarComponents;
294   length *= extent[1]-extent[0]+1;
295   length *= extent[3]-extent[2]+1;
296   if (this->GetFileDimensionality() == 3) length *= 
extent[5]-extent[4]+1;

297
298   if (length > VTK_INT_MAX)
299 {
300 vtkErrorMacro(<< "Cannot read more than " << VTK_INT_MAX
301   << " bytes at a time.");
302 }
303
304   // Do the read.  This is a coordinated parallel operation for 
efficiency.
305   MPICall(MPI_File_read_all(file.Handle, buffer, 
static_cast(length),

306 MPI_BYTE, MPI_STATUS_IGNORE));

the VTK code checks for over flow. however as that is not the error 
reported by the user, I have to admit that I am wrong about Sam's 
problem. Sorry about that.


Burlen


On 11/22/2016 02:11 PM, Moreland, Kenneth wrote:


Although we have certainly run into issues with communicating large 
messages, I’m not sure this is the issue with MPI-I/O. File sizes and 
linear offsets use a type MPI_Offset, which according to the 
specification should be large enough to hold the size of any file 
supported by the file system. Although it is true that creating the 3D 
subarray uses 32-bit indices, those are for each of the separate 
dimensions, and 2000 falls well below that limit.


Besides, it looks like that error happens when checking an ifstream 
object, so it looks like the reader is bypassing the MPI-I/O path anyway.


I would follow Berk’s suggesting of looking into the filesystem before 
diving into the guts of MPI-I/O.


-Ken

*From:*ParaView [mailto:paraview-boun...@paraview.org] *On Behalf Of 
*Burlen Loring

*Sent:* Tuesday, November 22, 2016 12:55 PM
*To:* Geveci, Berk (External Contact) <berk.gev...@kitware.com>; Keyes 
S.D. <s.d.ke...@soton.ac.uk>

*Cc:* paraview@paraview.org
*Subject:* [EXTERNAL] Re: [Paraview] RAW (binary) file import issues

I've hit that before. the RAW reader uses MPI-I/O, and MPI uses signed 
int everywhere in its API, so there are limits that you end up 
hitting. For instance to partition the data among processors one must 
give MPI-I/O the starting offset of the data in the file as a signed 
int, and that is limited to 2^31.


Burlen

On 11/22/2016 11:20 AM, Berk Geveci wrote:

Hmmm that happens to be around 4 GB which makes me wonder if there
is a limit somewhere in that reader... Any chance you can try this
on a Linux machine?

On Thu, Nov 17, 2016 at 10:30 AM, Keyes S.D.
<s.d.ke...@soton.ac.uk <mailto:s.d.ke...@soton.ac.uk>> wrote:

Dear all,

I am encountering issues when trying to import large 8 bit RAW
volumes to Paraview 5.1.2 (64 bit).

The file I wish to import has xyz dimensions of 2000x2000x1920
voxels (Unsigned char), 7.5GB.  I am running a machine with
192 GB RAM and 12 CPU cores.

I can import up to a 2000x2000x1000 crop of this file, but I
encounter the following message when I attempt larger z
dimensions:

ERROR: In
C:\bbd\df0abce0\source-paraview\VTK\IO\Image\vtkImageReader2.cxx,
line 592

vtkPVImageReader (07767F90): Initialize: Could not
open file

\\cseg_2\ERC\SLS_201606\Myco_2\CT2PpR3h1_\Hyphalseg_Raw_2000_2000_1920_8bit_SKELETON_FILT_PARAVIEW_TEST.raw




I cannot find an obvious memory ceiling within the paraview
settings - any ideas as to whether there is some effective
upper limit to import file size?

Sam

Samuel D Keyes, MEng, PhD
New Frontiers Fellow
Bioengineering / μVIS Centre for Computed Tomography
University of Southampton
E: s.d.ke...@soton.ac.uk
<mailto:s.d.ke...@soton.ac.uk><https://www.outlook.soton.ac.uk/owa/

<http://www.outlook.soton.ac.uk/owa/>redir.aspx?SURL=dhUg3da8XR77LeItLDzJQwhAwmH0Wx6PHrXeKfxx2tOD3LCr737TCG0AYQBpAGwAdABvADoAUwAuAEQALgBLAGUAeQBlAHMAQABzAG8AdABvAG4ALgBhAGMALgB1AGsA=mailto%3aS.D.Keyes%40soton.ac.uk>
T: 07898720248
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Pleas

Re: [Paraview] RAW (binary) file import issues

[Burlen Loring]

I've hit that before. the RAW reader uses MPI-I/O, and MPI uses signed 
int everywhere in its API, so there are limits that you end up hitting. 
For instance to partition the data among processors one must give 
MPI-I/O the starting offset of the data in the file as a signed int, and 
that is limited to 2^31.


Burlen

On 11/22/2016 11:20 AM, Berk Geveci wrote:
Hmmm that happens to be around 4 GB which makes me wonder if there is 
a limit somewhere in that reader... Any chance you can try this on a 
Linux machine?


On Thu, Nov 17, 2016 at 10:30 AM, Keyes S.D. <s.d.ke...@soton.ac.uk 
<mailto:s.d.ke...@soton.ac.uk>> wrote:


Dear all,

I am encountering issues when trying to import large 8 bit RAW
volumes to Paraview 5.1.2 (64 bit).

The file I wish to import has xyz dimensions of 2000x2000x1920
voxels (Unsigned char), 7.5GB.  I am running a machine with 192 GB
RAM and 12 CPU cores.

I can import up to a 2000x2000x1000 crop of this file, but I
encounter the following message when I attempt larger z dimensions:

ERROR: In
C:\bbd\df0abce0\source-paraview\VTK\IO\Image\vtkImageReader2.cxx,
line 592

vtkPVImageReader (07767F90): Initialize: Could not open
file

\\cseg_2\ERC\SLS_201606\Myco_2\CT2PpR3h1_\Hyphalseg_Raw_2000_2000_1920_8bit_SKELETON_FILT_PARAVIEW_TEST.raw


I cannot find an obvious memory ceiling within the paraview
settings - any ideas as to whether there is some effective upper
limit to import file size?

Sam

Samuel D Keyes, MEng, PhD
New Frontiers Fellow
Bioengineering / μVIS Centre for Computed Tomography
University of Southampton
E: s.d.ke...@soton.ac.uk

<mailto:s.d.ke...@soton.ac.uk><https://www.outlook.soton.ac.uk/owa/redir.aspx?SURL=dhUg3da8XR77LeItLDzJQwhAwmH0Wx6PHrXeKfxx2tOD3LCr737TCG0AYQBpAGwAdABvADoAUwAuAEQALgBLAGUAeQBlAHMAQABzAG8AdABvAG4ALgBhAGMALgB1AGsA=mailto%3aS.D.Keyes%40soton.ac.uk

<https://www.outlook.soton.ac.uk/owa/redir.aspx?SURL=dhUg3da8XR77LeItLDzJQwhAwmH0Wx6PHrXeKfxx2tOD3LCr737TCG0AYQBpAGwAdABvADoAUwAuAEQALgBLAGUAeQBlAHMAQABzAG8AdABvAG4ALgBhAGMALgB1AGsA=mailto%3aS.D.Keyes%40soton.ac.uk>>
T: 07898720248
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Re: [Paraview] associating table data with a Paraview source?

[Burlen Loring]

hey Cynthia,

if your data is in, or can be converted to, CSV format just open it up, 
and apply the table to points filter, followed by glyph filter. table to 
points you'll need to specify the coordinate arrays and check keep all 
arrays option. in the glyph filter properties you can select a sphere 
glyph and select glyph all points option. this will put a sphere at each 
point and you can scale and color them by any of the arrays.


Burlen

On 08/24/2016 03:41 PM, Hart, Cynthia Joyce - (cyndyb) wrote:


Hi folks, An ignorant question.  I know Paraview is great for 
visualizing existing complex data sets, but I have a simple problem 
wherein I need to create a dataset, and I would like to solve this 
problem using Paraview, but I am unsure how to do so.


In brief, I have been given point data of radiance values of 3 sensors 
placed in specific locations around a mesh.  I have no 3D object 
provided that represents the sensors, no 3d volume; just a spreadsheet 
of values of sensor readings over time. For illustrative purposes, it 
is desired to visualize the sensors as radiant spheres, and animate 
how the 3 sensor values change over time, by showing the sensor 
spheres varying in color.


It seems the way to go about this, is create source spheres in 
Paraview, at the proper locations around the mesh object.  This part 
is easy!  What is not clear to me, is if there is a way – and if so, 
what is it – to associate my data tables of changing sensor values 
with the Paraview sphere sources. Once I import the csv spreadsheet, 
how can I associate it with an object already in Paraview?   Can 
someone kindly point me in the right direction, or tell me this cannot 
be done.  Thank you!


Cynthia



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Re: [Paraview] Importing paraview.simple from python

[Burlen Loring]

fyi, a common way to encounter

Fatal Python error: PyThreadState_Get: no current thread
is when cmake's find Python modules mix two version of Python. this 
happen if you have two installs, one in a system location and one else 
where with interpreter in the path. You can identify it in the cmake 
cache. bug reports on this are found in the cmake Mantis tracker. The 
most informative is here  and 
in new bug tracker here 
. I've resorted to 
using python-config in cmake to work around, but this requires the 
environment to have the desired python in the path, ld lib path, dyld 
lib path and pkg config path.


On 08/10/2016 05:33 AM, Utkarsh Ayachit wrote:

Looks like the relative path specification has change which may make
this tricky. Ben, can you take  a look please? Thanks

Utkarsh

On Wed, Aug 10, 2016 at 5:29 AM, Zhou, Fangyi
 wrote:

Thanks to previous emails I have managed to get it running on Linux, but I have 
the similar problem on mac

% export 
DYLD_FALLBACK_FRAMEWORK_PATH=/Applications/paraview.app/Contents/Frameworks
% export 
DYLD_FALLBACK_LIBRARY_PATH=/Applications/paraview.app/Contents/Libraries
% export DYLD_LIBRARY_PATH=/Applications/paraview.app/Contents/Libraries/
% export 
PYTHONPATH=/Applications/paraview.app/Contents/Python:/Applications/paraview.app/Contents/Python/vtk:/Applications/paraview.app/Contents/Libraries

Home-brew python:

% which python
/usr/local/bin/python
% python
Python 2.7.12 (default, Jun 29 2016, 14:05:02)
[GCC 4.2.1 Compatible Apple LLVM 7.3.0 (clang-703.0.31)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

import paraview.simple

Fatal Python error: PyThreadState_Get: no current thread
[1]47104 abort  python

System python:

% /usr/bin/python
Python 2.7.10 (default, Oct 23 2015, 19:19:21)
[GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

import paraview.simple

Error: Could not import vtkCommonComputationalGeometry
Traceback (most recent call last):
   File "", line 1, in 
   File "/Applications/paraview.app/Contents/Python/paraview/simple.py", line 39, in 

 import servermanager
   File "/Applications/paraview.app/Contents/Python/paraview/servermanager.py", line 
52, in 
 from paraview import vtk
   File "/Applications/paraview.app/Contents/Python/paraview/vtk/__init__.py", line 
7, in 
 from vtkCommonCore import *
   File "/Applications/paraview.app/Contents/Python/paraview/vtk/vtkCommonCore.py", 
line 9, in 
 from vtkCommonCorePython import *
ImportError: 
dlopen(/Applications/paraview.app/Contents/Python/vtk/vtkCommonCorePython.so, 
2): Library not loaded: 
@executable_path/../Libraries/libvtkCommonCorePython27D-pv5.1.1.dylib
   Referenced from: 
/Applications/paraview.app/Contents/Python/vtk/vtkCommonCorePython.so
   Reason: unsafe use of @executable_path in 
/Applications/paraview.app/Contents/Python/vtk/vtkCommonCorePython.so with 
restricted binary

Thanks

Fangyi


On 9 Aug 2016, at 17:52, Mohammad Mirzadeh  wrote:

Thanks Utkarsh. Two issues:

1- Looks like I have to use OS X provided python (2.7)? Using any other python 
results in

Fatal Python error: PyThreadState_Get: no current thread

2- using system python I get some unresolved symbol issue with MPI.
Traceback (most recent call last):
   File "", line 1, in 
   File "/Applications/paraview.app/Contents/Python/paraview/simple.py", line 39, in 

 import servermanager
   File "/Applications/paraview.app/Contents/Python/paraview/servermanager.py", line 
55, in 
 from vtk.vtkPVServerImplementationCore import *
   File 
"/Applications/paraview.app/Contents/Python/paraview/vtk/vtkPVServerImplementationCore.py",
 line 9, in 
 from vtkPVServerImplementationCorePython import *
ImportError: 
dlopen(/Applications/paraview.app/Contents/Libraries/vtkPVServerImplementationCorePython.so,
 2): Symbol not found: _MPI_Group_size
   Referenced from: 
/Applications/paraview.app/Contents/Libraries/libmpich.3.3.dylib
   Expected in: flat namespace
  in /Applications/paraview.app/Contents/Libraries/libmpich.3.3.dylib

Any idea why that happens? I have open-mpi installed system-wide (/usr/local).


On Tue, Aug 9, 2016 at 12:15 PM, Utkarsh Ayachit  
wrote:
Attached is a script from an older email. The 5.1.* uses Python 2.7,
so you'll need to update the script accordingly. I haven't tested it
(as I don't have my Mac here), but it should give you some hints.

Utkarsh

On Tue, Aug 9, 2016 at 12:10 PM, Mohammad Mirzadeh  wrote:

Along the same lines, is this possible with prebuilt binaries on OS X? I
have tried including

export PYTHONPATH="$PYTHONPATH:/Applications/paraview.app/Contents/Python"
export

Re: [Paraview] problems using pvbatch in frozen build

[Burlen Loring]

certainly seems like a bug worth fixing. let me know if you want me to 
start a bug report.


On 07/08/2016 01:19 PM, Burlen Loring wrote:
Thanks Utakarsh. It sounds like it may be possible to work around the 
issue by not importing the lookuptable module from simple. However,  
it's "import math" that fails, and math seems like a fairly basic 
module that should always be present. Is there any chance it got left 
out of some packaging manifest used in the freeze process? having it 
be available might be a better solution.


On 07/08/2016 08:38 AM, Utkarsh Ayachit wrote:
I got over such problems by delaying importing of those modules until 
needed. They are not needed for most common use-cases.


See:
https://gitlab.kitware.com/paraview/paraview/commit/3af48fffd924bf5ffd11f576a261ef4eb3ff5897

On Tue, Jul 5, 2016 at 2:35 PM, Burlen Loring <blor...@lbl.gov 
<mailto:blor...@lbl.gov>> wrote:


Hi All,

I'm encountering some issues when trying to use pvbatch from a
frozen build(PARAVIEW_FREEZE_PYTHON=ON). Seems that certain key
python modules are missing.ie <http://missing.ie> math. However,
I can use Python shell feature in the GUI from the same build. Do
we have any idea about what may be wrong with pvbatch?


here is output from a simple test:

nid00048:~$pvbatch pvbatch-test.py
started
Traceback (most recent call last):
  File "pvbatch-test.py", line 3, in 
from paraview.simple import *
  File

"/usr/common/graphics/ParaView/builds/PV-4.4.0/lib/site-packages/paraview/simple.py",
line 40, in 
import lookuptable
  File

"/usr/common/graphics/ParaView/builds/PV-4.4.0/lib/site-packages/paraview/lookuptable.py",
line 21, in 
from math import sqrt
ImportError: No module named math

I tried this as well:

nid00048:~$pvpython
Python 2.7.9 (default, Jan  8 2015, 22:29:31)
[GCC 4.9.1 20140716 (Cray Inc.)] on linux2
Traceback (most recent call last):
  File "/etc/pythonstart", line 7, in 
import readline
ImportError: Excluded frozen object named readline
>>> import math
Traceback (most recent call last):
  File "", line 1, in 
ImportError: No module named math
>>>

Thanks
Burlen

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Re: [Paraview] [Non-DoD Source] making the leap to v5.1 on the cray

[Burlen Loring]

Thanks Rich! Have you had a good experience with 5 thus far?

I am more concerned with the usability aspect rather than the build. For 
instance if a user goes to volume render something and they see a 
trashed screen, they are likely to file  aticket which ccreates a bunch 
of work for me, and worse they are likely to switch to the competition's 
vis tool. Thus I'd rather see something slow but reliable, vs fast and 
flakey. I'm assuming 5 is maturing by now though...


B

On 07/07/2016 12:15 PM, Angelini, Richard C (Rick) CIV USARMY RDECOM ARL 
(US) wrote:

Burlen - we’ve successfully built 4.x and 5.x on a number of different
Crays.   We use the Superbuild and allow ParaView to pull whatever
versions of the dependent libraries it needs and build everything on the
fly.It looks like the recent builds used mesa-11.2.2 …..



Rick Angelini
USArmy Research Laboratory
CISD/HPC Architectures Team
Phone:  410-278-6266




-Original Message-
From: ParaView <paraview-boun...@paraview.org> on behalf of Burlen Loring
<blor...@lbl.gov>
Date: Tuesday, July 5, 2016 at 2:51 PM
To: ParaView <paraview@paraview.org>
Subject: [Non-DoD Source] [Paraview] making the leap to v5.1 on the cray

All active links contained in this email were disabled.  Please verify the
identity of the sender, and confirm the authenticity of all links
contained within the message prior to copying and pasting the address to a
Web browser.






Hi All,

first of all, is 5.1 production ready? or is 4.4 still the way to go in
a production environment? this would be the only install available for
users so it's important that it function reliably/correctly.

re: 5.1, I'm wondering what the recommended mesa config for use with pv
5.1 on cray is?  Which version of mesa have been tested/recommended? is
open swr an option yet? or is llvmpipe still a better bet?

Thanks
Burlen
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Re: [Paraview] making the leap to v5.1 on the cray

[Burlen Loring]

got it thanks!

On 07/05/2016 02:16 PM, Utkarsh Ayachit wrote:

first of all, is 5.1 production ready? or is 4.4 still the way to go in a 
production environment? this would be the only install available for users so 
it's important that it function reliably/correctly.

See this thread:
http://public.kitware.com/pipermail/paraview/2016-June/037389.html


re: 5.1, I'm wondering what the recommended mesa config for use with pv 5.1 on 
cray is?  Which version of mesa have been tested/recommended? is open swr an 
option yet? or is llvmpipe still a better bet?

11.2.* is recommended. OpenSWR is not yet in official release of
Mesa3D (it's still in the RC stage), llvmpipe would still be the best
bet.
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[Paraview] making the leap to v5.1 on the cray

[Burlen Loring]

Hi All,

first of all, is 5.1 production ready? or is 4.4 still the way to go in 
a production environment? this would be the only install available for 
users so it's important that it function reliably/correctly.


re: 5.1, I'm wondering what the recommended mesa config for use with pv 
5.1 on cray is?  Which version of mesa have been tested/recommended? is 
open swr an option yet? or is llvmpipe still a better bet?


Thanks
Burlen
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[Paraview] problems using pvbatch in frozen build

[Burlen Loring]

Hi All,

I'm encountering some issues when trying to use pvbatch from a frozen 
build(PARAVIEW_FREEZE_PYTHON=ON). Seems that certain key python modules 
are missing.ie math. However, I can use Python shell feature in the GUI 
from the same build. Do we have any idea about what may be wrong with 
pvbatch?



here is output from a simple test:

   nid00048:~$pvbatch pvbatch-test.py
   started
   Traceback (most recent call last):
  File "pvbatch-test.py", line 3, in 
from paraview.simple import *
  File
   
"/usr/common/graphics/ParaView/builds/PV-4.4.0/lib/site-packages/paraview/simple.py",
   line 40, in 
import lookuptable
  File
   
"/usr/common/graphics/ParaView/builds/PV-4.4.0/lib/site-packages/paraview/lookuptable.py",
   line 21, in 
from math import sqrt
   ImportError: No module named math

I tried this as well:

   nid00048:~$pvpython
   Python 2.7.9 (default, Jan  8 2015, 22:29:31)
   [GCC 4.9.1 20140716 (Cray Inc.)] on linux2
   Traceback (most recent call last):
  File "/etc/pythonstart", line 7, in 
import readline
   ImportError: Excluded frozen object named readline
>>> import math
   Traceback (most recent call last):
  File "", line 1, in 
   ImportError: No module named math
>>>

Thanks
Burlen
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Re: [Paraview] Memory leak with Catalyst

[Burlen Loring]

I think there is an api in the multi-block writer to disable writing 
metadata. Utkarsh knows, he's the one that figured it out. not sure how 
it applies to your use case. you may not even be using multi-block format...



On 05/23/2016 06:57 AM, Gallagher, Timothy P wrote:


Interesting -- I'd be willing to try it out if you have more details 
(commit hashtag, ticket, etc.), even if I have to figure out how to 
backport it from a newer version.



Thanks,


Tim




*From:* Burlen Loring <burlen.lor...@gmail.com>
*Sent:* Sunday, May 22, 2016 10:30 PM
*To:* Gallagher, Timothy P; Andy Bauer
*Cc:* paraview@paraview.org
*Subject:* Re: [Paraview] Memory leak with Catalyst
btw, we just had similar problem that was entirely explained by vtk 
writer attempting to gather a bunch of arrays to the root node. 
Utkarsh found a way to disable that behavior. I wonder if you are 
hitting the same.


On 5/20/2016 4:36 PM, Gallagher, Timothy P wrote:


Well... not going so well.


If I run a small simulation with massif and the Release build of 
paraview, I don't see any growing memory in time. I also get my VTK 
files and images.



If I run the same simulation linked against a Debug build with 
VTK_DEBUG_LEAKS on, there is a segfault inside one of the 
libvtkRendering libraries (it says libvtkRenderingOp but the rest of 
the name is cut off). If I take the image rendering out of my 
pipeline (comment out the RegisterView call) and leave the VTK file 
writing, it runs fine and doesn't report any leaks. I tried to get 
the segfault to drop a core file, but it won't do it.



I'm thinking that there is an issue in the rendering part causing the 
leak. I have no idea what it could be though -- this is the 4.4.0 
version, is anybody aware of any bug fixes between 4.4.0 and current 
versions that might be relevant?



Thanks for the help,


Tim






*From:* ParaView <paraview-boun...@paraview.org> on behalf of 
Gallagher, Timothy P <tim.gallag...@gatech.edu>

*Sent:* Friday, May 20, 2016 4:17 PM
*To:* Burlen Loring; Andy Bauer
*Cc:* paraview@paraview.org
*Subject:* Re: [Paraview] Memory leak with Catalyst

Thanks for the advice Burlen -- I haven't used Massif before, so this 
is a good opportunity to give it a try.



The initialize/finalize each time approach doesn't work either. I am 
calling the Finalize() routine on the vtkCPProcessor class but then 
when it tries to initialize again, it throws:



Warning: In 
/data4/ParaView/VTK/Parallel/Core/vtkSocketController.cxx, line 50

vtkSocketController (0xa4342f0): Already initialized.


and then crashes. So, hopefully I can sort out the memory leak rather 
than trying to debug why a hacked fix doesn't work!



Tim



--------
*From:* Burlen Loring <burlen.lor...@gmail.com>
*Sent:* Friday, May 20, 2016 3:46 PM
*To:* Gallagher, Timothy P; Andy Bauer
*Cc:* paraview@paraview.org
*Subject:* Re: [Paraview] Memory leak with Catalyst

VTK_DEBUG_LEAKS, although will catch some serious errors, will not 
catch all kinds of leaks. For example you can have leaks where data 
erroneously accumulates with each time step, but is deleted at 
program termination. VTK_DEBUG_LEAKS will not catch that kind of 
error. It's probably better to use massif to profile your code on a 
small one node run. There's an excellent tool called massif 
visualizer to aid in exploring the data generated.



$0.02


On 05/20/2016 11:56 AM, Gallagher, Timothy P wrote:


Hi Andy,


Thanks for the tips. I will get working on the VTK_DEBUG_LEAKS now 
and see what it turns up.



The initialize/finalize every time is definitely a hack and not for 
long-term use. But, sponsors want a report on Monday and we need to 
be able to visualize things for that -- the simulation is too big to 
write data files and post-process later. So I modified the code to 
do that for now until I can find a proper fix.



I'll let you know if I get stuck with the log file.


Thanks again,


Tim




*From:* Andy Bauer <andy.ba...@kitware.com>
*Sent:* Friday, May 20, 2016 2:39 PM
*To:* Gallagher, Timothy P
*Cc:* paraview@paraview.org
*Subject:* Re: [Paraview] Memory leak with Catalyst
Hi Tim,

If you build Catalyst with VTK_DEBUG_LEAKS enabled it is pretty good 
at finding VTK objects that aren't deleted properly. You should be 
able to run this with a small amount of calls to Catalyst as well. 
If you try this and want help understanding the output (if an object 
like a vtkUnstructuredGrid is leaked it will often give a whole 
bunch of false leaks that the unstructured grid is just holding the 
references to), just share your output file and I can take a look at 
it to try and narrow down the culprit. That may be slightly easier 

Re: [Paraview] Memory leak with Catalyst

[Burlen Loring]

btw, we just had similar problem that was entirely explained by vtk 
writer attempting to gather a bunch of arrays to the root node. Utkarsh 
found a way to disable that behavior. I wonder if you are hitting the same.


On 5/20/2016 4:36 PM, Gallagher, Timothy P wrote:


Well... not going so well.


If I run a small simulation with massif and the Release build of 
paraview, I don't see any growing memory in time. I also get my VTK 
files and images.



If I run the same simulation linked against a Debug build with 
VTK_DEBUG_LEAKS on, there is a segfault inside one of the 
libvtkRendering libraries (it says libvtkRenderingOp but the rest of 
the name is cut off). If I take the image rendering out of my pipeline 
(comment out the RegisterView call) and leave the VTK file writing, it 
runs fine and doesn't report any leaks. I tried to get the segfault to 
drop a core file, but it won't do it.



I'm thinking that there is an issue in the rendering part causing the 
leak. I have no idea what it could be though -- this is the 4.4.0 
version, is anybody aware of any bug fixes between 4.4.0 and current 
versions that might be relevant?



Thanks for the help,


Tim






*From:* ParaView <paraview-boun...@paraview.org> on behalf of 
Gallagher, Timothy P <tim.gallag...@gatech.edu>

*Sent:* Friday, May 20, 2016 4:17 PM
*To:* Burlen Loring; Andy Bauer
*Cc:* paraview@paraview.org
*Subject:* Re: [Paraview] Memory leak with Catalyst

Thanks for the advice Burlen -- I haven't used Massif before, so this 
is a good opportunity to give it a try.



The initialize/finalize each time approach doesn't work either. I am 
calling the Finalize() routine on the vtkCPProcessor class but then 
when it tries to initialize again, it throws:



Warning: In /data4/ParaView/VTK/Parallel/Core/vtkSocketController.cxx, 
line 50

vtkSocketController (0xa4342f0): Already initialized.


and then crashes. So, hopefully I can sort out the memory leak rather 
than trying to debug why a hacked fix doesn't work!



Tim



----
*From:* Burlen Loring <burlen.lor...@gmail.com>
*Sent:* Friday, May 20, 2016 3:46 PM
*To:* Gallagher, Timothy P; Andy Bauer
*Cc:* paraview@paraview.org
*Subject:* Re: [Paraview] Memory leak with Catalyst

VTK_DEBUG_LEAKS, although will catch some serious errors, will not 
catch all kinds of leaks. For example you can have leaks where data 
erroneously accumulates with each time step, but is deleted at program 
termination. VTK_DEBUG_LEAKS will not catch that kind of error. It's 
probably better to use massif to profile your code on a small one node 
run. There's an excellent tool called massif visualizer to aid in 
exploring the data generated.



$0.02


On 05/20/2016 11:56 AM, Gallagher, Timothy P wrote:


Hi Andy,


Thanks for the tips. I will get working on the VTK_DEBUG_LEAKS now 
and see what it turns up.



The initialize/finalize every time is definitely a hack and not for 
long-term use. But, sponsors want a report on Monday and we need to 
be able to visualize things for that -- the simulation is too big to 
write data files and post-process later. So I modified the code to do 
that for now until I can find a proper fix.



I'll let you know if I get stuck with the log file.


Thanks again,


Tim




*From:* Andy Bauer <andy.ba...@kitware.com>
*Sent:* Friday, May 20, 2016 2:39 PM
*To:* Gallagher, Timothy P
*Cc:* paraview@paraview.org
*Subject:* Re: [Paraview] Memory leak with Catalyst
Hi Tim,

If you build Catalyst with VTK_DEBUG_LEAKS enabled it is pretty good 
at finding VTK objects that aren't deleted properly. You should be 
able to run this with a small amount of calls to Catalyst as well. If 
you try this and want help understanding the output (if an object 
like a vtkUnstructuredGrid is leaked it will often give a whole bunch 
of false leaks that the unstructured grid is just holding the 
references to), just share your output file and I can take a look at 
it to try and narrow down the culprit. That may be slightly easier to 
use than Valgrind.


Beyond this, you could maybe try the same run but without doing any 
Catalyst work to see what happens then. That may be a lot of compute 
cycles but I'm not sure how else to try and bisect where the memory 
leak is occurring.


Initializing and finalizing Catalyst every time you want output would 
probably work but I'd think there may be significant overhead doing 
it like this. Plus, it's not really solving the problem -- just 
avoiding it.


Best,
Andy


On Fri, May 20, 2016 at 12:57 PM, Gallagher, Timothy P 
<tim.gallag...@gatech.edu <mailto:tim.gallag...@gatech.edu>> wrote:


Hi,


One of our users is running a very big simulation and writing out
images of two slices (two different views) every

Re: [Paraview] Memory leak with Catalyst

[Burlen Loring]

VTK_DEBUG_LEAKS, although will catch some serious errors, will not catch 
all kinds of leaks. For example you can have leaks where data 
erroneously accumulates with each time step, but is deleted at program 
termination. VTK_DEBUG_LEAKS will not catch that kind of error. It's 
probably better to use massif to profile your code on a small one node 
run. There's an excellent tool called massif visualizer to aid in 
exploring the data generated.



$0.02


On 05/20/2016 11:56 AM, Gallagher, Timothy P wrote:


Hi Andy,


Thanks for the tips. I will get working on the VTK_DEBUG_LEAKS now and 
see what it turns up.



The initialize/finalize every time is definitely a hack and not for 
long-term use. But, sponsors want a report on Monday and we need to be 
able to visualize things for that -- the simulation is too big to 
write data files and post-process later. So I modified the code to do 
that for now until I can find a proper fix.



I'll let you know if I get stuck with the log file.


Thanks again,


Tim




*From:* Andy Bauer 
*Sent:* Friday, May 20, 2016 2:39 PM
*To:* Gallagher, Timothy P
*Cc:* paraview@paraview.org
*Subject:* Re: [Paraview] Memory leak with Catalyst
Hi Tim,

If you build Catalyst with VTK_DEBUG_LEAKS enabled it is pretty good 
at finding VTK objects that aren't deleted properly. You should be 
able to run this with a small amount of calls to Catalyst as well. If 
you try this and want help understanding the output (if an object like 
a vtkUnstructuredGrid is leaked it will often give a whole bunch of 
false leaks that the unstructured grid is just holding the references 
to), just share your output file and I can take a look at it to try 
and narrow down the culprit. That may be slightly easier to use than 
Valgrind.


Beyond this, you could maybe try the same run but without doing any 
Catalyst work to see what happens then. That may be a lot of compute 
cycles but I'm not sure how else to try and bisect where the memory 
leak is occurring.


Initializing and finalizing Catalyst every time you want output would 
probably work but I'd think there may be significant overhead doing it 
like this. Plus, it's not really solving the problem -- just avoiding it.


Best,
Andy


On Fri, May 20, 2016 at 12:57 PM, Gallagher, Timothy P 
> wrote:


Hi,


One of our users is running a very big simulation and writing out
images of two slices (two different views) every 1000 iterations
and writing out the data for the two slices (two different data
writers) as VTK files every 5000 iterations. It is using Paraview
4.4.


After 21000 iterations, the simulation is killed because the
memory on the compute nodes fills up. I usually know how to track
down memory problems in our code using valgrind and related tools,
but is that the right way to go to try and find this problem?


Are there any tips on how to isolate where the problem may be? I
don't know if it is in the adapter, or in paraview itself. Has
anybody encountered problems with runaway memory using Catalyst in
4.4 when writing images or VTK files?


I know when we use pvpython to generate images and loop over many
files, sometimes the memory also blows up and so we usually move
the loop over the files outside the pvpython script and into a
driver script that executes a new pvpython for each file. Is there
a way to shut down/start up Catalyst each time it needs to write
something? Is that advisable?


Thanks,


Tim


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[Paraview] paraview crashes during startup

[Burlen Loring]

A fresh clone as of midday yesterday PV client fails to launch with the 
below error. I enabled mpi and python, everything else is default value.


libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast
X Error: BadValue (integer parameter out of range for operation) 2
  Extension:153 (Uknown extension)
  Minor opcode: 3 (Unknown request)
  Resource id:  0x0

apparently ParaView's attempting to load swrast,  a mesa renderer, 
although I have nvidia gpu and drivers. I also tried the OpenGL2 backend 
and encountered the same error. To work around this I manually located 
the nvidia headers and opengl library and forced cmake to use those.


I'm not sure if you want to call this a bug in ParaView or the CMake 
find opengl module. But ParaView should probably correctly detect and 
use nvidia drivers, and ignore mesa drivers, which are likely present on 
every system no matter if third party gpu/driver is installed or not.


Burlen


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Re: [Paraview] PYTHONPATH environmental variable

[Burlen Loring]

are you by chance mixing two python installs? like one from a paraview 
binary you didn't build yourself, and your system python?


On 06/17/2015 10:47 AM, Felix Salazar wrote:

Tried it, but for some reason, it breaks python

$ python
Could not find platform independent libraries prefix
Could not find platform dependent libraries exec_prefix
Consider setting $PYTHONHOME to prefix[:exec_prefix]
ImportError: No module named site

*
Félix Salazar
*/felix.sala...@polymtl.ca mailto:felix.sala...@polymtl.ca/*
*Étudiant au doctorat - PhD Student
/École Polytechnique de Montréal/
/LADYF/
//Lab. de dynamique des fluides
(514) 340 4711 ext 2489
Local: C-318.21.3*
*

On Wed, Jun 17, 2015 at 10:19 AM, Burlen Loring 
burlen.lor...@gmail.com mailto:burlen.lor...@gmail.com wrote:


You also have to prepend the paths with the .so's to
LD_LIBRARY_PATH before starting python.

Burlen


On 06/16/2015 07:19 PM, Felix Salazar wrote:

Hello community,

I normally run my Paraview scripts in pvpython, so far without
issues. But I got some problems using specific Python functions
(multiprocess), and decided to switch to import paraview
libraries directly within Python

I set my PYTHONPATH variable to the installation library where
the files are located. Got a few errors, and added more
directories, progressively clearing and decreasing the number of
errors, until a point where I'm getting this message

*Error: Could not import vtkCommonComputationalGeometryPython*
Traceback (most recent call last):
  File /home/pissarro/fesal/Tools/zReattachment-NP.py, line 4,
in module
except: from paraview.simple import *
  File

/apps/local-linux/paraview4.01/lib/paraview-4.0/site-packages/paraview/simple.py,
line 41, in module
import servermanager
  File

/apps/local-linux/paraview4.01/lib/paraview-4.0/site-packages/paraview/servermanager.py,
line 48, in module
import paraview, re, os, os.path, new, sys, atexit, vtk
  File

/apps/local-linux/paraview4.01/lib/paraview-4.0/site-packages/paraview/vtk/__init__.py,
line 7, in module
from vtkCommonCorePython import *
*ImportError: libvtkCommonCorePython27D-pv4.0.so.1: cannot open
shared object file: No such file or directory*

At this point my PYTHONPATH variable is:


PYTHONPATH=*/apps/local-linux/paraview4.01/lib/paraview-4.0*:/apps/local-linux/paraview4.01/lib/paraview-4.0/site-packages/paraview/vtk:/apps/local-linux/paraview4.01/lib/paraview-4.0/site-packages:/apps/local-linux/paraview4.01/bin

And the file libvtkCommonCorePython27D-pv4.0.so.1 is in
*/apps/local-linux/paraview4.01/lib/paraview-4.0/*

Hence, that location is part of the path variable, but for some
reason is not recognized. Is there any specific or recommended
order to load these directories in the PYTHONPATH variable?

Also, if I type help('modules') in a python console, I get this
error message before the list of modules

Please wait a moment while I gather a list of all available
modules...

Error: Could not import vtkCommonComputationalGeometryPython

Thanks,

*
Félix Salazar
*/felix.sala...@polymtl.ca mailto:felix.sala...@polymtl.ca/*
*Étudiant au doctorat - PhD Student
/École Polytechnique de Montréal/



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Re: [Paraview] PYTHONPATH environmental variable

[Burlen Loring]

You also have to prepend the paths with the .so's to LD_LIBRARY_PATH 
before starting python.


Burlen

On 06/16/2015 07:19 PM, Felix Salazar wrote:

Hello community,

I normally run my Paraview scripts in pvpython, so far without issues. 
But I got some problems using specific Python functions 
(multiprocess), and decided to switch to import paraview libraries 
directly within Python


I set my PYTHONPATH variable to the installation library where the 
files are located. Got a few errors, and added more directories, 
progressively clearing and decreasing the number of errors, until a 
point where I'm getting this message


*Error: Could not import vtkCommonComputationalGeometryPython*
Traceback (most recent call last):
  File /home/pissarro/fesal/Tools/zReattachment-NP.py, line 4, in 
module

except: from paraview.simple import *
  File 
/apps/local-linux/paraview4.01/lib/paraview-4.0/site-packages/paraview/simple.py, 
line 41, in module

import servermanager
  File 
/apps/local-linux/paraview4.01/lib/paraview-4.0/site-packages/paraview/servermanager.py, 
line 48, in module

import paraview, re, os, os.path, new, sys, atexit, vtk
  File 
/apps/local-linux/paraview4.01/lib/paraview-4.0/site-packages/paraview/vtk/__init__.py, 
line 7, in module

from vtkCommonCorePython import *
*ImportError: libvtkCommonCorePython27D-pv4.0.so.1: cannot open shared 
object file: No such file or directory*


At this point my PYTHONPATH variable is:

PYTHONPATH=*/apps/local-linux/paraview4.01/lib/paraview-4.0*:/apps/local-linux/paraview4.01/lib/paraview-4.0/site-packages/paraview/vtk:/apps/local-linux/paraview4.01/lib/paraview-4.0/site-packages:/apps/local-linux/paraview4.01/bin

And the file libvtkCommonCorePython27D-pv4.0.so.1 is in 
*/apps/local-linux/paraview4.01/lib/paraview-4.0/*


Hence, that location is part of the path variable, but for some reason 
is not recognized. Is there any specific or recommended order to load 
these directories in the PYTHONPATH variable?


Also, if I type help('modules') in a python console, I get this error 
message before the list of modules


Please wait a moment while I gather a list of all available modules...

Error: Could not import vtkCommonComputationalGeometryPython

Thanks,

*
Félix Salazar
*/felix.sala...@polymtl.ca mailto:felix.sala...@polymtl.ca/*
*Étudiant au doctorat - PhD Student
/École Polytechnique de Montréal/



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Re: [Paraview] Selecting volume rendering causes output to vanish

[Burlen Loring]

It's hard for me to say, I've never seen the stein mesh package, and 
googling doesn't turn anything up. Perhaps you could share the dataset 
itself? I'm sure someone here could quickly reproduce the issue and 
perhaps suggest a fix.


On 6/12/2015 3:27 PM, Jeff Becker wrote:

On 06/11/2015 01:05 PM, Burlen Loring wrote:

you ran out of memory.

You may need more than 1 node, and a parallel file format.

You mentioned that you had a grid of 500 x 500 points. You could save 
a lot of memory by using vtkImageData, vtkRectilinearMesh or 
vtkStructuredGrid if your data is amenable to one of those.


I switched to using vtkStructuredGrid. However, after reading the file 
in ParaView, and attempting to volume render I get the seg. fault in 
pvserver below. I am creating my grid in python as follows (steinmesh 
contains the grid coordinates):



import os
import numpy as np
import steinmesh as mesh
import itertools
import vtk
from vtk.util import numpy_support

in_fname='/nobackupp9/pmoran/stein/mhd48-1/dat/mhd48h1new_670.8.dat'
out_fname='/nobackup/jcbecker/steinBmag.vts'
f = open(in_fname,rb)
bx = 6
npoints = mesh.MX*mesh.MY*mesh.MZ
f.seek(bx*npoints*np.dtype('f4').itemsize,os.SEEK_SET)

steinbmag = np.square(np.fromfile(f,dtype=np.dtype('f4'),count=npoints))
steinbmag += np.square(np.fromfile(f,dtype=np.dtype('f4'),count=npoints))
steinbmag += np.square(np.fromfile(f,dtype=np.dtype('f4'),count=npoints))
steinbmag = np.sqrt(steinbmag)

f.close()

grid = [x for x in itertools.product(mesh.xcoords, mesh.ycoords, 
mesh.zcoords)]


pcoords = vtk.vtkDoubleArray()
pcoords.SetNumberOfComponents(3)
pcoords.SetNumberOfTuples(npoints)
for i in range(npoints):
   pcoords.SetTuple3(*((i,) + grid[i]))
pts = vtk.vtkPoints()
pts.SetData(pcoords)

sgrid = vtk.vtkStructuredGrid()
sgrid.SetDimensions(mesh.MX,mesh.MY,mesh.MZ)
sgrid.SetPoints(pts)

bmagV = numpy_support.numpy_to_vtk(steinbmag,deep=True)
bmagV.SetName('B field magnitude')
sgrid.GetPointData().SetScalars(bmagV)

writer = vtk.vtkXMLStructuredGridWriter()
writer.SetFileName(out_fname)
writer.SetInputData(sgrid)
writer.SetDataModeToBinary()
writer.Write()

Can anyone see what's wrong? Thanks.

-jeff


Program received signal SIGSEGV, Segmentation fault.
0x2fb1c327 in vtkDataArrayTemplatelong long::GetValue(long 
long) ()
   from 
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkCommonCore-pv4.3.so.1

(gdb) bt
#0  0x2fb1c327 in vtkDataArrayTemplatelong 
long::GetValue(long long)

()
   from 
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkCommonCore-pv4.3.so.1

#1  0x2e991d71 in vtkCellArray::GetMaxCellSize() ()
   from 
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkCommonDataModel-pv4.3.so.1

#2  0x2c44dde9 in vtkCellCenterDepthSort::ComputeCellCenters() ()
   from 
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1

#3  0x2c44e593 in vtkCellCenterDepthSort::InitTraversal() ()
   from 
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1
#4  0x2aaab82fc2dd in 
vtkOpenGLProjectedTetrahedraMapper::ProjectTetrahedra(vtkRenderer*, 
vtkVolume*) ()
   from 
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingVolumeOpenGL-pv4.3.so.1
#5  0x2aaab82f7997 in 
vtkOpenGLProjectedTetrahedraMapper::Render(vtkRenderer*, vtkVolume*) ()
   from 
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingVolumeOpenGL-pv4.3.so.1
#6  0x2c4d0118 in 
vtkVolume::RenderVolumetricGeometry(vtkViewport*) ()
   from 
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1
#7  0x2c4e1198 in 
vtkLODProp3D::RenderVolumetricGeometry(vtkViewport*)

()
   from 
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1
#8  0x2aaab4f3a4eb in 
vtkPVLODVolume::RenderVolumetricGeometry(vtkViewport*) ()
   from 
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVVTKExtensionsRendering-pv4.3.so.1

#9  0x2c4b94ee in vtkRenderer::UpdateGeometry() ()
   from 
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1
#10 0x2aaab4f2d751 in vtkPVDefaultPass::Render(vtkRenderState 
const*) ()
   from 
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVVTKExtensionsRendering-pv4.3.so.1

#11 0x2aaaba0d135b in vtkCameraPass::Render(vtkRenderState const*) ()
   from 
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingOpenGL-pv4.3.so.1

#12 0x2aaaba1436c0 in vtkOpenGLRenderer::DeviceRender() ()
   from 
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingOpenGL-pv4.3.so.1

#13 0x2c4bb18d in vtkRenderer::Render() ()
   from 
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1

#14 0x2c4b8429 in vtkRendererCollection::Render

Re: [Paraview] Selecting volume rendering causes output to vanish

[Burlen Loring]

500^3 should not be an issue. Still worth seeing if you can get the test 
data from wavelet source to display as a sanity check. Another thing 
that occasionally occurs, if the there is one or two extremely large 
outlying values in your dataset (say from writing random unitialized 
memory), the default transfer function makes the dataset invisible. 
Would be worth checking the range of your data and experimenting with 
transfer function as well.


On 06/10/2015 12:03 PM, David E DeMarle wrote:
Probably the content isn't amenable to volume rendering. To be so, the 
unstructured grid has to have volumetric cells in it (tets, voxels, 
etc). If it just has polys or lines or points in it, they won't 
appear. You'll have to resample of splat onto the data onto a 
volumetric grid in that case.





David E DeMarle
Kitware, Inc.
RD Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Wed, Jun 10, 2015 at 2:58 PM, Aashish Chaudhary 
aashish.chaudh...@kitware.com mailto:aashish.chaudh...@kitware.com 
wrote:


No, I don't think so. It would be nice if you can try Burlen
suggestion to see if it works for built in datasets / sources.

- Aashish

On Wed, Jun 10, 2015 at 2:49 PM, Jeff Becker
jeffrey.c.bec...@nasa.gov mailto:jeffrey.c.bec...@nasa.gov wrote:

On 06/10/2015 11:46 AM, Burlen Loring wrote:

Hmm. If Bunyk ray cast doesn't work some thing strange is
going on as that is a software(non gpu) algorithm and
should always work.

Can you get anything to show up using a small test data?
For example create a wavelet source and apply a threshold
(use default values) to convert to unstructured data. If
that works maybe something with your input data, or size
of it.


It's a 500 by 500 by 500 grid of floats - is that too big?


On 06/10/2015 11:27 AM, Jeff Becker wrote:

On 06/10/2015 11:06 AM, Burlen Loring wrote:

2 things to try: set the remote render threshold
to zero, and if that doesn't get it to show up,
change the mapper to Bunyk ray cast.  One of those
usually works depending on what the cause of the
issue is.


I have both of those set - no luck. BTW, this is
ParaView 4.3.1 on an NVIDIA backend. glxinfo shows:

$ glxinfo | head -30
name of display: :0.0
display: :0  screen: 0
direct rendering: Yes
server glx vendor string: NVIDIA Corporation
server glx version string: 1.4
server glx extensions:
GLX_EXT_visual_info, GLX_EXT_visual_rating,
GLX_SGIX_fbconfig,
GLX_SGIX_pbuffer, GLX_SGI_video_sync,
GLX_SGI_swap_control,
GLX_EXT_swap_control, GLX_EXT_swap_control_tear,
GLX_EXT_texture_from_pixmap, GLX_EXT_buffer_age,
GLX_ARB_create_context,
GLX_ARB_create_context_profile,
GLX_EXT_create_context_es_profile,
GLX_EXT_create_context_es2_profile,
GLX_ARB_create_context_robustness,
GLX_NV_delay_before_swap, GLX_EXT_stereo_tree,
GLX_ARB_multisample,
GLX_NV_float_buffer, GLX_ARB_fbconfig_float,
GLX_EXT_framebuffer_sRGB,
GLX_NV_multisample_coverage
client glx vendor string: NVIDIA Corporation
client glx version string: 1.4
client glx extensions:
GLX_ARB_get_proc_address, GLX_ARB_multisample,
GLX_EXT_visual_info,
GLX_EXT_visual_rating, GLX_EXT_import_context,
GLX_SGI_video_sync,
GLX_NV_swap_group, GLX_NV_video_out,
GLX_SGIX_fbconfig, GLX_SGIX_pbuffer,
GLX_SGI_swap_control, GLX_EXT_swap_control,
GLX_EXT_swap_control_tear,
GLX_EXT_buffer_age, GLX_ARB_create_context,
GLX_ARB_create_context_profile, GLX_NV_float_buffer,
GLX_ARB_fbconfig_float, GLX_EXT_fbconfig_packed_float,
GLX_EXT_texture_from_pixmap, GLX_EXT_framebuffer_sRGB,
GLX_NV_present_video, GLX_NV_copy_image,
GLX_NV_multisample_coverage,
GLX_NV_video_capture,
GLX_EXT_create_context_es_profile,
GLX_EXT_create_context_es2_profile,
GLX_ARB_create_context_robustness,
GLX_NV_delay_before_swap, GLX_EXT_stereo_tree


On 06/10/2015 11:00 AM, Jeff Becker wrote:

Hi. I have an unstructured grid file that
opens

Re: [Paraview] Selecting volume rendering causes output to vanish

[Burlen Loring]

2 things to try: set the remote render threshold to zero, and if that 
doesn't get it to show up, change the mapper to Bunyk ray cast.  One of 
those usually works depending on what the cause of the issue is.


On 06/10/2015 11:00 AM, Jeff Becker wrote:
Hi. I have an unstructured grid file that opens and displays in 
Surface Rendering mode. If I switch to Volume Rendering, I don't see 
any output. Any ideas?


Thanks.

-jeff
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Re: [Paraview] Selecting volume rendering causes output to vanish

[Burlen Loring]

Hmm. If Bunyk ray cast doesn't work some thing strange is going on as 
that is a software(non gpu) algorithm and should always work.


Can you get anything to show up using a small test data? For example 
create a wavelet source and apply a threshold (use default values) to 
convert to unstructured data. If that works maybe something with your 
input data, or size of it.


On 06/10/2015 11:27 AM, Jeff Becker wrote:

On 06/10/2015 11:06 AM, Burlen Loring wrote:
2 things to try: set the remote render threshold to zero, and if that 
doesn't get it to show up, change the mapper to Bunyk ray cast.  One 
of those usually works depending on what the cause of the issue is.


I have both of those set - no luck. BTW, this is ParaView 4.3.1 on an 
NVIDIA backend. glxinfo shows:


$ glxinfo | head -30
name of display: :0.0
display: :0  screen: 0
direct rendering: Yes
server glx vendor string: NVIDIA Corporation
server glx version string: 1.4
server glx extensions:
GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGIX_fbconfig,
GLX_SGIX_pbuffer, GLX_SGI_video_sync, GLX_SGI_swap_control,
GLX_EXT_swap_control, GLX_EXT_swap_control_tear,
GLX_EXT_texture_from_pixmap, GLX_EXT_buffer_age, 
GLX_ARB_create_context,

GLX_ARB_create_context_profile, GLX_EXT_create_context_es_profile,
GLX_EXT_create_context_es2_profile, 
GLX_ARB_create_context_robustness,

GLX_NV_delay_before_swap, GLX_EXT_stereo_tree, GLX_ARB_multisample,
GLX_NV_float_buffer, GLX_ARB_fbconfig_float, 
GLX_EXT_framebuffer_sRGB,

GLX_NV_multisample_coverage
client glx vendor string: NVIDIA Corporation
client glx version string: 1.4
client glx extensions:
GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_visual_info,
GLX_EXT_visual_rating, GLX_EXT_import_context, GLX_SGI_video_sync,
GLX_NV_swap_group, GLX_NV_video_out, GLX_SGIX_fbconfig, 
GLX_SGIX_pbuffer,
GLX_SGI_swap_control, GLX_EXT_swap_control, 
GLX_EXT_swap_control_tear,

GLX_EXT_buffer_age, GLX_ARB_create_context,
GLX_ARB_create_context_profile, GLX_NV_float_buffer,
GLX_ARB_fbconfig_float, GLX_EXT_fbconfig_packed_float,
GLX_EXT_texture_from_pixmap, GLX_EXT_framebuffer_sRGB,
GLX_NV_present_video, GLX_NV_copy_image, GLX_NV_multisample_coverage,
GLX_NV_video_capture, GLX_EXT_create_context_es_profile,
GLX_EXT_create_context_es2_profile, 
GLX_ARB_create_context_robustness,

GLX_NV_delay_before_swap, GLX_EXT_stereo_tree



On 06/10/2015 11:00 AM, Jeff Becker wrote:
Hi. I have an unstructured grid file that opens and displays in 
Surface Rendering mode. If I switch to Volume Rendering, I don't see 
any output. Any ideas?


Thanks.

-jeff
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Re: [Paraview] save 'Surface LIC' as texture

[Burlen Loring]

cd into VTK/Rendering/OpenGL and grep for  vtkTextureIO::Write, you'll 
find all the spots I was saving textures. There are some preprocessor 
macros to enable it. Good luck.


On 6/5/2015 1:34 AM, Göbbert, Jens Henrik wrote:

Hi Burlen,

thanks for your answer.
But somehow bad news for me :)

I will try to add this feature than - it might help others, too.
Can you give me some more hints where I can find this mechanism for 
sucking textures back from the gpu

and perhaps even how to use it for debugging?

Best
Jens Henrik


*From:* Burlen Loring [burlen.lor...@gmail.com]
*Sent:* Thursday, June 04, 2015 5:45 PM
*To:* Göbbert, Jens Henrik; paraview@paraview.org
*Subject:* Re: [Paraview] save 'Surface LIC' as texture

I think it could be done if you're willing to hack into PV. There is 
already some mechanism in there for sucking textures back from the gpu 
and writing them to disk for debugging. It's not exactly what you need 
but at least will illustrate pulling data from GPU.


a potential issue with this idea is that the result from the LIC is 
very view dependent, you may be restricted to use same view settings 
in your app/blender. maybe better just to write the LIC shader in blender.


On 06/04/2015 04:07 AM, Göbbert, Jens Henrik wrote:

Hello everyone,

I am using ParaView for some time now and love its representation of 
vector fields on surfaces by
'SurfaceLIC' 
(http://www.paraview.org/Wiki/ParaView/Line_Integral_Convolution). 
http://www.paraview.org/Wiki/ParaView/Line_Integral_Convolution%29.
Beyond that, lots of other representations of scientific data are of 
course simply great 


I would like to save this textures and the geometrie (incl. texture 
coordinates) of the surface
to view it later in our own OpenGL virtual reality application (or 
Blender).


ParaView can load textures 
(http://www.paraview.org/Wiki/ParaView:Texture),

but how can I save them ?

Does anyone has an idea ... including source code modifications, 
which might make things like that possible.


Best,
Jens Henrik



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Re: [Paraview] save 'Surface LIC' as texture

[Burlen Loring]

I think it could be done if you're willing to hack into PV. There is 
already some mechanism in there for sucking textures back from the gpu 
and writing them to disk for debugging. It's not exactly what you need 
but at least will illustrate pulling data from GPU.


a potential issue with this idea is that the result from the LIC is very 
view dependent, you may be restricted to use same view settings in your 
app/blender. maybe better just to write the LIC shader in blender.


On 06/04/2015 04:07 AM, Göbbert, Jens Henrik wrote:

Hello everyone,

I am using ParaView for some time now and love its representation of 
vector fields on surfaces by
'SurfaceLIC' 
(http://www.paraview.org/Wiki/ParaView/Line_Integral_Convolution). 
http://www.paraview.org/Wiki/ParaView/Line_Integral_Convolution%29.
Beyond that, lots of other representations of scientific data are of 
course simply great 


I would like to save this textures and the geometrie (incl. texture 
coordinates) of the surface
to view it later in our own OpenGL virtual reality application (or 
Blender).


ParaView can load textures 
(http://www.paraview.org/Wiki/ParaView:Texture),

but how can I save them ?

Does anyone has an idea ... including source code modifications, which 
might make things like that possible.


Best,
Jens Henrik



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Re: [Paraview] ParaView 4.3.1 client runs X out of memory

[Burlen Loring]

Hi Jeff,

It really sounds like you are unintentionally using X forwarding. It 
could be baked into your ssh config or a bash alias.

I see the window with the gears

if you are really doing remote rendering, you won't see the window.

you may be able to confirm accidental X forward using ssh with -vv 
option. there would be a bunch of X connection messages if it was in use.


also output of glxinfo may have some useful info. When I have remote 
rendering setup I see


   name of display: :0.0
   display: :0  screen: 0
   direct rendering: Yes

with ssh -X

   name of display: localhost:10.0
   display: localhost:10  screen: 0
   direct rendering: No (If you want to find out why, try setting
   LIBGL_DEBUG=verbose)

Burlen

On 05/22/2015 12:10 PM, Jeff Becker wrote:

On 05/22/2015 07:28 AM, Utkarsh Ayachit wrote:

Jeff,

Can you make sure the Remote Render Threshold is set to 0?

It is


Also, do you have an X server running (and accessible) on the backend
nodes? You're not using ssh -X to login to the backend nodes, right?


I do start an X server on the backend (and I don't use ssh -X). 
However, when I test the configuration using glxgears,
I see the window with the gears but they don't turn even though the 
app tells me how many frames

it rendered every 5 seconds.

My setup goes from my desktop (with GPU) through a front-end node 
(without GPU) to the backend (with GPU). Maybe some additional 
configuration is needed.


It seems like I need to get glxgears working properly before I try 
Paraview. What should I try? Thanks.


-jeff


On Thu, May 21, 2015 at 4:54 PM, Jeff Becker 
jeffrey.c.bec...@nasa.gov wrote:
Hi. I created a VTK unstructured grid (.vtu) file for a 500 by 500 
by 500
point data set. In order to visualize it, I fire up 8 pvservers on 
my GPU

multicore backend node using:

  mpirun -np 8 pvserver --client-host=XXX --use-offscreen-rendering

and connect to the root server from my ParaView client. I then open 
my vtu
file and hit apply, I can see the file gets read in, and then 
nothing much

else happens except X on my client grows to fill all of memory, and my
client system (my desktop) becomes unusable. I'm guessing that the 
client is

getting overwhelmed with X requests.

What am I doing wrong, and how to fix?

Thanks.

-jeff
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Re: [Paraview] Multiple GPUs per node

[Burlen Loring]

btw, here is an batch script 
https://github.com/burlen/pvserver-configs/blob/master/servers/nautilus/3.10.0-x/start_pvserver-x.qsub 
starting ParaView with pvservers assigned to GPU's round robin, from the 
SGI UV 1000 with 8 GPU. The other tricky aspect of running PV on 
multiple GPU is configuring X11. Here is the xorg.conf 
https://github.com/burlen/pvserver-configs/blob/master/servers/nautilus/3.10.0-x/xorg.conf 
on this system, each card has it's own device, screen, and layout.


Hope it helps.
Burlen

On 05/10/2015 09:30 PM, srikanth.nage...@stfc.ac.uk wrote:

Hi John,

You need to run 4 X servers, one X server per GPU card.
http://www.paraview.org/Wiki/Setting_up_a_ParaView_Server#Multiple_GPUs_Per_Nodehttp://www.paraview.org/Wiki/Setting_up_a_ParaView_Server#Multiple_GPUs_Per_Node

Sri

From: ParaView [paraview-boun...@paraview.org] on behalf of John Moore 
[johnpmoor...@gmail.com]
Sent: 08 May 2015 17:03
To: paraview@paraview.org
Subject: [Paraview] Multiple GPUs per node

I am trying to take advantage of all four GPUs on a 32 node Amazon ec2 cluster. 
However, I seem to only be able to utilize the first GPU.

I run pvserver as follows:

1)  Manually start an X display with the command :   sudo X :0 
2)  run pvserver with the following command (using OpenMPI's mpirun):
  mpirun -np 16 pvserver -display :0.0 : -np 16 pvserver -display :0.1

When I try to connect the client, I get an error saying that the client could 
not connect to the remote display. Everything works fine using display :0.0 
only.

Does anyone know what I might be doing wrong here? Thank you for your time!

John
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[Paraview] Fwd: Re: Fwd: Image Doesn't load correctly

[Burlen Loring]

 Forwarded Message 
Subject:Re: [Paraview] Fwd: Image Doesn't load correctly
Date:   Tue, 05 May 2015 09:14:06 -0700
From:   Burlen Loring blor...@lbl.gov
To: Dean, Kevin kevin.d...@decisionsciencescorp.com



ParaView should set it after it determines if the reader can read it. 
Did you also implement CanReadFile? Maybe the problem is in that function.


On 05/05/2015 09:09 AM, Dean, Kevin wrote:


-- Forwarded message --
From: *Dean, Kevin* kevin.d...@decisionsciencescorp.com 
mailto:kevin.d...@decisionsciencescorp.com

Date: Mon, May 4, 2015 at 5:10 PM
Subject: Re: [Paraview] Image Doesn't load correctly
To: Burlen Loring burlen.lor...@gmail.com 
mailto:burlen.lor...@gmail.com



awesome, thanks, that did it.

One more question. Is there a way to debug the FileName aspect of the 
reader. I can't figure out how it's supposed to get set. The only way 
I can get the image to show is by hard

coding it within the RequestData() function.

Thanks Again

Kevin E. Dean

On Mon, May 4, 2015 at 11:33 AM, Burlen Loring 
burlen.lor...@gmail.com mailto:burlen.lor...@gmail.com wrote:


Hi Kevin.

Your RequestInformation looks a little bare. Unless things have
changed recently, you might need to set WHOLE_EXTENT, ORIGIN,
SPACING, CAN_PRODUCE_SUB_EXTENT keys there. and if you support
parallel IO honor the requested extent in RequestData.

Burlen


On 05/04/2015 09:52 AM, Dean, Kevin wrote:

So I am still having a few issues with the reader. I have checked
the output from the information Panel. And it seems as if all the
information is the same. So maybe the data is getting deleted
somehow (I'm not sure, but here is a snippet of my code);

int vtkPVPROTOImageReader::RequestInformation (
   vtkInformation*,
   vtkInformationVector**,
   vtkInformationVector* outputVector)
{
   vtkInformation* outInfo = outputVector-GetInformationObject(0);
vtkDataObject::SetPointDataActiveScalarInfo(outInfo,
VTK_UNSIGNED_CHAR, 1);

   return 1;
}

int vtkPVPROTOImageReader::RequestData(vtkInformation
*vtkNotUsed(request),
vtkInformationVector **inputVector,
vtkInformationVector *outputVector)
{
   ... conversion code from protobuf

  /* Convert from protobuf to vtkImageData */
  vtkSmartPointervtkImageData image = function converting to
protobuf;

  vtkDataArray* scalars = image-GetPointData()-GetScalars();
scalars-SetName(ReconstructionData);

  /* Get the info object */
  vtkInformation *outInfo = outputVector-GetInformationObject(0);
outInfo-Set(vtkDataObject::DATA_TYPE_NAME(), vtkImageData);

  /* Get the output */
  vtkImageData* output = vtkImageData::GetData(outputVector);

// output-SetSpacing(image-GetSpacing());
// output-SetOrigin(image-GetOrigin());
// output-AllocateScalars(outInfo);
//
output-GetPointData()-SetScalars(image-GetPointData()-GetScalars());
// output-SetDimensions(image-GetDimensions());

  output-ShallowCopy(image);

  int* dimensions = output-GetDimensions();

  std::cout  \nNumber of points:  
output-GetNumberOfPoints()  std::endl;
  std::cout  Number of cells:   output-GetNumberOfCells()
 \n  std::endl;

// print out the pixel values to see if they are actually present
  for (int z = 0; z  dimensions[2]; z++)
  {
for (int y = 0; y  dimensions[1]; y++)
{
  for (int x = 0; x  dimensions[0]; x++)
  {
double* pixel =
static_castdouble*(output-GetScalarPointer(x,y,z));
// do something with v
std::cout  pixel value:   pixel[0]  \n;
  }
  std::cout  std::endl;
}
std::cout  std::endl;
  }

  // write output to file and compare in visualization window...
vtkSmartPointervtkXMLImageDataWriter vtk_writer =
vtkSmartPointervtkXMLImageDataWriter::New();
  vtk_writer-SetInputData(output);
  vtk_writer-SetFileName( /home/kdean/tmp/foo.vti );
  vtk_writer-Update();
  vtk_writer-Write();

  return 1;
}


Another Problem I ran into:
So I had to hardcode a file for the char *FileName into the
RequestData Function in order to read any protobuf file. I ran a
debugger on the code, and it seems like these functions from the
header file (of the reader):

vtkGetStringMacro(FileName);
vtkSetStringMacro(FileName);

they are never getting called.

Thanks,

Kevin

here are my xml too... it looks right, but maybe I am missing
something.

On Sun, May 3, 2015 at 7:04 AM, Utkarsh Ayachit
utkarsh.ayac...@kitware.com
mailto:utkarsh.ayac...@kitware.com wrote:

You can also use the Information panel to see what arrays are
being
read in and what their ranges are.

On Sat, May 2, 2015 at 7:06 PM, Dean, Kevin
kevin.d...@decisionsciencescorp.com

Re: [Paraview] Image Doesn't load correctly

[Burlen Loring]

Hi Kevin.

Your RequestInformation looks a little bare. Unless things have changed 
recently, you might need to set WHOLE_EXTENT, ORIGIN, SPACING, 
CAN_PRODUCE_SUB_EXTENT keys there. and if you support parallel IO honor 
the requested extent in RequestData.


Burlen

On 05/04/2015 09:52 AM, Dean, Kevin wrote:
So I am still having a few issues with the reader. I have checked the 
output from the information Panel. And it seems as if all the 
information is the same. So maybe the data is getting deleted somehow 
(I'm not sure, but here is a snippet of my code);


int vtkPVPROTOImageReader::RequestInformation (
   vtkInformation*,
   vtkInformationVector**,
   vtkInformationVector* outputVector)
{
   vtkInformation* outInfo = outputVector-GetInformationObject(0);
   vtkDataObject::SetPointDataActiveScalarInfo(outInfo, 
VTK_UNSIGNED_CHAR, 1);


   return 1;
}

int vtkPVPROTOImageReader::RequestData(vtkInformation 
*vtkNotUsed(request),

   vtkInformationVector **inputVector,
   vtkInformationVector *outputVector)
{
   ... conversion code from protobuf

  /* Convert from protobuf to vtkImageData */
  vtkSmartPointervtkImageData image = function converting to protobuf;

  vtkDataArray* scalars = image-GetPointData()-GetScalars();
  scalars-SetName(ReconstructionData);

  /* Get the info object */
  vtkInformation *outInfo = outputVector-GetInformationObject(0);
  outInfo-Set(vtkDataObject::DATA_TYPE_NAME(), vtkImageData);

  /* Get the output */
  vtkImageData* output = vtkImageData::GetData(outputVector);

//  output-SetSpacing(image-GetSpacing());
//  output-SetOrigin(image-GetOrigin());
//  output-AllocateScalars(outInfo);
// 
output-GetPointData()-SetScalars(image-GetPointData()-GetScalars());

//  output-SetDimensions(image-GetDimensions());

  output-ShallowCopy(image);

  int* dimensions = output-GetDimensions();

  std::cout  \nNumber of points:   output-GetNumberOfPoints() 
 std::endl;
  std::cout  Number of cells:   output-GetNumberOfCells()  
\n  std::endl;


// print out the pixel values to see if they are actually present
  for (int z = 0; z  dimensions[2]; z++)
  {
for (int y = 0; y  dimensions[1]; y++)
{
  for (int x = 0; x  dimensions[0]; x++)
  {
double* pixel = 
static_castdouble*(output-GetScalarPointer(x,y,z));

// do something with v
std::cout  pixel value:   pixel[0]  \n;
  }
  std::cout  std::endl;
}
std::cout  std::endl;
  }

  // write output to file and compare in visualization window...
  vtkSmartPointervtkXMLImageDataWriter vtk_writer = 
vtkSmartPointervtkXMLImageDataWriter::New();

  vtk_writer-SetInputData(output);
  vtk_writer-SetFileName( /home/kdean/tmp/foo.vti );
  vtk_writer-Update();
  vtk_writer-Write();

  return 1;
}


Another Problem I ran into:
So I had to hardcode a file for the char *FileName into the 
RequestData Function in order to read any protobuf file. I ran a 
debugger on the code, and it seems like these functions from the 
header file (of the reader):


vtkGetStringMacro(FileName);
vtkSetStringMacro(FileName);

they are never getting called.

Thanks,

Kevin

here are my xml too... it looks right, but maybe I am missing something.

On Sun, May 3, 2015 at 7:04 AM, Utkarsh Ayachit 
utkarsh.ayac...@kitware.com mailto:utkarsh.ayac...@kitware.com wrote:


You can also use the Information panel to see what arrays are being
read in and what their ranges are.

On Sat, May 2, 2015 at 7:06 PM, Dean, Kevin
kevin.d...@decisionsciencescorp.com
mailto:kevin.d...@decisionsciencescorp.com wrote:
 looked at the spreadsheet view in the GUI, and it looks like
none of the
 Point Data is actually being copied...

 On Sat, May 2, 2015 at 3:44 PM, Dean, Kevin
 kevin.d...@decisionsciencescorp.com
mailto:kevin.d...@decisionsciencescorp.com wrote:

 What's up Utkarsh?

 So I was able to write that plugin and convert my image to the
 vtkImageData. However, I am having trouble visualizing the
image. However,
 when I write out the output from my reader, the image gets written
 correctly... Here are some pictures to show the differences.
(All the
 information for the images is exactly the same) Do you have an
idea of how I
 can try to fix it? Thanks.

 Kevin E. Dean



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Re: [Paraview] default_servers.pvsc question

[Burlen Loring]

about (a): running multiple commands for each field could be annoying if 
for ex one was trying to query a server side value and the user had to 
enter their password more than once.


about (b), sounds OK but I'm not sure how it would work with the 
connections to remote site.


in all this, I think we want to make the low-level (ie ssh tunnel) 
connection once and make use of it from then on, for everything. as 
opposed to making a connection for querying and then making another 
connection for submitting/connecting to pvserver etc (or in your (a) 
many connections).


In my suggestion of allowing a script(or as you executable) to 
generate the pvsc xml, PV can use a pipe to communicate to first fetch 
the xml from the script then report the user selection back all while 
keeping the script alive, and same connection open.


On 04/14/2015 02:00 PM, Utkarsh Ayachit wrote:

Thanks Burlen/Rick.

After discussing it with a few folks here, how about the following options:

a. What if we make it possible to run an executable to obtain a
value for any attribute in the XML. One could indeed use a Python
script to produce that value or any other executable.

b. We provide a mechanism to add a Python function in the PVSC. Before
(and/or after) the PVSC is processed by the UI for display, it will
pass the XML to that function which can update the XML as appropriate.
This would mean that the Python code has to be aware of the PVSC's XML
structure, but shouldn't be a problem since the Python code is
embedded in the PVSC XML itself.

Both will allow 1 and 2. 1 may still be a little hard work on the PVSC
writer side, but it's a one time thing.

Burlen, I think 3 is a little independent of this task. I do agree, we
should embed all necessary tools in the paraview bundle -- something
we've been talking about for a while. We should address that, I just
don't want to commit to it just yet :).

Thoughts? The more I think about it, I think I am leaning towards (b).
For (a) the next logical question becomes how does one specify the
path to the executable to run and we're back to the same problem we're
trying to address :). What are your thoughts?

Utkarsh

On Mon, Apr 13, 2015 at 11:48 AM, Burlen Loring burlen.lor...@gmail.com wrote:

OK, I added some notes based on the above discussion.


On 04/13/2015 08:33 AM, Utkarsh Ayachit wrote:

Great, let's start here:


https://docs.google.com/a/kitware.com/document/d/1uzi3VzpCxiGslhqaUde3ZbKcx-9LLG_ly3BYvDiPPx0/edit?usp=sharing

Utkarsh



On Mon, Apr 13, 2015 at 11:29 AM, Burlen Loring burlen.lor...@gmail.com
wrote:

Great, that sounds like a good way to start.


On 04/13/2015 06:53 AM, Utkarsh Ayachit wrote:

Burlen/Rick,

I am totally open to adding  new features/refactoring the pvsc code.
It hasn't changed much in a few years, and I am sure we know more than
we did when we started with this :). Since you guys are the ones
actually using this code in the field, it'd be great if you can
identify the feature list of things missing or difficult to do in the
current implementation and we can decide which would be best way
forward.

Should I create a google-doc or something which all can edit to built
this
list?

Utkarsh

On Mon, Apr 13, 2015 at 8:19 AM, Angelini, Richard C (Rick) CIV USARMY
ARL (US) richard.c.angelini@mail.mil wrote:

Burlen/Utkarsh —— my preferred solution is also to not set an
environment
variable if possible.  For my particular issue, I’d much rather be able
to
do a `which ssh` (or equivalent) to get the answer than than asking the
user to set an environment variable.

Implementing a python-based default_servers definition opens things up
for
much more programmatic flexibility.

# take a guess at which ssh command to use

try:
   default_shell=os.popen(which ssh).read()
   default_shell=default_shell.rstrip(\r\n)
except:
   default_shell=/usr/krb5/bin/





Rick Angelini
USArmy Research Laboratory
CISD/HPC Architectures Team
Phone:  410-278-6266




-Original Message-
From: Burlen Loring burlen.lor...@gmail.com
Date: Sunday, April 12, 2015 at 10:34 PM
To: Utkarsh Ayachit utkarsh.ayac...@kitware.com, Rick Angelini
richard.c.angelini@mail.mil
Cc: paraview@paraview.org paraview@paraview.org
Subject: Re: [Paraview] default_servers.pvsc question

Hi Utkarsh,

I think environment variables are kind of a band aid around a larger
issue. In addition to leveraging the user's local environment, there's
also no way to get information from the server side environment. for
example list of account numbers a user can charge jobs to, or a list of
active queues. One thing I have been thinking about is  rather than
just
reading pvsc from an xml file, paraview could call a script to get the
pvsc xml. This script could query the user's local/remote environment
and generate the xml. A long time ago we had talked about a python
based
solution. What do you think?

Burlen

On 4/12/2015 11:31 AM, Utkarsh Ayachit

Re: [Paraview] default_servers.pvsc question

[Burlen Loring]

going back to your original question. when exec'ing new processes there 
are various flavors of exec, including one that uses your environment. 
Which made me wonder which flavor is PV using? I wrote a little pvsc to 
test this out(attached). Apparently PV does use the exec that includes 
your environment. So if you want to use the ssh that's in your path, 
don't give the path in your pvsc, in the example you gave change it to


   File default=ssh/

duh! (directed at myself)

I hope this discovery doesn't derail our discussion because the other 
features about being able to get information back from the server side 
we are discussing would be useful.


On 04/10/2015 01:09 PM, Angelini, Richard C (Rick) CIV USARMY ARL (US) 
wrote:

Question about the default_servers.pvsc file…..

I have this in my host profile:

  Server name=“My System resource=csrc://127.0.0.1
CommandStartup
  Options
Option name=SSHLOC label=Local SSH Command save=true
 File default=/usr/local/bin/ssh/
/Option

So, when the GUI pops up, the user has an opportunity to change the 
path to ssh.   But, rather than hard-coding the default value, or 
presenting blank field and have the user put in the correct path, is 
it possible to query the user’s environment and find `which ssh` and 
substitute in that value??






Rick Angelini
USArmy Research Laboratory
CISD/HPC Architectures Team
Phone:  410-278-6266


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Servers
  Server name=unix_test_my_paths resource=csrc://localhost:1
CommandStartup
  Command exec=xterm timeout=0 delay=0
Arguments
  Argument value=-T/
  Argument value=#x22;test/
  Argument value=paths#x22;/
  Argument value=-e/
  Argument value=bash/
  Argument value=-c/
  Argument value=#x22;echo/
  Argument value=PATH=$PATH/
  Argument value=#x26;#x26;/
  Argument value=echo/
  Argument value=#x26;#x26;/
  Argument value=echo/
  Argument value=which/
  Argument value=ssh=`which/
  Argument value=ssh`/
  Argument value=#x26;#x26;/
  Argument value=echo/
  Argument value=which/
  Argument value=xterm=`which/
  Argument value=xterm`/
  Argument value=#x26;#x26;/
  Argument value=sleep/
  Argument value=3000#x22;/
/Arguments
  /Command
/CommandStartup
  /Server
/Servers
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Re: [Paraview] default_servers.pvsc question

[Burlen Loring]

OK, I added some notes based on the above discussion.

On 04/13/2015 08:33 AM, Utkarsh Ayachit wrote:

Great, let's start here:

https://docs.google.com/a/kitware.com/document/d/1uzi3VzpCxiGslhqaUde3ZbKcx-9LLG_ly3BYvDiPPx0/edit?usp=sharing

Utkarsh



On Mon, Apr 13, 2015 at 11:29 AM, Burlen Loring burlen.lor...@gmail.com wrote:

Great, that sounds like a good way to start.


On 04/13/2015 06:53 AM, Utkarsh Ayachit wrote:

Burlen/Rick,

I am totally open to adding  new features/refactoring the pvsc code.
It hasn't changed much in a few years, and I am sure we know more than
we did when we started with this :). Since you guys are the ones
actually using this code in the field, it'd be great if you can
identify the feature list of things missing or difficult to do in the
current implementation and we can decide which would be best way
forward.

Should I create a google-doc or something which all can edit to built this
list?

Utkarsh

On Mon, Apr 13, 2015 at 8:19 AM, Angelini, Richard C (Rick) CIV USARMY
ARL (US) richard.c.angelini@mail.mil wrote:

Burlen/Utkarsh —— my preferred solution is also to not set an environment
variable if possible.  For my particular issue, I’d much rather be able
to
do a `which ssh` (or equivalent) to get the answer than than asking the
user to set an environment variable.

Implementing a python-based default_servers definition opens things up
for
much more programmatic flexibility.

# take a guess at which ssh command to use

try:
  default_shell=os.popen(which ssh).read()
  default_shell=default_shell.rstrip(\r\n)
except:
  default_shell=/usr/krb5/bin/





Rick Angelini
USArmy Research Laboratory
CISD/HPC Architectures Team
Phone:  410-278-6266




-Original Message-
From: Burlen Loring burlen.lor...@gmail.com
Date: Sunday, April 12, 2015 at 10:34 PM
To: Utkarsh Ayachit utkarsh.ayac...@kitware.com, Rick Angelini
richard.c.angelini@mail.mil
Cc: paraview@paraview.org paraview@paraview.org
Subject: Re: [Paraview] default_servers.pvsc question

Hi Utkarsh,

I think environment variables are kind of a band aid around a larger
issue. In addition to leveraging the user's local environment, there's
also no way to get information from the server side environment. for
example list of account numbers a user can charge jobs to, or a list of
active queues. One thing I have been thinking about is  rather than just
reading pvsc from an xml file, paraview could call a script to get the
pvsc xml. This script could query the user's local/remote environment
and generate the xml. A long time ago we had talked about a python based
solution. What do you think?

Burlen

On 4/12/2015 11:31 AM, Utkarsh Ayachit wrote:

Rick,

Alas no, this isn't currently supported. But should be fairly
straightforward to add. I've reported a bug:
http://www.paraview.org/Bug/view.php?id=15421

Utkarsh

On Fri, Apr 10, 2015 at 4:09 PM, Angelini, Richard C (Rick) CIV USARMY
ARL (US) richard.c.angelini@mail.mil wrote:

Question about the default_servers.pvsc file…..

I have this in my host profile:

 Server name=“My System resource=csrc://127.0.0.1
   CommandStartup
 Options
Option name=SSHLOC label=Local SSH Command save=true
File default=/usr/local/bin/ssh/
/Option

So, when the GUI pops up, the user has an opportunity to change the
path to
ssh.   But, rather than hard-coding the default value, or presenting
blank
field and have the user put in the correct path, is it possible to
query the
user’s environment and find `which ssh` and substitute in that value??





Rick Angelini
USArmy Research Laboratory
CISD/HPC Architectures Team
Phone:  410-278-6266

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Re: [Paraview] default_servers.pvsc question

[Burlen Loring]

Great, that sounds like a good way to start.

On 04/13/2015 06:53 AM, Utkarsh Ayachit wrote:

Burlen/Rick,

I am totally open to adding  new features/refactoring the pvsc code.
It hasn't changed much in a few years, and I am sure we know more than
we did when we started with this :). Since you guys are the ones
actually using this code in the field, it'd be great if you can
identify the feature list of things missing or difficult to do in the
current implementation and we can decide which would be best way
forward.

Should I create a google-doc or something which all can edit to built this list?

Utkarsh

On Mon, Apr 13, 2015 at 8:19 AM, Angelini, Richard C (Rick) CIV USARMY
ARL (US) richard.c.angelini@mail.mil wrote:

Burlen/Utkarsh —— my preferred solution is also to not set an environment
variable if possible.  For my particular issue, I’d much rather be able to
do a `which ssh` (or equivalent) to get the answer than than asking the
user to set an environment variable.

Implementing a python-based default_servers definition opens things up for
much more programmatic flexibility.

# take a guess at which ssh command to use

try:
 default_shell=os.popen(which ssh).read()
 default_shell=default_shell.rstrip(\r\n)
except:
 default_shell=/usr/krb5/bin/





Rick Angelini
USArmy Research Laboratory
CISD/HPC Architectures Team
Phone:  410-278-6266




-Original Message-
From: Burlen Loring burlen.lor...@gmail.com
Date: Sunday, April 12, 2015 at 10:34 PM
To: Utkarsh Ayachit utkarsh.ayac...@kitware.com, Rick Angelini
richard.c.angelini@mail.mil
Cc: paraview@paraview.org paraview@paraview.org
Subject: Re: [Paraview] default_servers.pvsc question

Hi Utkarsh,

I think environment variables are kind of a band aid around a larger
issue. In addition to leveraging the user's local environment, there's
also no way to get information from the server side environment. for
example list of account numbers a user can charge jobs to, or a list of
active queues. One thing I have been thinking about is  rather than just
reading pvsc from an xml file, paraview could call a script to get the
pvsc xml. This script could query the user's local/remote environment
and generate the xml. A long time ago we had talked about a python based
solution. What do you think?

Burlen

On 4/12/2015 11:31 AM, Utkarsh Ayachit wrote:

Rick,

Alas no, this isn't currently supported. But should be fairly
straightforward to add. I've reported a bug:
http://www.paraview.org/Bug/view.php?id=15421

Utkarsh

On Fri, Apr 10, 2015 at 4:09 PM, Angelini, Richard C (Rick) CIV USARMY
ARL (US) richard.c.angelini@mail.mil wrote:

Question about the default_servers.pvsc file…..

I have this in my host profile:

Server name=“My System resource=csrc://127.0.0.1
  CommandStartup
Options
Option name=SSHLOC label=Local SSH Command save=true
   File default=/usr/local/bin/ssh/
/Option

So, when the GUI pops up, the user has an opportunity to change the
path to
ssh.   But, rather than hard-coding the default value, or presenting
blank
field and have the user put in the correct path, is it possible to
query the
user’s environment and find `which ssh` and substitute in that value??





Rick Angelini
USArmy Research Laboratory
CISD/HPC Architectures Team
Phone:  410-278-6266

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Re: [Paraview] default_servers.pvsc question

[Burlen Loring]

Hi Utkarsh,

I think environment variables are kind of a band aid around a larger 
issue. In addition to leveraging the user's local environment, there's 
also no way to get information from the server side environment. for 
example list of account numbers a user can charge jobs to, or a list of 
active queues. One thing I have been thinking about is  rather than just 
reading pvsc from an xml file, paraview could call a script to get the 
pvsc xml. This script could query the user's local/remote environment 
and generate the xml. A long time ago we had talked about a python based 
solution. What do you think?


Burlen

On 4/12/2015 11:31 AM, Utkarsh Ayachit wrote:

Rick,

Alas no, this isn't currently supported. But should be fairly
straightforward to add. I've reported a bug:
http://www.paraview.org/Bug/view.php?id=15421

Utkarsh

On Fri, Apr 10, 2015 at 4:09 PM, Angelini, Richard C (Rick) CIV USARMY
ARL (US) richard.c.angelini@mail.mil wrote:

Question about the default_servers.pvsc file…..

I have this in my host profile:

   Server name=“My System resource=csrc://127.0.0.1
 CommandStartup
   Options
Option name=SSHLOC label=Local SSH Command save=true
  File default=/usr/local/bin/ssh/
/Option

So, when the GUI pops up, the user has an opportunity to change the path to
ssh.   But, rather than hard-coding the default value, or presenting blank
field and have the user put in the correct path, is it possible to query the
user’s environment and find `which ssh` and substitute in that value??





Rick Angelini
USArmy Research Laboratory
CISD/HPC Architectures Team
Phone:  410-278-6266

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Re: [Paraview] dlopen: cannot load anymore object with static TLS

[Burlen Loring]

I don't know the answer but you might try adding

   -fPIC -ftls-model=global-dynamic

to CMAKE_CXX_FLAGS and CMAKE_C_FLAGS vars when build PV and your plugin.

On 03/27/2015 09:36 AM, Kit Chambers wrote:

Hi All,

I have a ParaView plugin which in turn links against a couple of other 
shared libraries, these in turn use OpenMP for threading. After a 
recent re-build I get the following  error when the plugin is loaded.


dlopen: cannot load anymore object with static TLS

However, if I compile the supporting libraries without OpenMP it works 
fine.


Has anyone else come across this?

My system is:
Ubuntu 14.04 - (64bit)
kernel  = 3.13.0-46-generic
ParaView Version = 4.2


Cheers

Kit



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Re: [Paraview] Hardware suggestions for volume rendering

[Burlen Loring]

I have the same issue with unstructured grids(not using the new opengl 
work yet). A while back I wanted to volume render a large image dataset 
after clipping it. The clip made it unstructured. This was on a few 
hundered nodes on edison, I couldn't get the unstructured volume 
rendering to work, it appeared to hang(took so long I couldn't tell) and 
it crashed a few times as well(may have ran out of memory).  I think I 
tried a couple of the various mappers before I gave up. Would be nice to 
have it working better.


On 3/24/2015 8:43 AM, Armin Wehrfritz wrote:

Hey Kevin and Aashish,

I found this discussion rather interesting, especially since I'm 
basically facing the same problem as Kevin.


In almost all cases, we are dealing here with large unstructured grids 
(e.g. 12M cells) and the volume rendering is performance is extremely 
bad, not to say unusable, for these cases.


I only tested it with ParaView 4.3.1 and older versions, i.e. with the 
old OpenGL algorithms, but the performance is barely influenced by the 
actual volume renderer (i.e. GPU vs. CPU based).


For an unstructured grid the volume rendering seems to be CPU limited 
in any case, at least my CPU is at 100% for quite some time and the 
GPU load is negligible. ParaView's status bar indicates that it's busy 
with

OpenGLProjectedTetrahedraMapper.

This can be easily reproduced with the wavelet source (with e.g. 125k 
points) and tessellation filter.


So far I have resorted to resampling the data onto a structured grid. 
This has the clear drawback that a structured grid with the same 
resolution has about 70M grid points compared to the 12M points of the 
unstructured grid.
The volume rendering performance of a 70M unstructured grid is however 
already decent with the old OpenGL algorithms.


So is there a way to improve the rendering of unstructured grids to 
avoid the resampling?


Best regards,
Armin




On 03/24/2015 04:48 PM, Aashish Chaudhary wrote:

Hey Kevin,



On Fri, Mar 20, 2015 at 2:33 PM, Kevin Lau kevin.d@gmail.com
mailto:kevin.d@gmail.com wrote:

Dear Aashish,

Thanks for your reply.

(1)

We tried testing it with 2 different data sets of simulation data,
one medium sized and one very large:

Medium
Cells: 1309489
Points: 247984
Memory [MB]: 119.179
Geometry [MB]: 8.201

Very Large
Cells: 51937191
Points: 11019274
Memory [MB]: 4709.731
Geometry [MB]: 776.237

These datasets are unstructured grids (tetrahedral meshes) read into
ParaView using the Phasta data reader.

I see. Most of the performance improvements we have achieved is with GPU
RayCast Volume mapper (uses image data). If you can sample your data
into a strucuted grid then you will be able to use the new mapper.

Thanks,

(2)

The OS used was Ubuntu

(3)

The graphics card was a NVIDIA Quatro K6000 running the NVIDIA
drivers from the Ubuntu Repos (v 331.113)

(4)

We configured ParaView using the default CMake options, changing
VTK_RENDERING_BACKEND=OpenGL2 and disabling all the plug-ins. These
tests were run in serial, as building with MPI was throwing errors.

(5)

We expected that the OpenGL2 version of ParaView would be able to
volume render faster than the standard OpenGL version. However the
reported frame rates were the same in both builds when clicking and
dragging (~2 FPS).

This is a problem because we're mainly interested in visualising our
data and having users able to rotate the model and interact with it.
At these frame rates the response is a bit sluggish.

Also I've done serial test using an OpenGL2 build on Windows using
an old GeForce 8800 with the same medium sized data. On this machine
the frame rate was similar at around ~1.5 FPS.

(6)

ParaView was built by checking out the master from git. Sadly I'm
not on that test machine now, so I can't check the SHA

Many thanks for your help again.

Kevin


On 20 March 2015 at 10:33, Aashish Chaudhary
aashish.chaudh...@kitware.com
mailto:aashish.chaudh...@kitware.com wrote:

Hey Kevin,

On Thu, Mar 19, 2015 at 5:33 PM, Kevin Lau
kevin.d@gmail.com mailto:kevin.d@gmail.com wrote:

Dear Aashish,

Thanks for your reply, I've now managed to build ParaView
from the Master branch with VTK_RENDERING_BACKEND set to
OpenGL2 and I have noticed a visible difference in the
rendering.

However comparison of the rendering performance in the
interactive mode of builds with the standard OpenGL backend
vs the OpenGL2 backend, both show similar frame rates.


Depending on the card and features you are using you may not see
a huge bump in performance. On some systems we have seen 300
times performance improvements and on others there were close
specially when you have VSync 

Re: [Paraview] server configuration with two factor authentication?

[Burlen Loring]

there are 2 places I used netcat.

1) ssh policy on login node only allows us to connect to ssh tunnels 
from localhost. using ncat there fools ssh into thinking we are 
connecting on localhost. I think it's dumb that we have to do this, but 
our sys admins refuse to make the change. The ssh option is called 
GatewayPorts.


2) there is a different network protocol used on the compute nodes of 
our cray, the mom node understands that protocol and acts like a bridge 
to the login node. we create the tunnel from mom to login with netcat.


there are other ways to forward the connections beside netcat, but it's 
easy to build, install, and use, and it's fast.


On 03/20/2015 02:26 PM, Vanmoer, Mark W wrote:


Hi Burlen,

Are you using ncat to setup those connections because of a policy 
(like no outside network connections allowed) or for a technical reason?


Mark

*From:*Burlen Loring [mailto:burlen.lor...@gmail.com]
*Sent:* Thursday, March 19, 2015 4:48 PM
*To:* Vanmoer, Mark W; David E DeMarle
*Cc:* paraview@paraview.org
*Subject:* Re: [Paraview] server configuration with two factor 
authentication?


Hi Mark,

Yes to both. The way this could work on a simple cluster is: from the 
user's system which is assumed to be remote, the pvsc creates an ssh 
tunnel inside the xterm and calls the launch script on the compute 
system login node. the launch script submits the batch job. pvserver, 
when run in the batch script, connects back to the ssh tunnel on the 
login node. client host is the login node host name. server port 
is specified by the user in the pvsc.


There's a slight complication with some Cray systems that means we 
need to involve a special node called the mom node in the tunnel.


This will be clear if you see a complete example, for instance the 
following 3 scripts are used with NERSC's Cray Edison:pvsc 
https://github.com/burlen/pvserver-configs/blob/master/pvsc/edison-unix.pvsc, 
launch script 
https://github.com/burlen/pvserver-configs/blob/master/servers/edison/4.3.1/start_pvserver.sh, 
batch script 
https://github.com/burlen/pvserver-configs/blob/master/servers/edison/4.3.1/start_pvserver.qsub.


Burlen

On 03/19/2015 02:24 PM, Vanmoer, Mark W wrote:

This great, thanks for sharing, guys. Using xterm would have never
occurred to me.

Are you setting the pvserver –client-host somehow? My old pvsc
from Forge sent over the client’s hostname to the script. I tried
that on Blue Waters and it works, but do I not need to actually do
that? Also, are either of you setting –server-port in the launch
script?

*From:*David E DeMarle [mailto:dave.dema...@kitware.com]
*Sent:* Thursday, March 19, 2015 1:28 PM
*To:* Burlen Loring
*Cc:* Vanmoer, Mark W; paraview@paraview.org
mailto:paraview@paraview.org
*Subject:* Re: [Paraview] server configuration with two factor
authentication?

I liked this bit too as the windows version 'xterm -e ssh '.

Command exec=cmd.exe delay=10
Arguments
Argument value=/C/
Argument value=start/
Argument value=cmd.exe/
Argument value=/C/
Argument value=$SSH_EXEquot;/

Since windows isn't my first language, that took more hunting than
I'ld like to admit. :)


David E DeMarle
Kitware, Inc.
RD Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Thu, Mar 19, 2015 at 2:18 PM, Burlen Loring
burlen.lor...@gmail.com mailto:burlen.lor...@gmail.com wrote:

quot;C:\Program Files (x86)\PuTTY\plink.exequot;

  


so that's the secret to paths with spaces! nice, thanks for sharing 
that!

On 03/19/2015 09:22 AM, David E DeMarle wrote:

Howdy Mark,

Adding to what Burlen said.

You can grab pvsc examples for ORNL, ANL and NERSC via

paraview-File-Connect… Fetch servers.

//File-Conenct…FetchServers-Edit Sources replace with
pvsc http://www.paraview.org/files/pvscWindows Kitware
Inc. on windows.

Mac requires XQuartz, windows requires putty.

Let me know when you get it working, with your permission
I'ld love to add NCSA (and everywhere else) there so that
users get it by default.


David E DeMarle
Kitware, Inc.
RD Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909 tel:518-881-4909

On Thu, Mar 19, 2015 at 11:56 AM, Burlen Loring
burlen.lor...@gmail.com mailto:burlen.lor...@gmail.com
wrote:

Hi Mark,

This works without anything special if you launch in
an xterm. We did this at NICS which requires both ssh
authentication and rsa secure id token. Here is an
example

https://github.com/burlen/pvserver-configs/blob/master/pvsc/edison-unix.pvsc

Re: [Paraview] server configuration with two factor authentication?

[Burlen Loring]

quot;C:\Program Files (x86)\PuTTY\plink.exequot;

so that's the secret to paths with spaces! nice, thanks for sharing that!

On 03/19/2015 09:22 AM, David E DeMarle wrote:

Howdy Mark,

Adding to what Burlen said.

You can grab pvsc examples for ORNL, ANL and NERSC via
paraview-File-Connect… Fetch servers.
//File-Conenct…FetchServers-Edit Sources replace with pvsc 
http://www.paraview.org/files/pvscWindows Kitware Inc. on windows.

Mac requires XQuartz, windows requires putty.

Let me know when you get it working, with your permission I'ld love to 
add NCSA (and everywhere else) there so that users get it by default.




David E DeMarle
Kitware, Inc.
RD Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909 tel:518-881-4909

On Thu, Mar 19, 2015 at 11:56 AM, Burlen Loring 
burlen.lor...@gmail.com mailto:burlen.lor...@gmail.com wrote:


Hi Mark,

This works without anything special if you launch in an xterm. We
did this at NICS which requires both ssh authentication and rsa
secure id token. Here is an example

https://github.com/burlen/pvserver-configs/blob/master/pvsc/edison-unix.pvsc


Burlen


On 03/19/2015 06:50 AM, Vanmoer, Mark W wrote:


Hi, is there a way to set up the server XML so that it works with
two factor authentication, as in a token generator? This is for
the Blue Waters machine at NCSA. What I mean is, something like
how VisIt acts, which when doing the connection will prompt for
the password and token.

In the past, on machines without two factor auth, I’ve used


http://www.paraview.org/Wiki/ParaView:Server_Configuration#Case_Eleven:_Launch_pvserver_on_a_cluster_using_PBS_-_use_reverse_connection_to_client

but that requires having ssh keys set up.

Thanks,

Mark



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Re: [Paraview] server configuration with two factor authentication?

[Burlen Loring]

Hi Mark,

Yes to both. The way this could work on a simple cluster is: from the 
user's system which is assumed to be remote, the pvsc creates an ssh 
tunnel inside the xterm and calls the launch script on the compute 
system login node. the launch script submits the batch job. pvserver, 
when run in the batch script, connects back to the ssh tunnel on the 
login node. client host is the login node host name. server port is 
specified by the user in the pvsc.


There's a slight complication with some Cray systems that means we need 
to involve a special node called the mom node in the tunnel.


This will be clear if you see a complete example, for instance the 
following 3 scripts are used with NERSC's Cray Edison:pvsc 
https://github.com/burlen/pvserver-configs/blob/master/pvsc/edison-unix.pvsc, 
launch script 
https://github.com/burlen/pvserver-configs/blob/master/servers/edison/4.3.1/start_pvserver.sh, 
batch script 
https://github.com/burlen/pvserver-configs/blob/master/servers/edison/4.3.1/start_pvserver.qsub.


Burlen

On 03/19/2015 02:24 PM, Vanmoer, Mark W wrote:


This great, thanks for sharing, guys. Using xterm would have never 
occurred to me.


Are you setting the pvserver –client-host somehow? My old pvsc from 
Forge sent over the client’s hostname to the script. I tried that on 
Blue Waters and it works, but do I not need to actually do that? Also, 
are either of you setting –server-port in the launch script?


*From:*David E DeMarle [mailto:dave.dema...@kitware.com]
*Sent:* Thursday, March 19, 2015 1:28 PM
*To:* Burlen Loring
*Cc:* Vanmoer, Mark W; paraview@paraview.org
*Subject:* Re: [Paraview] server configuration with two factor 
authentication?


I liked this bit too as the windows version 'xterm -e ssh '.

Command exec=cmd.exe delay=10
Arguments
Argument value=/C/
Argument value=start/
Argument value=cmd.exe/
Argument value=/C/
Argument value=$SSH_EXEquot;/

Since windows isn't my first language, that took more hunting than 
I'ld like to admit. :)



David E DeMarle
Kitware, Inc.
RD Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Thu, Mar 19, 2015 at 2:18 PM, Burlen Loring 
burlen.lor...@gmail.com mailto:burlen.lor...@gmail.com wrote:


quot;C:\Program Files (x86)\PuTTY\plink.exequot;

  


so that's the secret to paths with spaces! nice, thanks for sharing that!

On 03/19/2015 09:22 AM, David E DeMarle wrote:

Howdy Mark,

Adding to what Burlen said.

You can grab pvsc examples for ORNL, ANL and NERSC via

paraview-File-Connect… Fetch servers.

//File-Conenct…FetchServers-Edit Sources replace with pvsc
http://www.paraview.org/files/pvscWindows Kitware Inc. on windows.

Mac requires XQuartz, windows requires putty.

Let me know when you get it working, with your permission I'ld
love to add NCSA (and everywhere else) there so that users get
it by default.


David E DeMarle
Kitware, Inc.
RD Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909 tel:518-881-4909

On Thu, Mar 19, 2015 at 11:56 AM, Burlen Loring
burlen.lor...@gmail.com mailto:burlen.lor...@gmail.com wrote:

Hi Mark,

This works without anything special if you launch in an
xterm. We did this at NICS which requires both ssh
authentication and rsa secure id token. Here is an example

https://github.com/burlen/pvserver-configs/blob/master/pvsc/edison-unix.pvsc


Burlen

On 03/19/2015 06:50 AM, Vanmoer, Mark W wrote:

Hi, is there a way to set up the server XML so that it
works with two factor authentication, as in a token
generator? This is for the Blue Waters machine at
NCSA. What I mean is, something like how VisIt acts,
which when doing the connection will prompt for the
password and token.

In the past, on machines without two factor auth, I’ve
used


http://www.paraview.org/Wiki/ParaView:Server_Configuration#Case_Eleven:_Launch_pvserver_on_a_cluster_using_PBS_-_use_reverse_connection_to_client

but that requires having ssh keys set up.

Thanks,

Mark

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Re: [Paraview] server configuration with two factor authentication?

[Burlen Loring]

Hi Mark,

This works without anything special if you launch in an xterm. We did 
this at NICS which requires both ssh authentication and rsa secure id 
token. Here is an example 
https://github.com/burlen/pvserver-configs/blob/master/pvsc/edison-unix.pvsc 



Burlen

On 03/19/2015 06:50 AM, Vanmoer, Mark W wrote:


Hi, is there a way to set up the server XML so that it works with two 
factor authentication, as in a token generator? This is for the Blue 
Waters machine at NCSA. What I mean is, something like how VisIt acts, 
which when doing the connection will prompt for the password and token.


In the past, on machines without two factor auth, I’ve used

http://www.paraview.org/Wiki/ParaView:Server_Configuration#Case_Eleven:_Launch_pvserver_on_a_cluster_using_PBS_-_use_reverse_connection_to_client

but that requires having ssh keys set up.

Thanks,

Mark



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Re: [Paraview] [EXTERNAL] Re: Trace recorder and presets (color table)

[Burlen Loring]

did you try including the code from the trace that set the opacity 
values? try adding that after the lut is set.



wavelet1Display.ScalarOpacityUnitDistance = 1.7320508075688779
rTDataPWF = GetOpacityTransferFunction('RTData')
rTDataPWF.Points = [37.35310363769531, 0.0, 0.5, 0.0, 
186.72914123535156, 1.0, 0.5, 0.0]



On 03/17/2015 04:48 PM, Scott, W Alan wrote:


Excellent!

One question – my user may want to use Opacity mapping.  The code 
below changes the Mapping Data view, removing the Opacity part of the 
view.  Is there a way to return it to normal, enabling Opacity Mapping?


Thanks

*From:*Burlen Loring [mailto:blor...@lbl.gov]
*Sent:* Tuesday, March 17, 2015 2:17 PM
*To:* Scott, W Alan; paraview@paraview.org
*Subject:* Re: [EXTERNAL] Re: [Paraview] Trace recorder and presets 
(color table)


Hi Alan,

The verbosity of the trace can be confusing, 90% of it is unnecessary, 
and can be removed. Here's how it looks in your example with 
unnecessary stuff removed and the 3 lines added to change the lut by name.


 import the simple module from the paraview
from paraview.simple import *

 disable automatic camera reset on 'Show'
paraview.simple._DisableFirstRenderCameraReset()

# create a new 'Wavelet'
wavelet1 = Wavelet()

# get active view
renderView1 = GetActiveViewOrCreate('RenderView')

# uncomment following to set a specific view size
# renderView1.ViewSize = [856, 797]

# show data in view
wavelet1Display = Show(wavelet1, renderView1)

# change representation type
wavelet1Display.SetRepresentationType('Surface')

*# change lookup table**
wavelet1Display.ColorArrayName = 'RTData'
w_arr = wavelet1.PointData.GetArray('RTData')
wavelet1Display.LookupTable = AssignLookupTable(w_arr, 'Rainbow 
Blended White')*


# show color bar/color legend
wavelet1Display.SetScalarBarVisibility(renderView1, True)

# reset view to fit data
renderView1.ResetCamera()

 uncomment the following to render all views
# RenderAllViews()
# alternatively, if you want to write images, you can use 
SaveScreenshot(...).


On 03/17/2015 11:46 AM, Scott, W Alan wrote:

Thanks Burlen!

Obviously, my ParaView Python fu is weak.  I tried to merge this
code into Python created by the trace recorder, but couldn’t. Say
a person does the following (which is sort of what my customer is
doing) :

·Trace recorder on.

·Wavelet. Apply.  Surface.  RTData.

·Color Editor/ Presets/ Blue to Red Rainbow.

·Trace Recorder off.

The line setting Blue to Red Rainbow doesn’t get recorded. What
code would I paste in there?

Here is the incorrect trace:

 import the simple module from the paraview

from paraview.simple import *

 disable automatic camera reset on 'Show'

paraview.simple._DisableFirstRenderCameraReset()

# create a new 'Wavelet'

wavelet1 = Wavelet()

# get active view

renderView1 = GetActiveViewOrCreate('RenderView')

# uncomment following to set a specific view size

# renderView1.ViewSize = [856, 797]

# show data in view

wavelet1Display = Show(wavelet1, renderView1)

# trace defaults for the display properties.

wavelet1Display.Representation = 'Outline'

wavelet1Display.ColorArrayName = ['POINTS', '']

wavelet1Display.ScalarOpacityUnitDistance = 1.7320508075688779

wavelet1Display.Slice = 10

# reset view to fit data

renderView1.ResetCamera()

# change representation type

wavelet1Display.SetRepresentationType('Surface')

# set scalar coloring

ColorBy(wavelet1Display, ('POINTS', 'RTData'))

# rescale color and/or opacity maps used to include current data range

wavelet1Display.RescaleTransferFunctionToDataRange(True)

# show color bar/color legend

wavelet1Display.SetScalarBarVisibility(renderView1, True)

# get color transfer function/color map for 'RTData'

rTDataLUT = GetColorTransferFunction('RTData')

rTDataLUT.RGBPoints = [37.35310363769531, 0.231373, 0.298039,
0.752941, 112.04112243652344, 0.865003, 0.865003, 0.865003,
186.72914123535156, 0.705882, 0.0156863, 0.14902]

rTDataLUT.ScalarRangeInitialized = 1.0

# get opacity transfer function/opacity map for 'RTData'

rTDataPWF = GetOpacityTransferFunction('RTData')

rTDataPWF.Points = [37.35310363769531, 0.0, 0.5, 0.0,
186.72914123535156, 1.0, 0.5, 0.0]

rTDataPWF.ScalarRangeInitialized = 1

 saving camera placements for all active views

# current camera placement for renderView1

renderView1.CameraPosition = [0.0, 0.0, 66.92130429902464]

renderView1.CameraParallelScale = 17.320508075688775

 uncomment the following to render all views

# RenderAllViews()

# alternatively, if you want to write images, you can use
SaveScreenshot(...).

*From:*Burlen Loring [mailto:blor...@lbl.gov]
*Sent:* Monday, March 16, 2015 4:45 PM
*To:* Scott, W Alan; paraview@paraview.org
mailto:paraview@paraview.org

Re: [Paraview] [EXTERNAL] Re: Trace recorder and presets (color table)

[Burlen Loring]

Hi Alan,

The verbosity of the trace can be confusing, 90% of it is unnecessary, 
and can be removed. Here's how it looks in your example with unnecessary 
stuff removed and the 3 lines added to change the lut by name.


 import the simple module from the paraview
from paraview.simple import *

 disable automatic camera reset on 'Show'
paraview.simple._DisableFirstRenderCameraReset()

# create a new 'Wavelet'
wavelet1 = Wavelet()

# get active view
renderView1 = GetActiveViewOrCreate('RenderView')

# uncomment following to set a specific view size
# renderView1.ViewSize = [856, 797]

# show data in view
wavelet1Display = Show(wavelet1, renderView1)

# change representation type
wavelet1Display.SetRepresentationType('Surface')

*# change lookup table**
**wavelet1Display.ColorArrayName = 'RTData'**
**w_arr = wavelet1.PointData.GetArray('RTData')**
**wavelet1Display.LookupTable = AssignLookupTable(w_arr, 'Rainbow 
Blended White')*


# show color bar/color legend
wavelet1Display.SetScalarBarVisibility(renderView1, True)

# reset view to fit data
renderView1.ResetCamera()

 uncomment the following to render all views
# RenderAllViews()
# alternatively, if you want to write images, you can use 
SaveScreenshot(...).



On 03/17/2015 11:46 AM, Scott, W Alan wrote:


Thanks Burlen!

Obviously, my ParaView Python fu is weak.  I tried to merge this code 
into Python created by the trace recorder, but couldn’t. Say a person 
does the following (which is sort of what my customer is doing) :


·Trace recorder on.

·Wavelet. Apply.  Surface.  RTData.

·Color Editor/ Presets/ Blue to Red Rainbow.

·Trace Recorder off.

The line setting Blue to Red Rainbow doesn’t get recorded.  What code 
would I paste in there?


Here is the incorrect trace:

 import the simple module from the paraview

from paraview.simple import *

 disable automatic camera reset on 'Show'

paraview.simple._DisableFirstRenderCameraReset()

# create a new 'Wavelet'

wavelet1 = Wavelet()

# get active view

renderView1 = GetActiveViewOrCreate('RenderView')

# uncomment following to set a specific view size

# renderView1.ViewSize = [856, 797]

# show data in view

wavelet1Display = Show(wavelet1, renderView1)

# trace defaults for the display properties.

wavelet1Display.Representation = 'Outline'

wavelet1Display.ColorArrayName = ['POINTS', '']

wavelet1Display.ScalarOpacityUnitDistance = 1.7320508075688779

wavelet1Display.Slice = 10

# reset view to fit data

renderView1.ResetCamera()

# change representation type

wavelet1Display.SetRepresentationType('Surface')

# set scalar coloring

ColorBy(wavelet1Display, ('POINTS', 'RTData'))

# rescale color and/or opacity maps used to include current data range

wavelet1Display.RescaleTransferFunctionToDataRange(True)

# show color bar/color legend

wavelet1Display.SetScalarBarVisibility(renderView1, True)

# get color transfer function/color map for 'RTData'

rTDataLUT = GetColorTransferFunction('RTData')

rTDataLUT.RGBPoints = [37.35310363769531, 0.231373, 0.298039, 
0.752941, 112.04112243652344, 0.865003, 0.865003, 0.865003, 
186.72914123535156, 0.705882, 0.0156863, 0.14902]


rTDataLUT.ScalarRangeInitialized = 1.0

# get opacity transfer function/opacity map for 'RTData'

rTDataPWF = GetOpacityTransferFunction('RTData')

rTDataPWF.Points = [37.35310363769531, 0.0, 0.5, 0.0, 
186.72914123535156, 1.0, 0.5, 0.0]


rTDataPWF.ScalarRangeInitialized = 1

 saving camera placements for all active views

# current camera placement for renderView1

renderView1.CameraPosition = [0.0, 0.0, 66.92130429902464]

renderView1.CameraParallelScale = 17.320508075688775

 uncomment the following to render all views

# RenderAllViews()

# alternatively, if you want to write images, you can use 
SaveScreenshot(...).


*From:*Burlen Loring [mailto:blor...@lbl.gov]
*Sent:* Monday, March 16, 2015 4:45 PM
*To:* Scott, W Alan; paraview@paraview.org
*Subject:* [EXTERNAL] Re: [Paraview] Trace recorder and presets (color 
table)


Hi Alan,

You can use the AssignLookupTable function to reference builtin lookup 
tables by name. For example see code between # marks below. There are 
a few other conveniences for working with the builtin tables as well, 
see this recipe 
http://www.paraview.org/Wiki/ParaView/Python/Lookup_tables


w = Wavelet()
w_rep = Show(w)
w_rep.Representation = 'Surface'
#
w_rep.ColorArrayName = 'RTData'
w_arr = w.PointData.GetArray('RTData')
w_rep.LookupTable = AssignLookupTable(w_arr, 'Rainbow Blended White')
#
Render().ResetCamera()

Burlen

On 03/16/2015 03:14 PM, Scott, W Alan wrote:

I have a user that needs to change the ParaView preset from
default (cool to warm) to another ParaView preset (Blue to Red
Rainbow).  He wants to do this in a python trace.  So, he used the
trace recorder to record his steps.  Unfortunately, changing
presets is not recorded with the trace recorder.

I have written this issue up as bug number
http://www.paraview.org/Bug

Re: [Paraview] Trace recorder and presets (color table)

[Burlen Loring]

Hi Alan,

You can use the AssignLookupTable function to reference builtin lookup 
tables by name. For example see code between # marks below. There are a 
few other conveniences for working with the builtin tables as well, see 
this recipe http://www.paraview.org/Wiki/ParaView/Python/Lookup_tables


w = Wavelet()
w_rep = Show(w)
w_rep.Representation = 'Surface'
#
w_rep.ColorArrayName = 'RTData'
w_arr = w.PointData.GetArray('RTData')
w_rep.LookupTable = AssignLookupTable(w_arr, 'Rainbow Blended White')
#
Render().ResetCamera()

Burlen

On 03/16/2015 03:14 PM, Scott, W Alan wrote:
I have a user that needs to change the ParaView preset from default 
(cool to warm) to another ParaView preset (Blue to Red Rainbow).  He 
wants to do this in a python trace. So, he used the trace recorder to 
record his steps. Unfortunately, changing presets is not recorded with 
the trace recorder.
I have written this issue up as bug number 
_http://www.paraview.org/Bug/view.php?id=15116_, but need to give the 
user the code that would have/ should have been produced.  Does anyone 
have the python code that changes presets?

Thanks all!
Alan


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Re: [Paraview] wiki issue

[Burlen Loring]

http://www.paraview.org/Wiki/ParaView/Line_Integral_Convolution

On 02/27/2015 02:16 PM, David E DeMarle wrote:

Looking…. can you point me at a specific page Burlen?

ty

On Fri, Feb 27, 2015 at 5:06 PM, Burlen Loring 
burlen.lor...@gmail.com mailto:burlen.lor...@gmail.com wrote:


Hi All,

I just noticed that math ml equations are no longer type set on
the wiki. instead tags and contents are displayed math ...
/math.  was this an accidental change?

Burlen
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Re: [Paraview] reducing startup time on cray

[Burlen Loring]

Thanks! I enabled this in my 4.3.1 installs.

On 02/23/2015 06:12 AM, Utkarsh Ayachit wrote:

Burlen,


I'm unfamiliar with freezing python and how it would work with pvserver,
pvbatch, or pvpython. Question: how/what do we freeze in the pvserver case?

Check this out: http://www.kitware.com/blog/home/post/517

Utkarsh
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Re: [Paraview] Minimum system requirement for PV 4.3 volume rendering?

[Burlen Loring]

Hi Ruq,

I'm not sure why it works in 4.2 and not 4.3. I assume someone else 
reading this who knows about the recent changes could comment.


The error message shows  some missing open gl extensions. Are you sure 
you have the latest driver installed?  GL_ARB_multitexture is not 
typically an issue, unless you are using the default MS driver. Also are 
you sure the error messages are the same on both systems? If not, it 
would be helpful to see all the messages on both systems.


Note: the AMD drivers have a bug that prevents projected tetrahedra from 
working. This should be disabled on the system with the AMD card.


In general when you have issues with one volume rendering method you 
could work around it by using a different one. In the properties panel 
under the display group there are some controls relating to the volume 
renderer. One labeled select mapper lets you chose different 
algorithms. For instance try to change it to Bunyk Ray Cast. In 
general the ray cast options are slower but more dependable.


Burlen

On 02/24/2015 11:18 PM, Xu, Ruqing wrote:

Hello,

I've installed PV 4.3 on a few PCs, all of them running Win 7 64-bit. 
What I've found is that volume rendering, curiously, works on some of 
them and fails on others. The error messages I got look like this:

=
ERROR: In 
C:\DBD\pvs-x64\paraview\src\paraview\VTK\Rendering\VolumeOpenGL\vtkOpenGLProjectedTetrahedraMapper.cxx, 
line 188


vtkOpenGLProjectedTetrahedraMapper (13AB80B0): The required 
extensions are not supported.




Warning: In 
C:\DBD\pvs-x64\paraview\src\paraview\VTK\Rendering\OpenGL\vtkOpenGLExtensionManager.cxx, 
line 781


vtkOpenGLExtensionManager (13567D60): Attempting to load 
GL_ARB_multitexture, which is not supported.




ERROR: In 
C:\DBD\pvs-x64\paraview\src\paraview\VTK\Rendering\OpenGL\vtkOpenGLExtensionManager.cxx, 
line 787


vtkOpenGLExtensionManager (13567D60): Extension 
GL_ARB_multitexture could not be loaded.


===


This seems to only happen to the relatively old PCs (~ 4 or 5 years 
old). For example one of them has graphics card of ATI Radeon HD 3450 
(Microsoft Corporation WDDM 1.1), driver version 7.14.10.0018; another 
laptop has Intel HD graphics, driver version 8.15.10.2559. - I'm 
wondering if these are considered insufficient for volume rendering to 
work with PV 4.3.


More curiously, volume rendering seems to run OK with PV 4.2 on these 
machines.


Thanks,

-Ruq


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Re: [Paraview] [Paraview-developers] min and max range mapping data in color map editor

[Burlen Loring]

also, usually ParaView colors by a scalar value and from your question 
it seems you are looking at position arrays (x,y,z). Do you have any 
scalar arrays defined? As Ken said,  would help to know more about your 
data.


On 02/18/2015 07:40 AM, Moreland, Kenneth wrote:

This question is probably more appropriate for the ParaView mailing list
rather than the developer's list, so I'm replying to it there.

I don't think there is enough information here to answer your question.
Any chance you could post an example data set?

-Ken



On 2/18/15, 7:56 AM, Laura Masse dragon.p...@gmail.com wrote:


Hello everybody,

I have a question about the limits in data range. I don´t understand how
paraview decide these limits, it seems there no any correspondence with
the
data value.

For example, in my case, data is a cloud points in a ply file, my real x,
y
,z range are :

X -1.3 to 14.6
Y -1.28 to 2.19
Z -60 to -50.1

Data range calculate by paraview is 159.49 to 382.243, I don´t understand
why .

I'm looking and looking the data but I don´t get the solution.

Anyone can help me ?

Advanced thanks !

Laura



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[Paraview] reducing startup time on cray

[Burlen Loring]

Hi All,

I want to share a performance issue related to PV start up time, which 
in general on our cray's is significant usability issue, especially on 
Hopper.


Earlier this week NERSC did some upgrades on one of our Crays which 
introduced some issues that prevent ParaView from starting. In the end 
we found that the issue is a system issue (file system or python 
problem) and not ParaView, but this exposed a performance issue in 
ParaView. ParaView would connect then hang when creating the render 
view. The debugger shows ParaView stuck in a python import call(stack is 
below) from vtkMatplotlibMathTextUtilities::CheckMPLAvailability. This 
function initializes the python interpreter and tries to import 
matplotlib.


Importing a python module (that's not built into the core of python) is 
an extremely expensive and unscalable operation in HPC setting. Software 
like python and ParaView, at least at NERSC, lives on slow remote file 
systems and in parallel the import hammers these file systems from each 
process. Python is essential for batch processing, but when using the 
interactive ParaView we should delay/avoid python imports as much as 
possible , especially during start up. This is a scalability issue in 
that most user aren't going to use the tex feature, but all users 
startup time is impacted, especially as job size grows.


I think in the case of ParaView's matplotlib tex features the run time 
check for matplotlib could probably be deferred until someone actually 
tries to use tex. What do you think? This would help keep startup time fast.


Burlen

proc_set{0}: #0 0x2e6b8fd0 in __open_nocancel
proc_set{0}: #1 0x2e65e483 in __GI__IO_file_open
proc_set{0}: #2 0x2e65e5fb in _IO_new_file_fopen
proc_set{0}: #3 0x2e6522f4 in __fopen_internal
proc_set{0}: #4 0x2ddb833c in find_module at Python/import.c:1556
proc_set{0}: #5 0x2ddba470 in import_submodule at 
Python/import.c:2689

proc_set{0}: #6 0x2ddbb0e3 in load_next at Python/import.c:2515
proc_set{0}: #7 0x2ddbb0e3 in import_module_level at 
Python/import.c:2224
proc_set{0}: #8 0x2ddbb0e3 in PyImport_ImportModuleLevel at 
Python/import.c:2288
proc_set{0}: #9 0x2dd998cf in builtin___import__ at 
Python/bltinmodule.c:49
proc_set{0}: #10 0x2dceae93 in PyObject_Call at 
Objects/abstract.c:2529
proc_set{0}: #11 0x2dd9b327 in PyEval_CallObjectWithKeywords at 
Python/ceval.c:3890
proc_set{0}: #12 0x2dd9e296 in PyEval_EvalFrameEx at 
Python/ceval.c:2333
proc_set{0}: #13 0x2dda198d in PyEval_EvalCodeEx at 
Python/ceval.c:3253

proc_set{0}: #14 0x2dda1ac2 in PyEval_EvalCode at Python/ceval.c:667
proc_set{0}: #15 0x2ddb924c in PyImport_ExecCodeModuleEx at 
Python/import.c:709
proc_set{0}: #16 0x2ddb95ae in load_source_module at 
Python/import.c:1099
proc_set{0}: #17 0x2ddba4a9 in import_submodule at 
Python/import.c:2700

proc_set{0}: #18 0x2ddbb0e3 in load_next at Python/import.c:2515
proc_set{0}: #19 0x2ddbb0e3 in import_module_level at 
Python/import.c:2224
proc_set{0}: #20 0x2ddbb0e3 in PyImport_ImportModuleLevel at 
Python/import.c:2288
proc_set{0}: #21 0x2dd998cf in builtin___import__ at 
Python/bltinmodule.c:49
proc_set{0}: #22 0x2dceae93 in PyObject_Call at 
Objects/abstract.c:2529
proc_set{0}: #23 0x2dd9b327 in PyEval_CallObjectWithKeywords at 
Python/ceval.c:3890
proc_set{0}: #24 0x2dd9e296 in PyEval_EvalFrameEx at 
Python/ceval.c:2333
proc_set{0}: #25 0x2dda198d in PyEval_EvalCodeEx at 
Python/ceval.c:3253

proc_set{0}: #26 0x2dda1ac2 in PyEval_EvalCode at Python/ceval.c:667
proc_set{0}: #27 0x2ddb924c in PyImport_ExecCodeModuleEx at 
Python/import.c:709
proc_set{0}: #28 0x2ddb95ae in load_source_module at 
Python/import.c:1099
proc_set{0}: #29 0x2ddba4a9 in import_submodule at 
Python/import.c:2700

proc_set{0}: #30 0x2ddbb567 in load_next at Python/import.c:2519
proc_set{0}: #31 0x2ddbb567 in import_module_level at 
Python/import.c:2224
proc_set{0}: #32 0x2ddbb567 in PyImport_ImportModuleLevel at 
Python/import.c:2288
proc_set{0}: #33 0x2dd998cf in builtin___import__ at 
Python/bltinmodule.c:49
proc_set{0}: #34 0x2dceae93 in PyObject_Call at 
Objects/abstract.c:2529
proc_set{0}: #35 0x2dd9b327 in PyEval_CallObjectWithKeywords at 
Python/ceval.c:3890
proc_set{0}: #36 0x2dd9e296 in PyEval_EvalFrameEx at 
Python/ceval.c:2333
proc_set{0}: #37 0x2dda198d in PyEval_EvalCodeEx at 
Python/ceval.c:3253

proc_set{0}: #38 0x2dda1ac2 in PyEval_EvalCode at Python/ceval.c:667
proc_set{0}: #39 0x2ddb924c in PyImport_ExecCodeModuleEx at 
Python/import.c:709
proc_set{0}: #40 0x2ddb95ae in load_source_module at 
Python/import.c:1099

proc_set{0}: #41 0x2ddba9e9 in load_package at Python/import.c:1166
proc_set{0}: #42

Re: [Paraview] reducing startup time on cray

[Burlen Loring]

Utkarsh, Berk,


It makes sense to me too.

Good, I will file a bug report so this doesn't get lost.

Having said that, wouldn't it be better to go to the next step and use 
a frozen Python?
Anything to improve the scalability of python would be huge and worth 
looking into.


NERSC maintains python and thing like mpi4py, numpy, matplotlib, etc. 
They chose to add the later stuff externally to their base python 
install (maybe it doesn't matter). When I build ParaView I have those 
modules loaded and cmake finds things as it needs. When I run ParaView I 
load the modules to bring the right versions/components into the 
environment.


I'm unfamiliar with freezing python and how it would work with pvserver, 
pvbatch, or pvpython. Question: how/what do we freeze in the pvserver case?


Thanks
Burlen

On 02/06/2015 12:19 PM, Berk Geveci wrote:

It makes sense to me too.

Having said that, wouldn't it be better to go to the next step and use 
a frozen Python? If all of the commonly used Python modules are frozen 
to the build, loading them will become much faster. The solution that 
you are proposing only defers the cost to later. Given that we are 
depending on Python more and more, I'd like to see it be usable 
everywhere.


Best,
-berk

On Fri, Feb 6, 2015 at 2:14 PM, Utkarsh Ayachit 
utkarsh.ayac...@kitware.com mailto:utkarsh.ayac...@kitware.com wrote:


 I think in the case of ParaView's matplotlib tex features the run time 
check
 for matplotlib could probably be deferred until someone actually
tries to
 use tex. What do you think? This would help keep startup time fast.

That makes total sense to me.
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Re: [Paraview] Writer plugin?

[Burlen Loring]

The WriterProxy may have a special file_name_method attribute that 
needs to be set. I'm not sure if that's required, optional, or long 
since obsolete since I haven't used our plugin in quite a while.


 13   WriterProxy name=vtkSQBOVWriter
 14 class=vtkSQBOVWriter
 15 file_name_method=SetFileName
 16 supports_parallel=1

On 1/28/2015 8:54 AM, David Thompson wrote:

Hi Andy,


I think you may be missing the FileName property. I thought that PV looked for 
that attribute to know that it should be classified as a writer. Also, you'll 
want to hide that property.

Adding the FileName property and hints did not work.

Thanks,
David


So:
   StringVectorProperty name=FileName
 command=SetFileName
 number_of_elements=1
 label=File Name
 Documentation
   The file name.
 /Documentation
   /StringVectorProperty


and:
   Hints
 Property name=Input show=0/
 Property name=FileName show=0/
 WriterFactory extensions=json file_description=JSON tabular data 
/
   /Hints




On Wed, Jan 28, 2015 at 11:34 AM, David Thompson david.thomp...@kitware.com 
wrote:
Hi all,

I have a ParaView plugin that contains a new writer which I would like to 
expose. However, while the plugin does properly expose a new view and 
representation, the writer does not appear to get added (when I try to save a 
vtkTable such as a statistics filter output, it doesn't appear as an option).

1. Is there any documentation for adding writers in plugins? This page has a 
comment or two but doesn't appear complete:

 http://www.paraview.org/Wiki/ParaView/Plugin_HowTo

2. If you're willing to look over the XML, I've attached it below. See any 
mistakes?

 Thanks,
 David

ServerManagerConfiguration
   !-- Other proxy groups for views and representations here --

   ProxyGroup name=writers
 WriterProxy
   class=vtkPJSONTableWriter
   name=PJSONTableWriter
   Documentation
 Write tabular data to a JSON file.
   /Documentation
   InputProperty
 command=SetInputConnection
 name=Input
 DataTypeDomain
   composite_data_supported=0
   name=input_type
   DataType value=vtkTable/
 /DataTypeDomain
 DocumentationThe input filter/source whose output dataset is to
 written to the file./Documentation
   /InputProperty
   Hints
 WriterFactory extensions=json file_description=JSON tabular data 
/
   /Hints
 /WriterProxy

   /ProxyGroup
/ServerManagerConfiguration

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[Paraview] building cosmo tools

[Burlen Loring]

Hi All,

I need to build CosmoTools extensions in ParaView. There are some 
dependencies that I'm having a hard time locating. For example 
GenericIO. Web search turns up nill, and the URL listed in the super 
build(git://kwsource.kitwarein.com/genericio/genericio.git) seems to be 
either private or bad. Anyone know where I can get this?


Thanks
Burlen
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Re: [Paraview] Python paraview.simple: Zoom To Data?

[Burlen Loring]

Hi Liam,

On 1/9/2015 10:52 AM, Liam wrote:
Just one more question. How do you define: far = config.camFac 


your question is a follow up to the script about automatically 
positioning the camera when viewing 2d axis aligned image data from thread

http://comments.gmane.org/gmane.comp.science.paraview.user/15091


in that post config.camFac was a variable for used for fine tuning the 
camera position. It could be 1.0 to go with default, less than 1.0 to 
move camera closer or greater than 1.0 to move the camera away.


Since I originally posted the script I had made improvements to it which 
I'll paste below. To remind of the context of the script below: I have 
2d axis aligned image data in the object named bovr. the script below 
automatically positions the camera and sizes the view according to the 
aspect ratio of the data. config_camZoom is a fine tuning parameter, 
and is documented here 
http://www.vtk.org/doc/nightly/html/classvtkCamera.html#a64512cc87555856a84f6c7d00abe0da9. 
1.0 is the value to start with.


hope this helps
Burlen

# run the pipeline here to get the bounds
rep = Show(bovr)
rep.Representation = 'Outline'
Render()

bounds = bovr.GetDataInformation().GetBounds()
bounds_dx = fabs(bounds[1] - bounds[0])
bounds_dy = fabs(bounds[3] - bounds[2])
bounds_dz = fabs(bounds[5] - bounds[4])
bounds_cx = (bounds[0] + bounds[1])/2.0
bounds_cy = (bounds[2] + bounds[3])/2.0
bounds_cz = (bounds[4] + bounds[5])/2.0

if (bounds_dx == 0):
  # yz
  dimMode = 2
  aspect = bounds_dz/bounds_dy

elif (bounds_dy == 0):
  # xz
  dimMode = 1
  aspect = bounds_dz/bounds_dx

elif (bounds_dz == 0):
  #xy
  dimMode = 0
  aspect = bounds_dy/bounds_dx

else:
  #3d
  dimMode = 3
  aspect = 1.0 # TODO

# position the camera
camFar=1.0

if (dimMode == 0):
  # xy
  camUp = [0.0, 1.0, 0.0]
  camDir = 2
  pos = max(bounds_dx, bounds_dy)
  camPos = [bounds_cx, bounds_cy, -pos*camFar]
  camFoc = [bounds_cx, bounds_cy, bounds_cz]

elif (dimMode == 1):
  # xz
  camUp = [0.0, 0.0, 1.0]
  camDir = 1
  pos = max(bounds_dx, bounds_dz)
  camPos = [bounds_cx, -pos*camFar,  bounds_cz]
  camFoc = [bounds_cx, bounds_cy, bounds_cz]

elif (dimMode == 2):
  # yz
  camUp = [0.0, 0.0, 1.0]
  camDir = 0
  pos = max(bounds_dy, bounds_dz)
  camPos = [ pos*camFar, bounds_cy, bounds_cz]
  camFoc = [bounds_cx, bounds_cy, bounds_cz]

else:
  # 3d
  print '3d cam position is yet TODO'

# configure the view
width = 1024
height = int(width*aspect)

view = GetRenderView()
view.CameraViewUp = camUp
view.CameraPosition = camPos
view.CameraFocalPoint = camFoc
view.UseOffscreenRenderingForScreenshots = 0
view.CenterAxesVisibility = 0
view.OrientationAxesVisibility = 0
view.ViewSize = [width, height]
Render()
view.ResetCamera()

# for fine tuning
config_camZoom = 1.0
cam = GetActiveCamera()
cam.Zoom(config_camZoom)

On 1/9/2015 10:52 AM, Liam wrote:

Hey guys,

Just one more question. How do you define:

far  = config.camFac

I cannot find in the code neither config nor camFac variable, so anybody
could explain me how to compute far variable?

This code has helped me so much.

Yhanks in advance,

Liam


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Re: [Paraview] Help with memory crash?

[Burlen Loring]

Hi Nikolaos,

One thing that I would suggest is to restructure your script so that you 
do not create new objects inside your loop. You can usually construct 
your rendering pipeline first then loop over the files(times, arrays, 
etc) modifying the existing pipeline objects and then calling Render 
followed by WriteImage. When you write your script that way you avoid 
the possibility of creating leaks. If you are convinced that there is a 
leak in ParaView we could advise on locating it, however I hesitate to 
give that advise prematurely. It's more likely that the issues are 
resulting from the way your script is structured.


Burlen

On 01/08/2015 09:57 AM, Nikolaos Beratlis wrote:
After reading about memory leaks I modified the script at the end by 
adding del after Delete:


  Delete(DataRepresentation4)
  del DataRepresentation4
  Delete(Contour2)
  del Contour2
  Delete(DataRepresentation3)
  del DataRepresentation3
  Delete(Q_VP_xmf)
  del Q_VP_xmf
  Delete(DataRepresentation2)
  del DataRepresentation2
  Delete(Contour1)
  del Contour1
  Delete(DataRepresentation1)
  del DataRepresentation1
  Delete(cf_VP_xmf)
  del cf_VP_xmf

That should fully delete the objects from the memory and it helped a 
little but I still have memory leaks. Before the script memory usage 
in the Memory Inspector is 1.4Gb and after one iteration it increases 
to 4Gb, compared to 10Gb without the del statements. After 4 
iterations the memory usage increases to 8Gb. Any ideas on how to 
track and eliminate completely the memory leaks? I am forgetting to 
delete an object from the script?




On Wed, Jan 7, 2015 at 9:17 PM, Nikolaos Beratlis 
nikos.berat...@gmail.com mailto:nikos.berat...@gmail.com wrote:


So I did some more tests by running the script interactively. I
used a smaller grid first, 2002 x 20 x 1000 points and ran it only
for 1 iteration. When Paraview loaded the memory usage on the
server was 1.04GB. After doing one iteration the memory usage
spiked to 10.42GB and remained like that when the script finished.
What I found out is the Delete statements make no difference at
all, with or without them the memory usage remained 10.42GB.
Performing more iterations in the script actually worsens this
problem, after 4 iterations the memory used increased to 14.32GB.
With a larger grid of 2002 x 100 x 1000 points the memory after
one iteration increased from 10.42GB before the script to 45.25GB
after the script. How can I properly delete all datasets and clear
the memory in Paraview?



On Wed, Jan 7, 2015 at 2:55 PM, Nikolaos Beratlis
nikos.berat...@gmail.com mailto:nikos.berat...@gmail.com wrote:

I am trying to run a script on a cluster with Paraview in
parallel. The cluster architecture is 16cores and 64GB per
node. The script reads in two XMF files, one contains a grid
of 2002x100x1000 points along with one variable. There is a
loop to perform two iterations:

try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()

RenderView1 = GetRenderView()
RenderView1.Background = [1.0, 1.0, 1.0]
view = GetActiveView()
view.ViewSize = [ 800, 500 ]

RenderView1.CenterAxesVisibility = 0
#RenderView1.OrientationAxesVisibility = 0

#Define variables
wdir =

'/lustre/groups/balarasgrp/nikosb/Research/Simulations/golfball/stationary/S120/Re20/gridC1/run_wm'
#wdir =

'/Users/nikosb/colone/Research/Simulations/golfball/stationary/S120/Re20/gridC1/run_wm'
#wdir =
'/Users/nikosb/Research/Simulations/SPHERE/Re100/gridC1/run'
Qval = 0.1
cfmin = -0.001
cfmax = 0.005

index = [None]*

m = 0
for i in range(0, 9):
  for j in range(0, 9):
for k in range(0, 9):
  for l in range(0, 9):
index[m] = chr(i+48)+chr(j+48)+chr(k+48)+chr(l+48)
m = m+1


for i in range(1,3):

  cf_VP_xmf = XDMFReader(
FileName=wdir+'/VPfield/XDMF/cf_VP'+index[i]+'.xmf' )

  cf_VP_xmf.Sets = []
  cf_VP_xmf.Grids = ['STL Grid']
  cf_VP_xmf.PointArrays = ['Cf']

  RenderView1 = GetRenderView()
  RenderView1.CenterOfRotation = [6.2286853790283203e-06,
2.5033950805664062e-06, 7.1227550506591797e-06]

  DataRepresentation1 = Show()
  DataRepresentation1.EdgeColor = [0.0, 0.0, 0.5762951094835]
DataRepresentation1.SelectionPointFieldDataArrayName = 'Cf'
  DataRepresentation1.ColorArrayName = ('POINT_DATA', 'Cf')
DataRepresentation1.ScalarOpacityUnitDistance =
0.03392870483226
  DataRepresentation1.ScaleFactor = 0.08557567596444

  a1_Cf_PVLookupTable = GetLookupTableForArray( Cf, 1,
RGBPoints=[-0.0099065126851201057

Re: [Paraview] paraview cmake can't find proper qt

[Burlen Loring]

Hi Jeff,

Here are the vars that I set:

   prepend-path PATH /work/apps/qt-4.8.2/bin
   prepend-path MANPATH :/work/apps/qt-4.8.2/man
   prepend-path LD_LIBRARY_PATH /work/apps/qt-4.8.2/lib
   prepend-path LD_RUN_PATH /work/apps/qt-4.8.2/lib

after sourcing this, typing which qmake in the shell where you're 
doing your build should print the path to your qt. then cmake should 
find your qt.


the above is an excerpt from a module file 
http://modules.sourceforge.net/ which provides a convenient way to 
manage multiple installs.


Burlen

On 01/09/2015 09:59 AM, Jeff Becker wrote:
Hi. My initial run of ccmake complained that my distro's qt was too 
old, so I downloaded and built/installed a supported version in 
/usr/local/Trolltech/Qt-4.8.6. Thus I set:


//Where can the qmake-qt4 library be found
QT_QMAKE_EXECUTABLE:FILEPATH=/usr/local/Trolltech/Qt-4.8.6/bin/qmake

However, even though ccmake completes (allowing the g key to be 
activated), the qt libraries/executables listed in CMakeCache.txt are 
all from the distro's versions (in /usr/lib64/qt4). E.g.,


//Path to a library.
QT_CUSTOMWIDGETPLUGIN_PLUGIN_RELEASE:FILEPATH=/usr/lib64/qt4/plugins/designer/libcustomwidgetplugin.so 



//Path to a program.
QT_DBUSCPP2XML_EXECUTABLE:FILEPATH=/usr/lib64/qt4/bin/qdbuscpp2xml

 Is there a QTHOME or similar variable I need to set to get the right 
libraries/executables? Thanks.


-jeff
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Re: [Paraview] Trace recorder missing color preset changes

[Burlen Loring]

Hi Alan,

Did you want to load a preset color lut by name from python? If so, this 
example shows how: 
http://www.paraview.org/Wiki/ParaView/Python/Lookup_tables


That commit was accepted as an interim measure, was never publicized, 
and Utkarsh may have a better way by now.


Burlen

On 12/22/2014 6:38 PM, Scott, W Alan wrote:
There is an issue with the trace recorder missing color preset 
changes.  I wrote up a bug here: 
_http://www.paraview.org/Bug/view.php?id=15116_. However, I need the 
python for a user so that he can manually edit the trace script and 
change color presets.  Does anyone either know the python I need, or 
where to find it?

Thanks,
Alan


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Re: [Paraview] paraview web issue

[Burlen Loring]

That did it! Thanks Sebastien!

On 11/25/2014 07:04 PM, Sebastien Jourdain wrote:
BTW, once you update the configuration file, you will need to restart 
that launcher process.

It is not smart enough to watch that file. ;-)

And down the road, if you want to use different machine for the Viz, 
you can issue some ssh command to remotely start that ParaView process 
even with mpi/pvserver.


Seb

On Tue, Nov 25, 2014 at 8:01 PM, Sebastien Jourdain 
sebastien.jourd...@kitware.com 
mailto:sebastien.jourd...@kitware.com wrote:


Found the issue! Or at least I think I do ;-)

The short answer is that the ready_line property inside your
launcher.json file should be Starting factory and not Starting
factory - XYZ for all the command lines. (Like written in the
documentation ;-)

The reason is that the launcher look for that exact String in the
output of the process that it runs. This allow to know when the
process is ready. And the line Starting factory - XYZ never show
up, hence the error message
Session did not start before timeout expired. Check session
logs. has it think the process is not ready.

Let me know if you run into something else.

Seb




On Tue, Nov 25, 2014 at 5:00 PM, Burlen Loring blor...@lbl.gov
mailto:blor...@lbl.gov wrote:

Hi Sebastien,

OK, I finally upgrade to Ubuntu 14.04 and apache 2.4! however,
I still have some issue. again I see the render window pop up
in the background, in the browser I have the ParaView web logo
and spinning wheel, now after a few seconds a dialog: Session
did not start before timeout expired. Check session logs.

I cranked up the log verbosity in apache. attached
everything.  Any idea what the problem is? how to get more
info? paraview has an error, how does that get reported?

Thanks
Burlen


On 11/24/2014 12:48 PM, Sebastien Jourdain wrote:

Apache 2.2 will probably be an issue as WS forwarding was not
properly supported with url rewrite.

You may need to build Apache yourself on that distribution.
The one that have all the fix and is supposed to work is 2.4.7+.

We have some additional documentation about that part here:


http://www.paraview.org/ParaView3/Doc/Nightly/www/js-doc/index.html#!/guide/apache_front_end

http://www.paraview.org/ParaView3/Doc/Nightly/www/js-doc/index.html#%21/guide/apache_front_end

Seb

On Mon, Nov 24, 2014 at 12:47 PM, Burlen Loring
blor...@lbl.gov mailto:blor...@lbl.gov wrote:

Hi Sebastien,

this is for a public deployment but I am testing in the
browser while it locally logged into the system. This
server is running ubuntu 11.04, apache 2.2.22. I hope
that this isn't a roadblock.I can't easily upgrade.

your instructions for 14.04 went off OK but in 2 spots I
had to find a work around:
1) proxy_wstunnel had to be installed manually, this went
without a hitch and it loaded up without error
2) in the apache config I had to comment #Require all
granted as that wasn't valid in 2.2

the session id was in the proxy.txt file and had the port
number 9100 which I see elsewhere in the logs, so that
looks OK.

I'm attaching the launcher config.

the apache config is pasted below.

131

333
132 VirtualHost *:80
133 ServerName paraview.lbl.gov http://paraview.lbl.gov
134 ServerAdmin blor...@lbl.gov mailto:blor...@lbl.gov
135 DocumentRoot /var/www/ParaView/www
136 ErrorLog /var/www/ParaView/logs/error.log
137 CustomLog /var/www/ParaView/logs/access.log common
138
139 Directory /var/www/ParaView/www
140 Options Indexes FollowSymLinks
141 Order allow,deny
142 Allow from all
143 AllowOverride None
144 #for ver = 2.4
145 #Require all granted
146 /Directory
147
148 # Handle launcher forwarding
149 ProxyPass /paraview http://localhost:8080/paraview
150
151 # Handle WebSocket forwarding
152 RewriteEngine On
153 RewriteMap session-to-port
txt:/var/www/ParaView/proxy.txt
154 RewriteCond %{QUERY_STRING} ^sessionId=(.*)$ [NC]
155 RewriteRule ^/proxy.*$
ws://${session-to-port:%1}/ws [P]
156 /VirtualHost


On 11/24/2014 10:02 AM, Sebastien Jourdain wrote:

Hi Burlen,

Just to make sure

Re: [Paraview] paraview web issue

[Burlen Loring]

Hi Sebastien,

OK, I finally upgrade to Ubuntu 14.04 and apache 2.4! however, I still 
have some issue. again I see the render window pop up in the background, 
in the browser I have the ParaView web logo and spinning wheel, now 
after a few seconds a dialog: Session did not start before timeout 
expired. Check session logs.


I cranked up the log verbosity in apache. attached everything. Any idea 
what the problem is? how to get more info? paraview has an error, how 
does that get reported?


Thanks
Burlen

On 11/24/2014 12:48 PM, Sebastien Jourdain wrote:
Apache 2.2 will probably be an issue as WS forwarding was not properly 
supported with url rewrite.


You may need to build Apache yourself on that distribution. The one 
that have all the fix and is supposed to work is 2.4.7+.


We have some additional documentation about that part here:

http://www.paraview.org/ParaView3/Doc/Nightly/www/js-doc/index.html#!/guide/apache_front_end 
http://www.paraview.org/ParaView3/Doc/Nightly/www/js-doc/index.html#%21/guide/apache_front_end


Seb

On Mon, Nov 24, 2014 at 12:47 PM, Burlen Loring blor...@lbl.gov 
mailto:blor...@lbl.gov wrote:


Hi Sebastien,

this is for a public deployment but I am testing in the browser
while it locally logged into the system. This server is running
ubuntu 11.04, apache 2.2.22. I hope that this isn't a roadblock.I
can't easily upgrade.

your instructions for 14.04 went off OK but in 2 spots I had to
find a work around:
1) proxy_wstunnel had to be installed manually, this went without
a hitch and it loaded up without error
2) in the apache config I had to comment #Require all granted as
that wasn't valid in 2.2

the session id was in the proxy.txt file and had the port number
9100 which I see elsewhere in the logs, so that looks OK.

I'm attaching the launcher config.

the apache config is pasted below.

131

333
132 VirtualHost *:80
133 ServerName paraview.lbl.gov http://paraview.lbl.gov
134 ServerAdmin blor...@lbl.gov mailto:blor...@lbl.gov
135 DocumentRoot /var/www/ParaView/www
136 ErrorLog /var/www/ParaView/logs/error.log
137 CustomLog /var/www/ParaView/logs/access.log common
138
139 Directory /var/www/ParaView/www
140 Options Indexes FollowSymLinks
141 Order allow,deny
142 Allow from all
143 AllowOverride None
144 #for ver = 2.4
145 #Require all granted
146 /Directory
147
148 # Handle launcher forwarding
149 ProxyPass /paraview http://localhost:8080/paraview
150
151 # Handle WebSocket forwarding
152 RewriteEngine On
153 RewriteMap  session-to-port txt:/var/www/ParaView/proxy.txt
154 RewriteCond %{QUERY_STRING} ^sessionId=(.*)$ [NC]
155 RewriteRule ^/proxy.*$ ws://${session-to-port:%1}/ws [P]
156 /VirtualHost


On 11/24/2014 10:02 AM, Sebastien Jourdain wrote:

Hi Burlen,

Just to make sure, you are performing the install on an Ubuntu
14.04 ?

Are you trying to try it locally first using localhost, or are
you targeting a real deploy with a real host name?

Can you share your config file for the launcher + apache?
(You can do it privately depending on your target deploy / security)

Moreover, can you validate that the session id
c3079f24-73f9-11e4-a023-002590202132  was properly mapped inside
the text file that is shared between Apache and the Python launcher?

Thanks,

Seb



On Mon, Nov 24, 2014 at 10:29 AM, burlen burlen.lor...@gmail.com
mailto:burlen.lor...@gmail.com wrote:

Hi All,

Making an attempt to install ParaView web. I need some
assistance in trouble shooting. I am attaching a set of logs
from a single attempt. I'm following theinstructions for
Ubuntu 14.04

http://www.paraview.org/ParaView3/Doc/Nightly/www/js-doc/index.html#%21/guide/ubuntu_14_04.
I see the x11 render window open, but the web page shows nothing.

from the error log
[Mon Nov 24 08:48:53 2014] [error] [client 131.243.240.15]
File does not exist: /var/www/ParaView/www/ws:

from the access log
131.243.240.15 - - [24/Nov/2014:08:48:53 -0800] GET
/ws://localhost:9100/ws?sessionId=c3079f24-73f9-11e4-a023-002590202132
HTTP/1.1 404 513
131.243.240.15 - - [24/Nov/2014:08:48:53 -0800] GET
/proxy?sessionId=c3079f24-73f9-11e4-a023-002590202132
HTTP/1.1 404 457

Seems that the problem potentially relates to web sockets.
How can I get further info about what's failing? Can anyone
give some hint on troubleshooting this issue?

Burlen

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[Paraview] paraview web issue

[burlen]

Hi All,

Making an attempt to install ParaView web. I need some assistance in 
trouble shooting. I am attaching a set of logs from a single attempt. 
I'm following theinstructions for Ubuntu 14.04 
http://www.paraview.org/ParaView3/Doc/Nightly/www/js-doc/index.html#%21/guide/ubuntu_14_04. 
I see the x11 render window open, but the web page shows nothing.


from the error log
[Mon Nov 24 08:48:53 2014] [error] [client 131.243.240.15] File does not 
exist: /var/www/ParaView/www/ws:


from the access log
131.243.240.15 - - [24/Nov/2014:08:48:53 -0800] GET 
/ws://localhost:9100/ws?sessionId=c3079f24-73f9-11e4-a023-002590202132 
HTTP/1.1 404 513
131.243.240.15 - - [24/Nov/2014:08:48:53 -0800] GET 
/proxy?sessionId=c3079f24-73f9-11e4-a023-002590202132 HTTP/1.1 404 457


Seems that the problem potentially relates to web sockets. How can I get 
further info about what's failing? Can anyone give some hint on 
troubleshooting this issue?


Burlen
131.243.240.15 - - [24/Nov/2014:08:48:06 -0800] GET / HTTP/1.1 304 211
131.243.240.15 - - [24/Nov/2014:08:48:06 -0800] GET /resources/css/app-d837b293d081641aaa2111b87080b6d6.css HTTP/1.1 304 211
131.243.240.15 - - [24/Nov/2014:08:48:06 -0800] GET /extjs/ext-all.js HTTP/1.1 304 213
131.243.240.15 - - [24/Nov/2014:08:48:06 -0800] GET /data-0d50d2ddb5aba49a18815a3ab4cc9c10.js HTTP/1.1 304 211
131.243.240.15 - - [24/Nov/2014:08:48:06 -0800] GET /app-9096a86b4ef476d85905927d55b2fdef.js HTTP/1.1 304 212
131.243.240.15 - - [24/Nov/2014:08:48:06 -0800] GET /custom.css HTTP/1.1 304 210
131.243.240.15 - - [24/Nov/2014:08:48:06 -0800] GET /images/PVW_Slide.png HTTP/1.1 304 189
131.243.240.15 - - [24/Nov/2014:08:48:06 -0800] GET /images/compatible_ie.gif HTTP/1.1 304 186
131.243.240.15 - - [24/Nov/2014:08:48:06 -0800] GET /images/compatible_firefox.gif HTTP/1.1 304 186
131.243.240.15 - - [24/Nov/2014:08:48:06 -0800] GET /images/compatible_chrome.gif HTTP/1.1 304 186
131.243.240.15 - - [24/Nov/2014:08:48:06 -0800] GET /images/compatible_opera.gif HTTP/1.1 304 186
131.243.240.15 - - [24/Nov/2014:08:48:06 -0800] GET /images/compatible_safari.gif HTTP/1.1 304 186
131.243.240.15 - - [24/Nov/2014:08:48:07 -0800] GET /resources/images/loading.gif HTTP/1.1 304 187
131.243.240.15 - - [24/Nov/2014:08:48:07 -0800] GET /resources/images/logo.png HTTP/1.1 304 186
131.243.240.15 - - [24/Nov/2014:08:48:07 -0800] GET /extjs/resources/themes/images/default/form/trigger.gif HTTP/1.1 304 186
131.243.240.15 - - [24/Nov/2014:08:48:07 -0800] GET /extjs/resources/themes/images/default/form/exclamation.gif HTTP/1.1 304 186
131.243.240.15 - - [24/Nov/2014:08:48:07 -0800] GET /extjs/resources/themes/images/default/grid/grid3-hd-btn.gif HTTP/1.1 304 186
131.243.240.15 - - [24/Nov/2014:08:48:07 -0800] GET /extjs/resources/themes/images/default/form/checkbox.gif HTTP/1.1 304 186
131.243.240.15 - - [24/Nov/2014:08:48:07 -0800] GET /resources/images/search-box.png HTTP/1.1 304 186
131.243.240.15 - - [24/Nov/2014:08:48:07 -0800] GET /resources/images/tabs.png HTTP/1.1 304 187
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /apps/FileViewer/ HTTP/1.1 200 1410
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /apps/FileViewer/style.css HTTP/1.1 200 997
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /ext/pure/pure.min.js HTTP/1.1 200 5074
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /lib/widgets/FileBrowser/vtkweb-widget-filebrowser.js HTTP/1.1 200 2483
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /lib/widgets/FileBrowser/vtkweb-widget-filebrowser.tpl HTTP/1.1 200 900
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /lib/css/paraview.ui.toolbar.css HTTP/1.1 200 1033
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /lib/widgets/FileBrowser/vtkweb-widget-filebrowser.css HTTP/1.1 200 618
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /ext/jscolor/jscolor.js HTTP/1.1 200 7455
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /lib/css/paraview.ui.toolbar.vcr.css HTTP/1.1 200 572
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /lib/css/paraview.ui.toolbar.viewport.css HTTP/1.1 200 855
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /lib/css/paraview.ui.toolbar.connect.css HTTP/1.1 200 520
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /lib/js/paraview.ui.toolbar.js HTTP/1.1 200 1034
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /lib/js/paraview.ui.toolbar.vcr.js HTTP/1.1 200 1959
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /lib/js/paraview.ui.toolbar.viewport.js HTTP/1.1 200 2048
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /lib/js/paraview.ui.toolbar.connect.js HTTP/1.1 200 2336
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /apps/FileViewer/open.png HTTP/1.1 200 1813
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /lib/css/paraview/toolbar/common/logo.png HTTP/1.1 200 2371
131.243.240.15 - - [24/Nov/2014:08:48:47 -0800] GET /lib/css/paraview/toolbar/common/loading.gif HTTP/1.1 200 2
131.243.240.15 - - [24/Nov/2014:08:48:48 -0800] POST

Re: [Paraview] paraview web issue

[Burlen Loring]

Hi Sebastien,

this is for a public deployment but I am testing in the browser while it 
locally logged into the system. This server is running ubuntu 11.04, 
apache 2.2.22. I hope that this isn't a roadblock.I can't easily upgrade.


your instructions for 14.04 went off OK but in 2 spots I had to find a 
work around:
1) proxy_wstunnel had to be installed manually, this went without a 
hitch and it loaded up without error
2) in the apache config I had to comment #Require all granted as that 
wasn't valid in 2.2


the session id was in the proxy.txt file and had the port number 9100 
which I see elsewhere in the logs, so that looks OK.


I'm attaching the launcher config.

the apache config is pasted below.

131 
333

132 VirtualHost *:80
133 ServerName paraview.lbl.gov
134 ServerAdmin blor...@lbl.gov
135 DocumentRoot /var/www/ParaView/www
136 ErrorLog /var/www/ParaView/logs/error.log
137 CustomLog /var/www/ParaView/logs/access.log common
138
139 Directory /var/www/ParaView/www
140 Options Indexes FollowSymLinks
141 Order allow,deny
142 Allow from all
143 AllowOverride None
144 #for ver = 2.4
145 #Require all granted
146 /Directory
147
148 # Handle launcher forwarding
149 ProxyPass /paraview http://localhost:8080/paraview
150
151 # Handle WebSocket forwarding
152 RewriteEngine On
153 RewriteMap  session-to-port txt:/var/www/ParaView/proxy.txt
154 RewriteCond %{QUERY_STRING} ^sessionId=(.*)$ [NC]
155 RewriteRule ^/proxy.*$ ws://${session-to-port:%1}/ws [P]
156 /VirtualHost

On 11/24/2014 10:02 AM, Sebastien Jourdain wrote:

Hi Burlen,

Just to make sure, you are performing the install on an Ubuntu 14.04 ?

Are you trying to try it locally first using localhost, or are you 
targeting a real deploy with a real host name?


Can you share your config file for the launcher + apache?
(You can do it privately depending on your target deploy / security)

Moreover, can you validate that the session id 
c3079f24-73f9-11e4-a023-002590202132  was properly mapped inside the 
text file that is shared between Apache and the Python launcher?


Thanks,

Seb



On Mon, Nov 24, 2014 at 10:29 AM, burlen burlen.lor...@gmail.com 
mailto:burlen.lor...@gmail.com wrote:


Hi All,

Making an attempt to install ParaView web. I need some assistance
in trouble shooting. I am attaching a set of logs from a single
attempt. I'm following theinstructions for Ubuntu 14.04

http://www.paraview.org/ParaView3/Doc/Nightly/www/js-doc/index.html#%21/guide/ubuntu_14_04.
I see the x11 render window open, but the web page shows nothing.

from the error log
[Mon Nov 24 08:48:53 2014] [error] [client 131.243.240.15] File
does not exist: /var/www/ParaView/www/ws:

from the access log
131.243.240.15 - - [24/Nov/2014:08:48:53 -0800] GET
/ws://localhost:9100/ws?sessionId=c3079f24-73f9-11e4-a023-002590202132
HTTP/1.1 404 513
131.243.240.15 - - [24/Nov/2014:08:48:53 -0800] GET
/proxy?sessionId=c3079f24-73f9-11e4-a023-002590202132 HTTP/1.1
404 457

Seems that the problem potentially relates to web sockets. How can
I get further info about what's failing? Can anyone give some hint
on troubleshooting this issue?

Burlen

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launcher.json
Description: application/json
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Re: [Paraview] volume color transfer table.

[Burlen Loring]

that is indeed annoying, and would be very nice to be able to save the 
opacity table. A work around is use a state file. The opacity tables 
will be saved/restored. note: 4.2 has a bug in state file loading re: 
time. depending on your scenario you may need to use 4.1.


On 11/07/2014 08:33 AM, Anderson, Lawrence S. wrote:

thanks for the attention!  I should also point out that i have tried the import/export 
options on the color table editing feature- opacity is not preserved.  i.e. when i export 
a table to an xml file, the opacities all revert to 1.0, and when i import an xml file, 
any ' o=x.xx ' value is ignored, and whatever opacity function in the editor 
from previous work is applied instead.
cheers-
-lawrence a.


From: Utkarsh Ayachit [utkarsh.ayac...@kitware.com]
Sent: Friday, November 07, 2014 9:01 AM
To: Anderson, Lawrence S.; Aashish Chaudhary
Cc: paraview@paraview.org
Subject: Re: [Paraview] volume color transfer table.

To the best of my knowledge, the current volume mappers in
VTK/ParaView need to use a color/opacity transfer functions. Aashish,
is that changing with the new volume rendering code?

Utkarsh

On Wed, Nov 5, 2014 at 3:12 PM, Anderson, Lawrence S.
lawrence.ander...@utoledo.edu wrote:

hi-  i have seen this question on various blogs, but not the answer in a
usable form for me...
i provide project data to paraview via vtk legacy files in ascii.  the
default color mapping functions provided by paraview do not decouple opacity
from color, so i am providing my own look_up table of RGBa values organized
in such a way that i can apply different opacities to the same color, and
different colors to the same opacity.  it works for surface rendering, but
not for volume rendering- i.e. when choosing the volume option, the
rendering reverts back to one of the default tables.  how do i apply my
scalar color table in the vtk file to volumes?
i could laboriously enter 120x4 values into the paraview mapping editor, but
that seems silly...
thank you!
and as i am new to paraview and this list mail option, feel free to refer me
to an old post.
-lawrence anderson, university of toledo



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Re: [Paraview] HPC paraview

[Burlen Loring]

to verify make a small job on 1 node. In the shell you are starting 
pvserver in, after you've done all the environment settings you need to 
to setup for paraview, run glxinfo and look for the gl vendor, gl 
version and gl renderer strings. these should give you info about your 
tesla. that can be done from your batch script or at the command prompt. 
some systems like cray mpiexec command (aprun) runs the program on a  
different set of nodes than the batch script itself, so for a system 
like that run aprun -n 1 glxinfo.


On 10/29/2014 08:29 PM, R C Bording wrote:

HI Burlen,
  Thanks again.  Is there and easy way to verify that Paraview is 
using the GPU ours are TESLA C2075?


Should I need to change the MOD(?) setting so it is rendering rather 
than compute?


R. Christopher Bording
Supercomputing Team-iVEC@UWA
E: cbord...@ivec.org mailto:cbord...@ivec.org
T: +61 8 6488 6905

26 Dick Perry Avenue,
Technology Park
Kensington, Western Australia.
6151





On 27/10/2014, at 11:10 PM, Burlen Loring wrote:


Hi Christopher,

Are you by any chance logged in with ssh X11 forwarding (ssh -X ...)? 
It seems the error you report comes up often in that context. X 
forwarding would not be the right way to run PV on your cluster.


Depending on how your cluster is setup you may need to start up the 
xserver before launching PV, and make sure to close it after PV 
exits. IUn that scenario your xorg.conf would specify the nvidia 
driver and a screen for each gpu which you would refernece in the 
shell used to start PV through the DISPLAY variable. If you already 
have x11 running and screens configured then it's just a matter of 
setting the display variable correctly. When there are multiple GPU's 
per node then you'd need to set the display using mpi rank modulo the 
number of gpus per node.


I'm not sure it matters that much but I don't think that you want 
--use-offscreen-rendering option.


Burlen

On 10/26/2014 10:23 PM, R C Bording wrote:

Hi,
 Managed to get a working version of Paraview-4.2.0.1 on our GPU 
cluster but when I try to run the
parallelSphere.py script on more than one node it just hangs.  Work 
like it is supposed to up to 12 cores on a single node.  I am still 
trying work out if I a running on the GPU tesla- C2070).


Here is the list of cake configurations

IBS_TOOL_CONFIGURE='-DCMAKE_BUILD_TYPE=Release \
-DParaView_FROM_GIT=OFF \
-DParaView_URL=$MYGROUP/vis/src/ParaView-v4.2.0-source.tar.gz \
-DENABLE_boost=ON \
-DENABLE_cgns=OFF \
-DENABLE_ffmpeg=ON \
-DENABLE_fontconfig=ON \
-DENABLE_freetype=ON \
-DENABLE_hdf5=ON \
-DENABLE_libxml2=ON \
-DENABLE_matplotlib=ON \
-DENABLE_mesa=OFF \
-DENABLE_mpi=ON \
-DENABLE_numpy=ON \
-DENABLE_osmesa=OFF \
-DENABLE_paraview=ON \
-DENABLE_png=ON \
-DENABLE_python=ON \
-DENABLE_qhull=ON \
-DENABLE_qt=ON \
-DENABLE_silo=ON \
-DENABLE_szip=ON \
-DENABLE_visitbridge=ON \
-DMPI_CXX_LIBRARIES:STRING=$MPI_HOME/lib/libmpi_cxx.so \
-DMPI_C_LIBRARIES:STRING=$MPI_HOME/lib/libmpi.so \
-DMPI_LIBRARY:FILEPATH=$MPI_HOME/lib/libmpi_cxx.so \
-DMPI_CXX_INCLUDE_PATH:STRING=$MPI_HOME/include \
-DMPI_C_INCLUDE_PATH:STRING=$MPI_HOME/include \
-DUSE_SYSTEM_mpi=ON \
-DUSE_SYSTEM_python=OFF \
-DUSE_SYSTEM_qt=OFF \
-DUSE_SYSTEM_zlib=OFF '

The goal is to be able to support batch rendering on the whole 
cluster ~96 nodes.


Also do I need set another environment variable in my Paraview 
module to make the Xlib

warning go away?

[cbording@f100 Paraview]$ mpirun -n 12 pvbatch 
--use-offscreen-rendering parallelSphere.py

Xlib:  extension NV-GLX missing on display localhost:50.0.
Xlib:  extension NV-GLX missing on display localhost:50.0.
Xlib:  extension NV-GLX missing on display localhost:50.0.
Xlib:  extension NV-GLX missing on display localhost:50.0.
Xlib:  extension NV-GLX missing on display localhost:50.0.
Xlib:  extension NV-GLX missing on display localhost:50.0.

Is this related to my not being able to run across multiple nodes?

R. Christopher Bording
Supercomputing Team-iVEC@UWA
E: cbord...@ivec.org mailto:cbord...@ivec.org
T: +61 8 6488 6905

26 Dick Perry Avenue,
Technology Park
Kensington, Western Australia.
6151







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Re: [Paraview] PV 4.2.0 Color legend disappearing

[Burlen Loring]

yep I've seen that and a hosty of other flakeyness that I haven't had 
time to make bug reports about. using 4.1 for now.


On 10/29/2014 04:26 PM, Scott, W Alan wrote:
In ParaView 4.2.0, I have found a few cases where the color legend 
disappears, and I can’t get it back.  Has anyone else seen this, and 
found a way to replicate it? Mind passing the voodoo on how to 
replicate this bug?

Thanks,
Alan


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Re: [Paraview] HPC paraview

[Burlen Loring]

Hi Chris,

your reply makes me suspicious that you may not really be rendering on 
your tesla yet. LIBGL_ALWAYS_INDIRECT should not be needed and as far as 
I know this is a Mesa specific variable. Even in an interactive batch 
job you shouldn't use x11 forwarding for ParaView (I couldn't tell if 
you are using it or not, but I wanted to be clear about that because it 
doesn't scale well). If I were you I'd verify that you're really using 
the your tesla by examining the output of glxinfo.


Burlen

On 10/28/2014 02:52 AM, R C Bording wrote:

HI Burlen,
  Yes I am for the purpose of testing on our debug queue.  But you are 
bang on with setting the DISPLAY environment variable.


so setting in the preview module
setenv LIBGL_ALWAYS_INDIRECT 1
or in bash in the job script
export LIBGL_ALWAYS_INDIRECT 1

but also adding
export DISPLAY=:1
is needed to render on the GPU.

Renders the parallelSphere.py example with no errors across multiple 
nodes.


my mpirun command looks like this

mpirun pvbatch parallelSphere.py

note we have PBSpro installed so it determines the -np ##-number of 
processors/cores based on the

#PBS -l select=.

So now to see if I can render something awesome!

Chris B

On 27/10/2014, at 11:10 PM, Burlen Loring wrote:


Hi Christopher,

Are you by any chance logged in with ssh X11 forwarding (ssh -X ...)? 
It seems the error you report comes up often in that context. X 
forwarding would not be the right way to run PV on your cluster.


Depending on how your cluster is setup you may need to start up the 
xserver before launching PV, and make sure to close it after PV 
exits. IUn that scenario your xorg.conf would specify the nvidia 
driver and a screen for each gpu which you would refernece in the 
shell used to start PV through the DISPLAY variable. If you already 
have x11 running and screens configured then it's just a matter of 
setting the display variable correctly. When there are multiple GPU's 
per node then you'd need to set the display using mpi rank modulo the 
number of gpus per node.


I'm not sure it matters that much but I don't think that you want 
--use-offscreen-rendering option.


Burlen

On 10/26/2014 10:23 PM, R C Bording wrote:

Hi,
 Managed to get a working version of Paraview-4.2.0.1 on our GPU 
cluster but when I try to run the
parallelSphere.py script on more than one node it just hangs.  Work 
like it is supposed to up to 12 cores on a single node.  I am still 
trying work out if I a running on the GPU tesla- C2070).


Here is the list of cake configurations

IBS_TOOL_CONFIGURE='-DCMAKE_BUILD_TYPE=Release \
-DParaView_FROM_GIT=OFF \
-DParaView_URL=$MYGROUP/vis/src/ParaView-v4.2.0-source.tar.gz \
-DENABLE_boost=ON \
-DENABLE_cgns=OFF \
-DENABLE_ffmpeg=ON \
-DENABLE_fontconfig=ON \
-DENABLE_freetype=ON \
-DENABLE_hdf5=ON \
-DENABLE_libxml2=ON \
-DENABLE_matplotlib=ON \
-DENABLE_mesa=OFF \
-DENABLE_mpi=ON \
-DENABLE_numpy=ON \
-DENABLE_osmesa=OFF \
-DENABLE_paraview=ON \
-DENABLE_png=ON \
-DENABLE_python=ON \
-DENABLE_qhull=ON \
-DENABLE_qt=ON \
-DENABLE_silo=ON \
-DENABLE_szip=ON \
-DENABLE_visitbridge=ON \
-DMPI_CXX_LIBRARIES:STRING=$MPI_HOME/lib/libmpi_cxx.so \
-DMPI_C_LIBRARIES:STRING=$MPI_HOME/lib/libmpi.so \
-DMPI_LIBRARY:FILEPATH=$MPI_HOME/lib/libmpi_cxx.so \
-DMPI_CXX_INCLUDE_PATH:STRING=$MPI_HOME/include \
-DMPI_C_INCLUDE_PATH:STRING=$MPI_HOME/include \
-DUSE_SYSTEM_mpi=ON \
-DUSE_SYSTEM_python=OFF \
-DUSE_SYSTEM_qt=OFF \
-DUSE_SYSTEM_zlib=OFF '

The goal is to be able to support batch rendering on the whole 
cluster ~96 nodes.


Also do I need set another environment variable in my Paraview 
module to make the Xlib

warning go away?

[cbording@f100 Paraview]$ mpirun -n 12 pvbatch 
--use-offscreen-rendering parallelSphere.py

Xlib:  extension NV-GLX missing on display localhost:50.0.
Xlib:  extension NV-GLX missing on display localhost:50.0.
Xlib:  extension NV-GLX missing on display localhost:50.0.
Xlib:  extension NV-GLX missing on display localhost:50.0.
Xlib:  extension NV-GLX missing on display localhost:50.0.
Xlib:  extension NV-GLX missing on display localhost:50.0.

Is this related to my not being able to run across multiple nodes?

R. Christopher Bording
Supercomputing Team-iVEC@UWA
E: cbord...@ivec.org mailto:cbord...@ivec.org
T: +61 8 6488 6905

26 Dick Perry Avenue,
Technology Park
Kensington, Western Australia.
6151







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Re: [Paraview] Paravew on XC30

[Burlen Loring]

Hi Christopher,

I can't help you with the superbuild, but I can show you how to build PV 
on the XC30. here's the script 
https://github.com/burlen/pvserver-configs/blob/master/servers/edison/builds/config-pv-mesa.sh 
I used to build ParaView 4.2 with PrgEnv-gnu/5.2.25 on our XC30


You'll see a bunch of paths that need to be set specific to the version 
of PrgEnv-gnu that you are running. The easiest way to figure out these 
is to look at the CRAY_LD_LIBRARY_PATH environment variable. If for some 
reason that isn't set then you can alway look at the output of CC 
--verbose. You also need to point to an OSMesa install 
http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D.


Burlen

On 10/26/2014 10:22 PM, R C Bording wrote:

Hi,
 Trying to build Paraview on our XC30,
here is the end of the build log where it goes pear-shape,

Making install in test
/usr/bin/install -c -m 644 fonts.dtd 
'/group/director100/cbording/vis/cle52/build/osmesa-ParaViewSuperbuild-4.2.0/ParaViewSuperbuild-4.2.0-build/install/etc/fonts'
/usr/bin/install -c -m 644 ./fonts.conf 
/group/director100/cbording/vis/cle52/build/osmesa-ParaViewSuperbuild-4.2.0/ParaViewSuperbuild-4.2.0-build/install/etc/fonts/fonts.conf
/group/director100/cbording/vis/cle52/build/osmesa-ParaViewSuperbuild-4.2.0/ParaViewSuperbuild-4.2.0-build/install/bin/fc-cache 
-s -f -v

/usr/share/fonts: caching, new cache contents: 0 fonts, 10 dirs
/usr/share/fonts/100dpi: /bin/sh: line 9: 16194 Illegal instruction 
/group/director100/cbording/vis/cle52/build/osmesa-ParaViewSuperbuild-4.2.0/ParaViewSuperbuild-4.2.0-build/install/bin/fc-cache 
-s -f -v

make[5]: *** [install-data-local] Error 132
make[4]: *** [install-am] Error 2
make[3]: *** [install-recursive] Error 1
make[2]: *** [fontconfig/src/fontconfig-stamp/fontconfig-install] Error 2
make[1]: *** [CMakeFiles/fontconfig.dir/all] Error 2
make: *** [all] Error 2

Here is the cmake build flags for the paraviewsuperbuild script.

IBS_TOOL_CONFIGURE='-DCMAKE_BUILD_TYPE=Release \
-DParaView_FROM_GIT=OFF \
-DParaView_URL=$MYGROUP/vis/cle52/src/ParaView-v4.2.0-source.tar.gz \
-DENABLE_boost=ON \
-DENABLE_cgns=OFF \
-DENABLE_ffmpeg=ON \
-DENABLE_fontconfig=ON \
-DENABLE_freetype=ON \
-DENABLE_hdf5=ON \
-DENABLE_libxml2=ON \
-DENABLE_matplotlib=OFF \
-DENABLE_mesa=OFF \
-DENABLE_mpi=ON \
-DENABLE_numpy=ON \
-DENABLE_osmesa=ON \
-DENABLE_paraview=ON \
-DENABLE_png=ON \
-DENABLE_python=ON \
-DENABLE_qhull=ON \
-DENABLE_qt=OFF \
-DENABLE_silo=ON \
-DENABLE_szip=ON \
-DENABLE_visitbridge=ON \
-DMPI_CXX_LIBRARIES:STRING=/opt/cray/mpt/7.0.0/gni/mpich2-gnu/49/lib/libmpichcxx.so 
\
-DMPI_C_LIBRARIES:STRING=/opt/cray/mpt/7.0.0/gni/mpich2-gnu/49/mpt/lib/libmpich.so 
\
-DMPI_LIBRARY:FILEPATH=/opt/cray/mpt/7.0.0/gni/mpich2-gnu/49/lib/libmpichcxx.so 
\
-DMPI_CXX_INCLUDE_PATH:STRING=/opt/cray/mpt/7.0.0/gni/mpich2-gnu/49/include 
\
-DMPI_C_INCLUDE_PATH:STRING=/opt/cray/mpt/7.0.0/gni/mpich2-gnu/49/include 
\

-DUSE_SYSTEM_mpi=ON \
-DUSE_SYSTEM_python=OFF \
-DUSE_SYSTEM_zlib=ON '

Is there other CRAY specific libraries that I should check for before 
I try again to install paraview?

Our Cray does NOT have any GPUS!

R. Christopher Bording
Supercomputing Team-iVEC@UWA
E: cbord...@ivec.org mailto:cbord...@ivec.org
T: +61 8 6488 6905

26 Dick Perry Avenue,
Technology Park
Kensington, Western Australia.
6151







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Re: [Paraview] HPC paraview

[Burlen Loring]

Hi Christopher,

Are you by any chance logged in with ssh X11 forwarding (ssh -X ...)? It 
seems the error you report comes up often in that context. X forwarding 
would not be the right way to run PV on your cluster.


Depending on how your cluster is setup you may need to start up the 
xserver before launching PV, and make sure to close it after PV exits. 
IUn that scenario your xorg.conf would specify the nvidia driver and a 
screen for each gpu which you would refernece in the shell used to start 
PV through the DISPLAY variable. If you already have x11 running and 
screens configured then it's just a matter of setting the display 
variable correctly. When there are multiple GPU's per node then you'd 
need to set the display using mpi rank modulo the number of gpus per node.


I'm not sure it matters that much but I don't think that you want 
--use-offscreen-rendering option.


Burlen

On 10/26/2014 10:23 PM, R C Bording wrote:

Hi,
 Managed to get a working version of Paraview-4.2.0.1 on our GPU 
cluster but when I try to run the
parallelSphere.py script on more than one node it just hangs.  Work 
like it is supposed to up to 12 cores on a single node.  I am still 
trying work out if I a running on the GPU tesla- C2070).


Here is the list of cake configurations

IBS_TOOL_CONFIGURE='-DCMAKE_BUILD_TYPE=Release \
-DParaView_FROM_GIT=OFF \
-DParaView_URL=$MYGROUP/vis/src/ParaView-v4.2.0-source.tar.gz \
-DENABLE_boost=ON \
-DENABLE_cgns=OFF \
-DENABLE_ffmpeg=ON \
-DENABLE_fontconfig=ON \
-DENABLE_freetype=ON \
-DENABLE_hdf5=ON \
-DENABLE_libxml2=ON \
-DENABLE_matplotlib=ON \
-DENABLE_mesa=OFF \
-DENABLE_mpi=ON \
-DENABLE_numpy=ON \
-DENABLE_osmesa=OFF \
-DENABLE_paraview=ON \
-DENABLE_png=ON \
-DENABLE_python=ON \
-DENABLE_qhull=ON \
-DENABLE_qt=ON \
-DENABLE_silo=ON \
-DENABLE_szip=ON \
-DENABLE_visitbridge=ON \
-DMPI_CXX_LIBRARIES:STRING=$MPI_HOME/lib/libmpi_cxx.so \
-DMPI_C_LIBRARIES:STRING=$MPI_HOME/lib/libmpi.so \
-DMPI_LIBRARY:FILEPATH=$MPI_HOME/lib/libmpi_cxx.so \
-DMPI_CXX_INCLUDE_PATH:STRING=$MPI_HOME/include \
-DMPI_C_INCLUDE_PATH:STRING=$MPI_HOME/include \
-DUSE_SYSTEM_mpi=ON \
-DUSE_SYSTEM_python=OFF \
-DUSE_SYSTEM_qt=OFF \
-DUSE_SYSTEM_zlib=OFF '

The goal is to be able to support batch rendering on the whole cluster 
~96 nodes.


Also do I need set another environment variable in my Paraview module 
to make the Xlib

warning go away?

[cbording@f100 Paraview]$ mpirun -n 12 pvbatch 
--use-offscreen-rendering parallelSphere.py

Xlib:  extension NV-GLX missing on display localhost:50.0.
Xlib:  extension NV-GLX missing on display localhost:50.0.
Xlib:  extension NV-GLX missing on display localhost:50.0.
Xlib:  extension NV-GLX missing on display localhost:50.0.
Xlib:  extension NV-GLX missing on display localhost:50.0.
Xlib:  extension NV-GLX missing on display localhost:50.0.

Is this related to my not being able to run across multiple nodes?

R. Christopher Bording
Supercomputing Team-iVEC@UWA
E: cbord...@ivec.org mailto:cbord...@ivec.org
T: +61 8 6488 6905

26 Dick Perry Avenue,
Technology Park
Kensington, Western Australia.
6151







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Re: [Paraview] Segmentation Fault when using the vtkPVDReader

[Burlen Loring]

Unless something's changed in the pipeline recently that I'm unaware of, 
when dealing with multiblock data you still need to force the composite 
data pipeline first. that may or or may not be the cause of your 
segfault, but you need to do it.


On 10/27/2014 03:56 AM, Bogdan Daqui Herrera wrote:

Hi Burlen,

Yes, it is a stand-alone C++ application, which makes use of VTK and Paraview 
as libraries, linking against them and calling functionality to interpret the 
data.
I am not setting up any pipeline (as of now). Is this from the TestExodusTime 
or TestTemporalFractal examples. I will try adding this.

Currently I need to read and traverse the dataset without adding any filters or 
processing the data. I it still needed to create a pipeline in this case?

Kind regards,
Bogdan

On 10/24/2014 06:14 PM, Burlen Loring wrote:

Hi Bogdan,

You are writing a stand alone C++ app right? Are you setting up to run the 
composite data pipeline as in the following example?

100   vtkCompositeDataPipeline* cexec=vtkCompositeDataPipeline::New();
101   vtkAlgorithm::SetDefaultExecutivePrototype(cexec);
102   cexec-Delete();

Burlen

On 10/23/2014 06:37 PM, Sebastien Jourdain wrote:

Thanks Bogdan,

that's not helping me but someone else might have some idea.

Seb

On Thu, Oct 23, 2014 at 12:19 PM, Bogdan Daqui Herrera bda...@simscale.de 
mailto:bda...@simscale.de wrote:

 Certainly. I should mention, I am using a pre-compiled version of Paraview 
4.1 bundled with Salome (Ubuntu package).

 Here it is (using pReader-SetForceOutputTypeToMultiBlock(1)):
 ERROR: In 
/misc/dn47/SALOME/PRODUCTS/7x/opt/Ubuntu.13.10.64/7.4.0/tmp/ParaView-4.1.0_SRC/ParaViewCore/VTKExtensions/Default/vtkXMLCollectionReader.cxx,
 line 316
 vtkPVDReader (0x6559e0): Error creating vtkXMLMultiBlockDataReader using 
vtkPVInstantiator.

 Program received signal SIGSEGV, Segmentation fault.
 0x765c4270 in vtkXMLCollectionReader::ReadXMLDataImpl() ()
from 
/opt/salomeUbuntu_740/ParaView-4.1.0/lib/paraview-4.1/libvtkPVVTKExtensionsDefault-pv4.1.so.1
 #0  0x765c4270 in vtkXMLCollectionReader::ReadXMLDataImpl() ()
from 
/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkPVVTKExtensionsDefault-pv4.1.so.1
 #1  0x768cc128 in vtkXMLReader::RequestData(vtkInformation*, 
vtkInformationVector**, vtkInformationVector*) () from
 /opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkIOXML-pv4.1.so.1
 #2  0x768cd35d in vtkXMLReader::ProcessRequest(vtkInformation*, 
vtkInformationVector**, vtkInformationVector*) () from
 /opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkIOXML-pv4.1.so.1
 #3  0x77b97fd0 in vtkExecutive::CallAlgorithm(vtkInformation*, 
int, vtkInformationVector**, vtkInformationVector*) ()
from 
/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkCommonExecutionModel-pv4.1.so.1
 #4  0x77b93447 in 
vtkDemandDrivenPipeline::ExecuteData(vtkInformation*, vtkInformationVector**, 
vtkInformationVector*) ()
from 
/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkCommonExecutionModel-pv4.1.so.1
 #5  0x77b91181 in 
vtkCompositeDataPipeline::ExecuteData(vtkInformation*, vtkInformationVector**, 
vtkInformationVector*) ()
from 
/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkCommonExecutionModel-pv4.1.so.1
 #6  0x77b95bb1 in 
vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, 
vtkInformationVector**, vtkInformationVector*) ()
from 
/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkCommonExecutionModel-pv4.1.so.1
 #7  0x77ba8c21 in 
vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, 
vtkInformationVector**, vtkInformationVector*) ()
from 
/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkCommonExecutionModel-pv4.1.so.1
 #8  0x77b9486d in vtkDemandDrivenPipeline::UpdateData(int) ()
from 
/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkCommonExecutionModel-pv4.1.so.1
 #9  0x77ba9765 in vtkStreamingDemandDrivenPipeline::Update(int) ()
from 
/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkCommonExecutionModel-pv4.1.so.1
 #10 0x00414fbf in testing::TestingIO::read (this=0x652b30, 
fileName=..., pMultiBlockDataSet=...)
 at /home/.../someProject/src/testing.cpp:85


 Please let me know if you need something additional
 On 10/23/2014 07:51 PM, Sebastien Jourdain wrote:
  If you provide the stack trace, that may be helpful.
 
  Seb
 
  On Thu, Oct 23, 2014 at 10:36 AM, Bogdan Daqui Herrera bda...@simscale.de 
mailto:bda...@simscale.de mailto:bda...@simscale.de
 mailto:bda...@simscale.de wrote:
 
  Hi Seb,
 
  Thanks for the quick reply. Yes the project is managed with CMake. I 
have not however been able to find the relevant posts by Marcus (in the users
 list). Is
  that in the users

Re: [Paraview] Paravew on XC30

[Burlen Loring]

Hi Rick,

It doesn't look like you're building for the compute nodes, either that 
or you've got GPU's. for example Qt is on and OSMesa is off. I'm 
unfamiliar with the superbuild process but normally that would produce a 
binary that couldn't be run on the compute node without gpu's.


I'm expecting my installs to work with the Kitware provided client 
binaries. For that in the past at least we need to match their build 
options to some some extent. For example the VisIt bridge would be on. I 
know there have been some updates to how the server capabilities are 
exposed so I'm not sure how much of an issue that is in 4.2.


Burlen

On 10/27/2014 08:22 AM, Angelini, Richard C (Rick) CIV USARMY ARL (US) 
wrote:

Chris - I’ve been able to build on 3 different XC30 systems … here’s my
script.  I’m using
PrgEnv-gnu/5.2.14
cray-mpich/6.3.1
gcc/4.8.2



#!/bin/csh

module unload PrgEnv-cray
module load PrgEnv-gnu
module load cray-mpich
module load pbs
module list


setenv gcc gcc
setenv gplusplus g++
setenv gfortran gfortran

setenv CC $gcc
setenv CXX $gplusplus
setenv FC $gfortran
setenv F70 $gfortran
setenv F77 $gfortran
setenv F90 $gfortran
setenv F95 $gfortran

set version=4.2.0

if (! -d Build_${version}_mesa) mkdir Build_${version}_mesa

cd Build_${version}_mesa

if (! -d install) mkdir install

set INSTALLPATH=`pwd`/install

#Build the latest version of CMAKE
if (! -e install/bin/cmake) then
 echo Need to build cmake
 cp ../Downloads/cmake-2.8.11.tar.gz .
 tar xzvf cmake-2.8.11.tar.gz
 cd cmake-2.8.11
 ./bootstrap --prefix=$INSTALLPATH
 make -j 8 install
 cd ..
endif

setenv PATH ${INSTALLPATH}/bin:$PATH

cmake \
-DCMAKE_INSTALL_PREFIX:PATH=${HOME}/pv-test/${version}_mesa \
-DCMAKE_BUILD_TYPE=Release \
-DParaView_FROM_GIT=OFF \
-Ddownload_location=`pwd`/../Downloads \
-DParaView_URL=`pwd`/../Downloads/ParaView-v4.2.0-source.tar.gz \
-DENABLE_boost=ON \
-DENABLE_cgns=OFF \
-DENABLE_ffmpeg=ON \
-DENABLE_fontconfig=ON \
-DENABLE_freetype=ON \
-DENABLE_hdf5=ON \
-DENABLE_libxml2=ON \
-DENABLE_matplotlib=OFF \
-DENABLE_osmesa=OFF \
-DENABLE_mesa=ON \
-DENABLE_qt=ON \
-DENABLE_mpi=ON \
-DENABLE_numpy=ON \
-DENABLE_paraview=ON \
-DENABLE_png=ON \
-DENABLE_python=ON \
-DENABLE_qhull=ON \
-DENABLE_silo=ON \
-DENABLE_szip=ON \
-DENABLE_visitbridge=OFF \
-DMPI_CXX_LIBRARIES:STRING=/opt/cray/mpt/6.3.1/gni/mpich2-gnu/48/lib/libmp
ichcxx.so \
-DMPI_C_LIBRARIES:STRING=/opt/cray/mpt/6.3.1/gni/mpich2-gnu/48/lib/libmpic
h.so \
-DMPI_LIBRARY:FILEPATH=/opt/cray/mpt/6.3.1/gni/mpich2-gnu/48/lib/libmpichc
xx.so \
-DMPI_CXX_INCLUDE_PATH:STRING=/opt/cray/mpt/6.3.1/gni/mpich2-gnu/48/includ
e/ \
-DMPI_C_INCLUDE_PATH:STRING=/opt/cray/mpt/6.3.1/gni/mpich2-gnu/48/include/
 \
-DUSE_SYSTEM_mpi=ON \
-DUSE_SYSTEM_python=ON \
-DUSE_SYSTEM_zlib=ON \
../Source

make -j 4 install


Rick Angelini
USArmy Research Laboratory
CISD/HPC Architectures Team
Phone:  410-278-6266




On 10/27/14, 11:00 AM, Burlen Loring blor...@lbl.gov wrote:




Hi Christopher,

I can't help you with the superbuild, but I can show you how to build PV
on the XC30. here's

the script
https://github.com/burlen/pvserver-configs/blob/master/servers/edison/bui
lds/config-pv-mesa.sh I used to build ParaView 4.2 with
PrgEnv-gnu/5.2.25 on our XC30

You'll see a bunch of paths that need to be set specific to the version
of PrgEnv-gnu that you are running. The easiest way to figure out these
is to look at the CRAY_LD_LIBRARY_PATH environment variable. If for some
reason that isn't set then you can alway
look at the output of CC --verbose. You also need to point to an
OSMesa install
http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D.

Burlen

On 10/26/2014 10:22 PM, R C Bording wrote:


Hi,
Trying to build Paraview on our XC30,
here is the end of the build log where it goes pear-shape,

Making install in test
/usr/bin/install -c -m 644 fonts.dtd
'/group/director100/cbording/vis/cle52/build/osmesa-ParaViewSuperbuild-4.2
.0/ParaViewSuperbuild-4.2.0-build/install/etc/fonts'
/usr/bin/install -c -m 644 ./fonts.conf
/group/director100/cbording/vis/cle52/build/osmesa-ParaViewSuperbuild-4.2.
0/ParaViewSuperbuild-4.2.0-build/install/etc/fonts/fonts.conf
/group/director100/cbording/vis/cle52/build/osmesa-ParaViewSuperbuild-4.2.
0/ParaViewSuperbuild-4.2.0-build/install/bin/fc-cache -s -f -v
/usr/share/fonts: caching, new cache contents: 0 fonts, 10 dirs
/usr/share/fonts/100dpi: /bin/sh: line 9: 16194 Illegal instruction
/group/director100/cbording/vis/cle52/build/osmesa-ParaViewSuperbuild-4.2.
0/ParaViewSuperbuild-4.2.0-build/install/bin/fc-cache -s -f -v
make[5]: *** [install-data-local] Error 132
make[4]: *** [install-am] Error 2
make[3]: *** [install-recursive] Error 1
make[2]: *** [fontconfig/src/fontconfig-stamp/fontconfig-install] Error 2
make[1]: *** [CMakeFiles/fontconfig.dir/all] Error 2
make: *** [all] Error 2

Here is the cmake build flags for the paraviewsuperbuild script

Re: [Paraview] Segmentation Fault when using the vtkPVDReader

[Burlen Loring]

Hi Bogdan,

You are writing a stand alone C++ app right? Are you setting up to run 
the composite data pipeline as in the following example?


100   vtkCompositeDataPipeline* cexec=vtkCompositeDataPipeline::New();
101   vtkAlgorithm::SetDefaultExecutivePrototype(cexec);
102   cexec-Delete();

Burlen

On 10/23/2014 06:37 PM, Sebastien Jourdain wrote:

Thanks Bogdan,

that's not helping me but someone else might have some idea.

Seb

On Thu, Oct 23, 2014 at 12:19 PM, Bogdan Daqui Herrera 
bda...@simscale.de mailto:bda...@simscale.de wrote:


Certainly. I should mention, I am using a pre-compiled version of
Paraview 4.1 bundled with Salome (Ubuntu package).

Here it is (using pReader-SetForceOutputTypeToMultiBlock(1)):
ERROR: In

/misc/dn47/SALOME/PRODUCTS/7x/opt/Ubuntu.13.10.64/7.4.0/tmp/ParaView-4.1.0_SRC/ParaViewCore/VTKExtensions/Default/vtkXMLCollectionReader.cxx,
line 316
vtkPVDReader (0x6559e0): Error creating
vtkXMLMultiBlockDataReader using vtkPVInstantiator.

Program received signal SIGSEGV, Segmentation fault.
0x765c4270 in vtkXMLCollectionReader::ReadXMLDataImpl() ()
   from

/opt/salomeUbuntu_740/ParaView-4.1.0/lib/paraview-4.1/libvtkPVVTKExtensionsDefault-pv4.1.so.1
#0  0x765c4270 in vtkXMLCollectionReader::ReadXMLDataImpl() ()
   from

/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkPVVTKExtensionsDefault-pv4.1.so.1
#1  0x768cc128 in
vtkXMLReader::RequestData(vtkInformation*, vtkInformationVector**,
vtkInformationVector*) () from
/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkIOXML-pv4.1.so.1
#2  0x768cd35d in
vtkXMLReader::ProcessRequest(vtkInformation*,
vtkInformationVector**, vtkInformationVector*) () from
/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkIOXML-pv4.1.so.1
#3  0x77b97fd0 in
vtkExecutive::CallAlgorithm(vtkInformation*, int,
vtkInformationVector**, vtkInformationVector*) ()
   from

/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkCommonExecutionModel-pv4.1.so.1
#4  0x77b93447 in
vtkDemandDrivenPipeline::ExecuteData(vtkInformation*,
vtkInformationVector**, vtkInformationVector*) ()
   from

/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkCommonExecutionModel-pv4.1.so.1
#5  0x77b91181 in
vtkCompositeDataPipeline::ExecuteData(vtkInformation*,
vtkInformationVector**, vtkInformationVector*) ()
   from

/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkCommonExecutionModel-pv4.1.so.1
#6  0x77b95bb1 in
vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*,
vtkInformationVector**, vtkInformationVector*) ()
   from

/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkCommonExecutionModel-pv4.1.so.1
#7  0x77ba8c21 in
vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*,
vtkInformationVector**, vtkInformationVector*) ()
   from

/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkCommonExecutionModel-pv4.1.so.1
#8  0x77b9486d in vtkDemandDrivenPipeline::UpdateData(int) ()
   from

/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkCommonExecutionModel-pv4.1.so.1
#9  0x77ba9765 in
vtkStreamingDemandDrivenPipeline::Update(int) ()
   from

/opt/salome_740/ParaView-4.1.0/lib/paraview-4.1/libvtkCommonExecutionModel-pv4.1.so.1
#10 0x00414fbf in testing::TestingIO::read (this=0x652b30,
fileName=..., pMultiBlockDataSet=...)
at /home/.../someProject/src/testing.cpp:85


Please let me know if you need something additional
On 10/23/2014 07:51 PM, Sebastien Jourdain wrote:
 If you provide the stack trace, that may be helpful.

 Seb

 On Thu, Oct 23, 2014 at 10:36 AM, Bogdan Daqui Herrera
bda...@simscale.de mailto:bda...@simscale.de
mailto:bda...@simscale.de mailto:bda...@simscale.de wrote:

 Hi Seb,

 Thanks for the quick reply. Yes the project is managed with
CMake. I have not however been able to find the relevant posts by
Marcus (in the users list). Is
 that in the users or developers mailing list?

 It does sound like it could be a problem with some
initialization, as you can see below.

 One short update, it looks like setting
ForceMultiBlockDataSet Output with:
 pReader-SetForceOutputTypeToMultiBlock(1);
 leads to the segmentation fault at Update() (The deepcopy is
never reached). With or without setting the previous line, the error
 vtkPVDReader (0x1cb49e0): Error creating
vtkXMLMultiBlockDataReader using vtkPVInstantiator.

 The code looks like this now:
 vtkSmartPointer  vtkPVDReader  pReader =
vtkSmartPointer  vtkPVDReader ::New();
  pReader-SetFileName(/some/file.pvd);
 pReader-Update(); (where the error is triggered

Re: [Paraview] Filter to keep points, dropping topology

[Burlen Loring]

don't forget to add vertex type cells, or you will not be able to see 
the points,  and that it's going to be more complicated if you're 
starting from data types that have implicit points.



On 10/22/2014 07:52 AM, Biddiscombe, John A. wrote:

Output-SetPoints(input-GetPoints());

Or

Output-CopyStructure(input);
Output-SetCells(NULL)

Then copy point field data etc


On 22/10/14 16:19, B.W.H. van Beest b...@xs4all.nl wrote:


Hello,

I need a filter that only keeps the 3D points of a certain source (e.g.
coming from  an stl file).
The topology of the data set may go.

I thought that the following filter, only passing through the pointdata,
would do the job,
but that appears not to be the case (no points after the filter!)
What's going wrong and how should I change the filter?

Kind Regards,
Bertwim



int FilterPoints::RequestData( vtkInformation*,
 vtkInformationVector**
inputVector,
 vtkInformationVector*
outputVector)
{
   // Get the input and output data objects.
   vtkDataSet* input = vtkDataSet::GetData( inputVector[0] );
   vtkDataSet* output = vtkDataSet::GetData( outputVector );

   // output-CopyStructure( input );
   output-GetPointData()-PassData( input-GetPointData() );
  
   return 1;

}

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Re: [Paraview] Filter to keep points, dropping topology

[Burlen Loring]

you can have just points, they'll be ignored during rendering without 
vertex type cells.


On 10/22/2014 08:15 AM, B.W.H. van Beest wrote:

Are you saying that one cannot have just points?

In my case, I want to  snap the points to a structured grid,
but haven't done that yet, as I wanted to see the
points first, and do the snapping as a next step.
So that is not a good idea? I need to do it all in one go?

Regards,
Bertwim





On 10/22/2014 04:58 PM, Burlen Loring wrote:

don't forget to add vertex type cells, or you will not be able to see
the points,  and that it's going to be more complicated if you're
starting from data types that have implicit points.


On 10/22/2014 07:52 AM, Biddiscombe, John A. wrote:

Output-SetPoints(input-GetPoints());

Or

Output-CopyStructure(input);
Output-SetCells(NULL)

Then copy point field data etc


On 22/10/14 16:19, B.W.H. van Beest b...@xs4all.nl wrote:


Hello,

I need a filter that only keeps the 3D points of a certain source (e.g.
coming from  an stl file).
The topology of the data set may go.

I thought that the following filter, only passing through the
pointdata,
would do the job,
but that appears not to be the case (no points after the filter!)
What's going wrong and how should I change the filter?

Kind Regards,
Bertwim



int FilterPoints::RequestData( vtkInformation*,
  vtkInformationVector**
inputVector,
  vtkInformationVector*
outputVector)
{
// Get the input and output data objects.
vtkDataSet* input = vtkDataSet::GetData( inputVector[0] );
vtkDataSet* output = vtkDataSet::GetData( outputVector );

// output-CopyStructure( input );
output-GetPointData()-PassData( input-GetPointData() );
  return 1;
}

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Re: [Paraview] BOX - volume?

[Burlen Loring]

Hi Bertwim,

The problem you're experiencing is not an issue of missing extensions, 
but rather a bug in ATI's driver. Projected tetrahedra is disabled when 
an ATI device is detected to avoid that bug(ParaView will hang). However 
it's not a big deal. because you can use the Bunyk raycast algrothim 
instead. After your data is on screen scroll to the bottom of the 
properties panel and look for the field Select mapper, set that to 
Bunyk ray cast, then change the representation to volume.


Burlen


On 10/15/2014 06:58 PM, B.W.H. van Beest wrote:
I am still busy with finding out which etensions are needed, and how I 
can enable them.

THis opebnGL-world is a bit alien to me, so it will take some time.

Regards,
Bertwim

On 10/14/2014 11:07 PM, Aashish Chaudhary wrote:
Looks like certain extensions are still not quite working on yours 
system even with the proprietary driver. I will see if I can run your 
code on my laptop but that would be for tomorrow.


** Assuming that this is not data dependent issue (which it should not).

I think its probably this line causing the issue:

bool driverSupport

#if defined(__APPLE__)

= true;

#else

= !(extensions-DriverIsATI()

 (extensions-GetDriverGLVersionMajor() = 3))

|| extensions-GetIgnoreDriverBugs(ATI texturing bug);

#endif



On line number 181: can you change this code to :

this-HasHardwareSupport=renwin!=NULLthis-IsSupported(renwin);
to
this-HasHardwareSupport=1;

- Aashish



On Tue, Oct 14, 2014 at 4:53 PM, B.W.H. van Beest b...@xs4all.nl 
mailto:b...@xs4all.nl wrote:


Progress indeed. But I don't understand what you are saying about
the transfer function.

I' starting to wonder if I have two issues occurring simultaneously.
In a new thread I just posted I described my problem in getting
the colours in place.
I need to write to a vtk file first and load it back.  I just
found that when I just did that
and then switched fo volume rendering, an error was there about
the absence
of an opengl extension:

ERROR: In

/usr/local/git/ParaView/VTK/Rendering/VolumeOpenGL/vtkOpenGLProjectedTetrahedraMapper.cxx,
line 185
vtkOpenGLProjectedTetrahedraMapper (0x58ae490): The required
extensions are not supported.

 This is complete unknown terrain for me.

Regards,
Bertwim



On 10/14/2014 09:58 PM, Burlen Loring wrote:

progress!  it sounds like volume rendering is working on the
wavelet dataset.

You do need the scalars for volume rendering, so make sure you
have those when you try. You need to select the scalars in the
drop down also, I usually do this before changing to the volume
representation. You also may need to edit the transfer function.
For testing you could make the opacity over the entire scalar
range in which case you should see a solid cube.

If you've done all that and don't see anything it's likely that
the dataset is messed up.  Add a dataset-Print(cerr) statement
to the end of your request data,  look in the information panel
and verify correct number of points and scalar ranges.

If all else fails post the dataset to the list. After creating
your cube go to the file menu and save data.


On 10/14/2014 10:40 AM, B.W.H. van Beest wrote:

Hi Burlen,

I have upgraded to the AMD drivers. Thanks for the hint. It has
improved the situation a bit.

Furthermore, I created the wavelet source. When selecting
volume representation, I do see a three 3 picture, in all 5
volume rendering mode (smart, raycast and texture mapping, ray
cast only, texture mapping only, GPU based). The picture a
rather fuzzy, but then I don't know what I'm supposed to see
here. The good news is that the openGL errors I had before when
displaying a wavelet, now have gone.

The situation with my own cube, though, has unchanged.
unfortunately.
The cube disappears in volume representation node, also when
I  re-inserted scalar values for each of the 8 vertices.

Regards,
Bertwim

On 10/14/2014 06:06 PM, Burlen Loring wrote:

Hi Bertwim,

In recent releases of ParaView I have experienced
issues/flakeyness with volume rendering. Something you should
try: Create the wavelet source, then in the properties panel
find volume rendering mode and set it to ray cast only. 
This has worked for me on a number of systems. may or may not

work, but worth a try.

The output you pasted below shows that although you've got a
sweet ATI GPU you're not taking advantage of it! You're using
the Intel integrated GPU with Mesa drivers. If I were you I
would install proprietary the AMD drivers
http://support.amd.com/en-us/download. This should give you
nice performance boost and may even solve the OpenGL errors
you reported, which these days are as often (or more) a result
of bugs in the Mesa

Re: [Paraview] BOX - volume?

[Burlen Loring]

You could try it without modifying any code by setting  the following 
cmake variable.


VTK_IGNORE_GLDRIVER_BUGS:BOOL=ON

and recompile ParaView. With my ATI Radeon HD7780 projected tetrahedra 
just hangs.


Burlen

On 10/14/2014 02:07 PM, Aashish Chaudhary wrote:
Looks like certain extensions are still not quite working on yours 
system even with the proprietary driver. I will see if I can run your 
code on my laptop but that would be for tomorrow.


** Assuming that this is not data dependent issue (which it should not).

I think its probably this line causing the issue:

bool driverSupport

#if defined(__APPLE__)

= true;

#else

= !(extensions-DriverIsATI()

 (extensions-GetDriverGLVersionMajor() = 3))

|| extensions-GetIgnoreDriverBugs(ATI texturing bug);

#endif



On line number 181: can you change this code to :

this-HasHardwareSupport=renwin!=NULLthis-IsSupported(renwin);
to
this-HasHardwareSupport=1;

- Aashish



On Tue, Oct 14, 2014 at 4:53 PM, B.W.H. van Beest b...@xs4all.nl 
mailto:b...@xs4all.nl wrote:


Progress indeed. But I don't understand what you are saying about
the transfer function.

I' starting to wonder if I have two issues occurring simultaneously.
In a new thread I just posted I described my problem in getting
the colours in place.
I need to write to a vtk file first and load it back.  I just
found that when I just did that
and then switched fo volume rendering, an error was there about
the absence
of an opengl extension:

ERROR: In

/usr/local/git/ParaView/VTK/Rendering/VolumeOpenGL/vtkOpenGLProjectedTetrahedraMapper.cxx,
line 185
vtkOpenGLProjectedTetrahedraMapper (0x58ae490): The required
extensions are not supported.

 This is complete unknown terrain for me.

Regards,
Bertwim



On 10/14/2014 09:58 PM, Burlen Loring wrote:

progress!  it sounds like volume rendering is working on the
wavelet dataset.

You do need the scalars for volume rendering, so make sure you
have those when you try. You need to select the scalars in the
drop down also, I usually do this before changing to the volume
representation. You also may need to edit the transfer function.
For testing you could make the opacity over the entire scalar
range in which case you should see a solid cube.

If you've done all that and don't see anything it's likely that
the dataset is messed up.  Add a dataset-Print(cerr) statement
to the end of your request data,  look in the information panel
and verify correct number of points and scalar ranges.

If all else fails post the dataset to the list. After creating
your cube go to the file menu and save data.


On 10/14/2014 10:40 AM, B.W.H. van Beest wrote:

Hi Burlen,

I have upgraded to the AMD drivers. Thanks for the hint. It has
improved the situation a bit.

Furthermore, I created the wavelet source. When selecting
volume representation, I do see a three 3 picture, in all 5
volume rendering mode (smart, raycast and texture mapping, ray
cast only, texture mapping only, GPU based). The picture a
rather fuzzy, but then I don't know what I'm supposed to see
here. The good news is that the openGL errors I had before when
displaying a wavelet, now have gone.

The situation with my own cube, though, has unchanged.
unfortunately.
The cube disappears in volume representation node, also when
I  re-inserted scalar values for each of the 8 vertices.

Regards,
Bertwim

On 10/14/2014 06:06 PM, Burlen Loring wrote:

Hi Bertwim,

In recent releases of ParaView I have experienced
issues/flakeyness with volume rendering. Something you should
try: Create the wavelet source, then in the properties panel
find volume rendering mode and set it to ray cast only. 
This has worked for me on a number of systems. may or may not

work, but worth a try.

The output you pasted below shows that although you've got a
sweet ATI GPU you're not taking advantage of it! You're using
the Intel integrated GPU with Mesa drivers. If I were you I
would install proprietary the AMD drivers
http://support.amd.com/en-us/download. This should give you
nice performance boost and may even solve the OpenGL errors you
reported, which these days are as often (or more) a result of
bugs in the Mesa drivers than in VTK.

Burlen

On 10/13/2014 11:44 AM, B.W.H. van Beest wrote:



OS:   OpenSuSe 13.1

# lspci | grep -i vga
00:02.0 VGA compatible controller: Intel Corporation 4th Gen
Core Processor Integrated Graphics Controller (rev 06)
01:00.0 VGA compatible controller: Advanced Micro Devices,
Inc. [AMD/ATI] Mars [Radeon HD 8670A/8670M/8750M]

# glxinfo
name of display: :0
display: :0  screen: 0
direct rendering: Yes
server glx vendor string: SGI

Re: [Paraview] Disappearing volume rendering?

[Burlen Loring]

do you have any scalars? those are not optional for volume rendering. 
Additionally you may need to adjust the transfer function,


On 10/13/2014 10:22 AM, B.W.H. van Beest wrote:

No, it doesn't work. The filter creates tets, which are visible in the
wireframe representation,
but when I select Volume  representation the image disappears.

I can't imagine it is so difficult to render a volume in Paraview. I
must be doing something wrong

Regards,
Bertwim

On 10/13/2014 05:36 PM, Cory Quammen wrote:

Bertwim,

I'm not sure that the volume renderer can handle VTK_HEXAHEDRON
elements. Try the Tetrahedralize filter on your source and see if
the Volume representation works.

Thanks,
Cory

On Mon, Oct 13, 2014 at 10:19 AM, B.W.H. van Beest b...@xs4all.nl wrote:

Hi,

I'm struggling to get a proper 3D view of my model system (yes,
embarrassing!)
but must admit my defeat.
After stripping almost everything, keeping the minimum to exhibit the
issue,
I'm left with the following:

I have created a simple box source. To get a 3D representation, I
sub-classed
the code for this Source from vtkUnstructuredGridAlgorithm.

In the RequestData method, I define the 8 point of the unit cube. I
added the points to the
underlying unstructed grid, and I specified the cell topology.

This all seems to work: when instantiating this box Source, I *do* get the
expected cube in the representations (Surface, wireframe, Points).

However, when I select the Volume representation, *the image disappears*
What am I doing wrong?

As the code is not too long and very simple, I take the freedom to paste
it below.

Kind regards.
Bertwim

=

  int sphBoxSourceC::RequestData( vtkInformation *vtkNotUsed(request),
 vtkInformationVector
**vtkNotUsed(inputVector),
 vtkInformationVector *outputVector)
{
// Get the info object
vtkInformation *outInfo = outputVector-GetInformationObject(0);
vtkUnstructuredGrid *umesh = vtkUnstructuredGrid::SafeDownCast(
outInfo-Get( vtkDataObject::DATA_OBJECT() ) );

// Pre-allocate some memory
umesh-Allocate( 1024 );

// Specify points.
double r0[] = { 0.0, 0.0, 0.0 };
double r1[] = { 1.0, 0.0, 0.0 };
double r2[] = { 0.0, 1.0, 0.0 };
double r3[] = { 1.0, 1.0, 0.0 };
double r4[] = { 0.0, 0.0, 1.0 };
double r5[] = { 1.0, 0.0, 1.0 };
double r6[] = { 0.0, 1.0, 1.0 };
double r7[] = { 1.0, 1.0, 1.0 };

// Collect the points in a vtk data structures.
{
   vtkSmartPointervtkPoints points = vtkSmartPointervtkPoints::New();
   points-SetDataType( VTK_DOUBLE );

   points-InsertNextPoint( r0 );
   points-InsertNextPoint( r1 );
   points-InsertNextPoint( r2 );
   points-InsertNextPoint( r3 );
   points-InsertNextPoint( r4 );
   points-InsertNextPoint( r5 );
   points-InsertNextPoint( r6 );
   points-InsertNextPoint( r7 );

   // Transfer points to umesh.
   umesh-SetPoints( points );
}

// Cell Topology
vtkIdType vtx[8] = { 0, 1, 3, 2, 4, 5, 7, 6 };
umesh-InsertNextCell( VTK_HEXAHEDRON, 8, vtx );

return 1;
}



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Re: [Paraview] new Source plugin: no show!

[Burlen Loring]

Hi Bertwim,

I should have explained the cells better. The cells are descriptions of 
how points are combined into geometric primitives that can be rendered 
by OpenGL (or converted into those understood by OpenGL). Here is an 
excerpt http://www.vtk.org/VTK/img/file-formats.pdf of the User Guide 
describing VTK's cells, see p9-10.


Burlen

On 10/5/2014 8:17 AM, B.W.H. van Beest wrote:

Hi Burlen,

Thanks for your reply. On the cell-info:  I now (finally) understood 
what was there to be. After implementing the cells, I indeed got the 
expected display. On the book: what keeps me from buying is that it 
seems outdated (because it refers to version 3).
The texture coordinates I had found on Google indeed. What I needed 
was how to apply it in Paraview/VTK. I will look into that again Maybe 
it becomes clear now.


Thanks
Bertwim


On 10/05/2014 05:05 AM, Burlen Loring wrote:
I assume in your request data you are generating a vtkPolyData 
dataset. At the end of request data call dataset-Print(cerr); . 
That's the one of the best debug method when you don't see what you 
think you should in PV while developing a new filter/source/reader 
what ever. The information tab in the GUI gives a subset of that, 
also useful.


texture coordinates are usually for applying an image to the surface. 
google it and you'll find volumes of info. In pv they are optional.


the cell array I'm afraid is not. when generating poly or 
unstructured data. If you have no cells what do you expect to see?


normals are per point.

some of your questions suggest that the book VTK user guide 
http://www.kitware.com/products/books/vtkguide.html would be a good 
investment for you.


Hope I didn't miss anything. ;-)

On 10/4/2014 8:30 AM, B.W.H. van Beest wrote:

Hello,

I need to write a new Source, representing a 'TriPrism,
i.e. a prism where the top and bottom planes are triangles. So far, I
failed.

Being unable to find appropriate documentation, I used the source code
of vtkCubeSource as an example, thinking it would be an easy change.
Wrong! The prism doesn't show on the screen. The
properties panel behaves as expected (and ok, as far I can see).

The member function 'RequestData' seems to be the important method.
But the code of the example (as well as other source examples) is on
closer inspection not clear to me at all.

The following is happening in the vtkCubeSource:

a)   The point of the cube are generated.  This is straightforward and
easily
 translates to the triprism.
The new points are updated via a call output-setPoints(
newPoints );

b)   The normals (to the side planes of the cube) are being calculated.
The new normals are updated via a call
output-GetPointData()-SetNormals(newNormals);
 This is also straightforward for the triprism, but:

Q: although calculating the normals is straightforward,
 in which order are they supposed to be given?

c) Also, texture coordinates (TCoords) are calculated.
  Q: What are these?  Are these mandatory?

d) Also, a new vtkCellArray is being created. ('newPolys')
   Q: Same question. No clue what I should do here.

As usual, any clue of how to attack this is greatly appreciated.

Bertwim



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Re: [Paraview] new Source plugin: no show!

[Burlen Loring]

I assume in your request data you are generating a vtkPolyData dataset. 
At the end of request data call dataset-Print(cerr); . That's the one 
of the best debug method when you don't see what you think you should in 
PV while developing a new filter/source/reader what ever. The 
information tab in the GUI gives a subset of that, also useful.


texture coordinates are usually for applying an image to the surface. 
google it and you'll find volumes of info. In pv they are optional.


the cell array I'm afraid is not. when generating poly or unstructured 
data. If you have no cells what do you expect to see?


normals are per point.

some of your questions suggest that the book VTK user guide 
http://www.kitware.com/products/books/vtkguide.html would be a good 
investment for you.


Hope I didn't miss anything. ;-)

On 10/4/2014 8:30 AM, B.W.H. van Beest wrote:

Hello,

I need to write a new Source, representing a 'TriPrism,
i.e. a prism where the top and bottom planes are triangles. So far, I
failed.

Being unable to find appropriate documentation, I used the source code
of vtkCubeSource as an example, thinking it would be an easy change.
Wrong! The prism doesn't show on the screen. The
properties panel behaves as expected (and ok, as far I can see).

The member function 'RequestData' seems to be the important method.
But the code of the example (as well as other source examples) is on
closer inspection not clear to me at all.

The following is happening in the vtkCubeSource:

a)   The point of the cube are generated.  This is straightforward and
easily
 translates to the triprism.
The new points are updated via a call output-setPoints(
newPoints );

b)   The normals (to the side planes of the cube) are being calculated.
The new normals are updated via a call
output-GetPointData()-SetNormals(newNormals);
 This is also straightforward for the triprism, but:

Q: although calculating the normals is straightforward,
 in which order are they supposed to be given?

c) Also, texture coordinates (TCoords) are calculated.
  Q: What are these?  Are these mandatory?

d) Also, a new vtkCellArray is being created. ('newPolys')
   Q: Same question. No clue what I should do here.

As usual, any clue of how to attack this is greatly appreciated.

Bertwim



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Re: [Paraview] Paraview-Wiki: OSMesa

[Burlen Loring]

Hi Gerrit,

The code on the Wiki has been tested with PV 4.0.0, but it sounds like 
it no longer works. The issue is that if you do not put *something in 
the GL library then CMake will fill it in with the system libGL. That is 
the wrong thing to do when using OSMesa and can lead to run time issues 
if you don't set LD_LIBRARY_PATH. In recent builds I've been putting 
libOSMesa in place of the empty string and that has worked. We can 
update the Wiki, however the real solution will be to remove linking of 
libGL and X11 libraries when using OSMesa.


Burlen

On 9/26/2014 7:49 AM, Gerrit Laube wrote:

Hi Paraview Users, developers or wiki-maintainers (whoever that is),

not sure, who's editing the paraview-wiki, but I think, I came across 
a problematic statement on the OSMesa-page:


here
http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D
in chapter Configuring ParaView for use with OSMesa it says:
...
-DOPENGL_gl_LIBRARY=\\ \
...
but here
http://www.paraview.org/pipermail/paraview/2013-November/029961.html
it says, that you should avoid empty quotes in this variable. I 
experienced similar problems and i think

...
-DOPENGL_gl_LIBRARY= \
...
finally fixed it. You might want to correct or mention this issue in 
the wiki.


Regards!

Gerrit
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Re: [Paraview] proper formatting of 2D data

[Burlen Loring]

Hi Robert,

Good one! The slice rep uses GPU textures and this behavior looks a bug 
in the logic that sets up the texture. You should file a bug report.


There's an easy workaround. Convert to a positive spacing and adjust the 
origin accordinigly. The data will the occupy the same region. Here's 
how your file looks then:


--8--
# vtk DataFile Version 2.0
testing
ASCII
DATASET STRUCTURED_POINTS
DIMENSIONS 3 4 1
ORIGIN 0.0 -2.25 0.0
SPACING 0.5 0.75 1.0
POINT_DATA 12
SCALARS test float
LOOKUP_TABLE default
0.0
1.0
2.0
1.0
2.0
3.0
2.0
3.0
4.0
3.0
4.0
5.0
--8--

Burlen

On 09/18/2014 11:56 PM, Robert-Zoltan Szasz wrote:

Hi,

I tried to visualize 2D structured point data when I observed a 
strange behavior. If the spacing in Y direction is negative, the data 
is flipped upside-down in 'Slice' representation mode but shown 
properly as a  'Surface' representation. Tried in v. 4.0.1 and 4.2rc1 
on Linux 64 bit. Here is a small VTK file to test:


--8--
# vtk DataFile Version 2.0
testing
ASCII
DATASET STRUCTURED_POINTS
DIMENSIONS 3 4 1
ORIGIN 0.0 0.0 0.0
SPACING 0.5 -0.75 1.0
POINT_DATA 12
SCALARS test float
LOOKUP_TABLE default
0.0
1.0
2.0
1.0
2.0
3.0
2.0
3.0
4.0
3.0
4.0
5.0
--8--

I am wondering if I missed something when formatting the file or if 
you have any ideas how to avoid this behavior?

Thanks,
Robert



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Re: [Paraview] Quadrature Points filters

[Burlen Loring]

Hi Ken,

Those are for visualizing data at locations used internally by FE 
solvers. The menu category was added a while back (3.98?) when I fixed a 
couple of bugs reported here on the user list. The filters themselves 
have been around for a while. 
http://www.vtk.org/Wiki/images/7/78/VTK-Quadrature-Point-Design-Doc.pdf


Burlen


On 08/26/2014 11:38 AM, Moreland, Kenneth wrote:
In the nightly builds of ParaView I notice that there is a new filter 
category named Quadrature Points. Can someone briefly explain what 
these filters do?


-Ken

     Kenneth Moreland
***  Sandia National Laboratories
***
*** *** ***  email: kmo...@sandia.gov mailto:kmo...@sandia.gov
**  ***  **  phone: (505) 844-8919
***  web: http://www.sandia.gov/~kmorel 
http://www.sandia.gov/%7Ekmorel




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Re: [Paraview] Strange opacity behavior

[Burlen Loring]

I have the same issue, I reported back in may
http://public.kitware.com/pipermail/paraview/2014-May/031007.html


On 08/25/2014 03:57 PM, Yi Chen wrote:

Hi Ken,

Thanks a lot for your fascinating answer. In my application of 
visualizing multi-floor buildings a higher peel number is necessary. 
However, I found I can enable or disable Depth Peeling but not to 
adjust the Number ( tried both Ubuntu and Windows )


Inline image 1

Should I use the nightly build instead of 4.10? It seems that it is 
adjustable on Mac since I found the following figure on wiki,


Inline image 2

Yi



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Re: [Paraview] A Forward Connection Over two ssh Tunnel

[Burlen Loring]

One thing to be aware of is the additional overhead of ssh compared to 
something like ncat or portfwd. ssh encrypts/unencrypts it's data which 
adds unnecessary overhead. I ran the 2 ssh tunnel solution at nersc for 
a while on Hopper. The performance was noticeably better with ncat which 
pipes data through untouched. The issue in large part because of the 
heavy loading and heavy network traffic on mom nodes where second tunnel 
ran. this is cray thing, you may not notice the difference between ssh 
and ncat on a typical cluster or if the system is not hammered by 1000's 
of simultaneous users as ours are. Still I think ncat is the best practice.


On 08/18/2014 08:56 PM, Utkarsh Ayachit wrote:

Very cool! Thanks for sharing, Axel. It will be nice to link this page
from the Wiki as a reference/example, if that's okay.

Utkarsh

On Mon, Aug 18, 2014 at 6:12 PM, Huebl, Axel a.hu...@hzdr.de wrote:

Dear Ehsan,

I use a similar setup as Burlen, tunneling twice over a login node to
our cluster's head node.

It also needs `GatewayPorts clientspecified` in the head node's
sshd_config to work with maximum comfort.
Feel free to check our wiki:

https://github.com/ComputationalRadiationPhysics/picongpu/wiki/ParaView

Best,
Axel

On 18.08.2014 22:43, Burlen Loring wrote:

Hi Utkarsh,

Sure I can do that.

Burlen

On 08/18/2014 01:36 PM, Utkarsh Ayachit wrote:

Burlen,

Very cool. When you get the chance, mind updating the Wiki?

Thanks
Utkarsh

On Mon, Aug 18, 2014 at 12:37 PM, Burlen Loring blor...@lbl.gov wrote:

Hi Ehsan,

As Utkarsh says you need to use a reverse connection. I suggest ncat
instead
of portfwd because portfwd is a long dead project with no support and
it's
failed to compile on some systems I used. Here's a schematic of the
setup

[work station]  [  login node]  [ compute node ]
[  paraview  ]-- ssh -R --[ ncat + ncat -l ]-[ pvserver -rc ]

in more detail:
in your pvsc on the client
ssh -R ${PORT}:localhost:${PORT} ${LOGIN_HOST} ...

on the login node in a shell script referenced by the client's pvsc:
let LOGIN_PORT=${PORT}+1
ncat -l ${LOGIN_HOST} ${LOGIN_PORT} --sh-exec=ncat localhost $PORT 
qsub ...

on the compute node in your batch script
mpirun ... pvserver --reverse-connection --client-host ${LOGIN_HOST}
--server-port ${LOGIN_PORT} ...

You could skip ncat if you have control over the sshd config, you
need to
enable GatewayPorts.

Burlen


On 08/18/2014 08:18 AM, Utkarsh Ayachit wrote:

It does boil down to using reverse connection and setting up recursive
tunnels so that the pvserver and tunnel back to the client. See the
following on the need for portfwd and how it could potentially be
helpful here.

http://www.paraview.org/Wiki/Reverse_connection_and_port_forwarding#Reverse_Connection_over_a_Reverse_ssh_Tunnel_with_portfwd


On Mon, Aug 18, 2014 at 11:15 AM, ehsan saei ehsan.s...@gmail.com
wrote:

Dear Utkarsh,
Thanks for your respond. I tried the section :  A forward connection
over
an ssh tunnel 
but it doesn't work. The problem is that I have to ssh to one system and
then ssh to the cluster again and finally I can submit a job. Do you
have
any other suggestions?

thanks in advance,
Ehsan


On Mon, Aug 18, 2014 at 4:29 PM, Utkarsh Ayachit
utkarsh.ayac...@kitware.com wrote:

This may be of help:
http://www.paraview.org/Wiki/Reverse_connection_and_port_forwarding

Utkarsh

On Mon, Aug 18, 2014 at 5:52 AM, ehsan saei ehsan.s...@gmail.com
wrote:

Hi all,

I'm new to paraview. I try to run pvserver on a cluster. The problem is
that
I need to ssh twice to get access to the cluster. To use pvserver I
submit a
job on the cluster and then I run pvserver using the command
mpirun -np 12 pvserver
then I pick the name and port from terminal and use it in paraview
client.
but paraview can't find the pvserver. Is there any way to establish a
connection via these two ssh tunnels?

Thanks in advance,
Ehsan

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Re: [Paraview] A Forward Connection Over two ssh Tunnel

[Burlen Loring]

Hi Ehsan,

As Utkarsh says you need to use a reverse connection. I suggest ncat 
http://nmap.org/ncat/ instead of portfwd because portfwd is a long 
dead project with no support and it's failed to compile on some systems 
I used. Here's a schematic of the setup


[work station]  [  login node]  [ compute node ]
[  paraview  ]-- ssh -R --[ ncat+ncat-l]-[ pvserver -rc ]

in more detail:
in your pvsc on the client
ssh -R ${PORT}:localhost:${PORT} ${LOGIN_HOST} ...

on the login node in a shell script referenced by the client's pvsc:
let LOGIN_PORT=${PORT}+1
ncat -l ${LOGIN_HOST} ${LOGIN_PORT} --sh-exec=ncat localhost $PORT 
qsub ...

on the compute nodein your batch script
mpirun ... pvserver --reverse-connection --client-host ${LOGIN_HOST} 
--server-port ${LOGIN_PORT} ...


You could skip ncat if you have control over the sshd config, you need 
to enable GatewayPorts.


Burlen

On 08/18/2014 08:18 AM, Utkarsh Ayachit wrote:

It does boil down to using reverse connection and setting up recursive
tunnels so that the pvserver and tunnel back to the client. See the
following on the need for portfwd and how it could potentially be
helpful here.

http://www.paraview.org/Wiki/Reverse_connection_and_port_forwarding#Reverse_Connection_over_a_Reverse_ssh_Tunnel_with_portfwd

On Mon, Aug 18, 2014 at 11:15 AM, ehsan saei ehsan.s...@gmail.com wrote:

Dear Utkarsh,
Thanks for your respond. I tried the section :  A forward connection over
an ssh tunnel 
but it doesn't work. The problem is that I have to ssh to one system and
then ssh to the cluster again and finally I can submit a job. Do you have
any other suggestions?

thanks in advance,
Ehsan


On Mon, Aug 18, 2014 at 4:29 PM, Utkarsh Ayachit
utkarsh.ayac...@kitware.com wrote:

This may be of help:
http://www.paraview.org/Wiki/Reverse_connection_and_port_forwarding

Utkarsh

On Mon, Aug 18, 2014 at 5:52 AM, ehsan saei ehsan.s...@gmail.com wrote:

Hi all,

I'm new to paraview. I try to run pvserver on a cluster. The problem is
that
I need to ssh twice to get access to the cluster. To use pvserver I
submit a
job on the cluster and then I run pvserver using the command
mpirun -np 12 pvserver
then I pick the name and port from terminal and use it in paraview
client.
but paraview can't find the pvserver. Is there any way to establish a
connection via these two ssh tunnels?

Thanks in advance,
Ehsan

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Re: [Paraview] A Forward Connection Over two ssh Tunnel

[Burlen Loring]

Hi Utkarsh,

Sure I can do that.

Burlen

On 08/18/2014 01:36 PM, Utkarsh Ayachit wrote:

Burlen,

Very cool. When you get the chance, mind updating the Wiki?

Thanks
Utkarsh

On Mon, Aug 18, 2014 at 12:37 PM, Burlen Loring blor...@lbl.gov wrote:

Hi Ehsan,

As Utkarsh says you need to use a reverse connection. I suggest ncat instead
of portfwd because portfwd is a long dead project with no support and it's
failed to compile on some systems I used. Here's a schematic of the setup

[work station]  [  login node]  [ compute node ]
[  paraview  ]-- ssh -R --[ ncat + ncat -l ]-[ pvserver -rc ]

in more detail:
in your pvsc on the client
ssh -R ${PORT}:localhost:${PORT} ${LOGIN_HOST} ...

on the login node in a shell script referenced by the client's pvsc:
let LOGIN_PORT=${PORT}+1
ncat -l ${LOGIN_HOST} ${LOGIN_PORT} --sh-exec=ncat localhost $PORT 
qsub ...

on the compute node in your batch script
mpirun ... pvserver --reverse-connection --client-host ${LOGIN_HOST}
--server-port ${LOGIN_PORT} ...

You could skip ncat if you have control over the sshd config, you need to
enable GatewayPorts.

Burlen


On 08/18/2014 08:18 AM, Utkarsh Ayachit wrote:

It does boil down to using reverse connection and setting up recursive
tunnels so that the pvserver and tunnel back to the client. See the
following on the need for portfwd and how it could potentially be
helpful here.

http://www.paraview.org/Wiki/Reverse_connection_and_port_forwarding#Reverse_Connection_over_a_Reverse_ssh_Tunnel_with_portfwd

On Mon, Aug 18, 2014 at 11:15 AM, ehsan saei ehsan.s...@gmail.com wrote:

Dear Utkarsh,
Thanks for your respond. I tried the section :  A forward connection over
an ssh tunnel 
but it doesn't work. The problem is that I have to ssh to one system and
then ssh to the cluster again and finally I can submit a job. Do you have
any other suggestions?

thanks in advance,
Ehsan


On Mon, Aug 18, 2014 at 4:29 PM, Utkarsh Ayachit
utkarsh.ayac...@kitware.com wrote:

This may be of help:
http://www.paraview.org/Wiki/Reverse_connection_and_port_forwarding

Utkarsh

On Mon, Aug 18, 2014 at 5:52 AM, ehsan saei ehsan.s...@gmail.com wrote:

Hi all,

I'm new to paraview. I try to run pvserver on a cluster. The problem is
that
I need to ssh twice to get access to the cluster. To use pvserver I
submit a
job on the cluster and then I run pvserver using the command
mpirun -np 12 pvserver
then I pick the name and port from terminal and use it in paraview
client.
but paraview can't find the pvserver. Is there any way to establish a
connection via these two ssh tunnels?

Thanks in advance,
Ehsan

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Re: [Paraview] [ParaView] Unofficial ParaView 4.1.0 SDK for Windows 32 and 64-bit

[Burlen Loring]

makes me wonder if the installer could also install python binaries? ;-)

I'm not sure which compiler you should use, I tend to think the newer 
compiler would potentially generate better code, but I don't know if 
there are other factors that you need to consider when creating binaries.


On 08/13/2014 07:07 AM, Utkarsh Ayachit wrote:

Good to know. I think we'll make the switch at the same time when we
upgrade the VS compiler we're using for the binaries. We are switching
to using CMakified Python soon and then we wouldn't need to use
VS2008. Any thoughts on which is the most common VS compiler? Qt
distributes binaries for 2010, 2012, 2013. I suppose we can pick 2012
:).

On Tue, Aug 12, 2014 at 11:50 PM, Burlen Loring burlen.lor...@gmail.com wrote:

Ahh, that may be, I wouldn't have noticed it since I have admin on my
account.

as far as the version of the standard implemented by MS MPI in HPC Pack 2012
(internal ver 256), it's 2.0. The TestSystemCaps regression test has the
code to report.


On 8/11/2014 9:53 AM, Utkarsh Ayachit wrote:

Additionally, you need to run the installer as admin since it installs
a daemon (I believe). I think it would make sense to put out two
version of Windows binaries (without MPI and with MS MPI) and then
include the MSMPI installer as a part of the installation process,
esp. since no other Windows MPI is officially supported any more.

Something to think about for 4.3, not sure I want to make the plunge
for 4.2 -- but we'll keep the options open :).

Utkarsh





On Mon, Aug 11, 2014 at 12:46 PM, Burlen Loring blor...@lbl.gov wrote:

Hi Utkarsh,

I think it does implement MPI2. At least my codes make heavy use of MPI 2
and it works fine. However, I'll look into it and report back.

Microsoft's documentation says:

You may also redistribute this MS-MPI installation package with your own
applications, to facilitate having an application that can run on a
stand-alone workstation and easily take advantage of an HPC Pack 2012
R2-based cluster. Please refer to the license agreement for additional
details.


Sounds like if you use an installer it could handle the dependency.

Burlen


On 08/11/2014 08:03 AM, Utkarsh Ayachit wrote:

The ParaView dev team switched from Open-MPI 1.6.2 backwards to 1.4.4,
precisely because the support was dropped.

That is correct. That's  precisely why we've stuck with 1.4.4. I spent
a lot of time trying to packing 1.6.* on Windows to no success and
then decided to just stick with 1.4.4.

Problem is that the source code for the current MS-MPI builds does not
seem
to be publicly available,

The problem with using MS-MPI is two fold:
1. I can't remember if its support MPIv2 API. I don't think so, but I
may be wrong.
2. The license (at least when I checked) doesn't allow us to packing
the dlls in our binaries. In other words, we would always have to have
the user manually install using the installer distributed by MS.

Utkarsh



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Re: [Paraview] [ParaView] Unofficial ParaView 4.1.0 SDK for Windows 32 and 64-bit

[Burlen Loring]

I was thinking along the lines that the ParaView installer, could 
leverage the python official installer behind the scenes, but direct it 
into the ParaView specific location...


On 08/13/2014 07:59 AM, Utkarsh Ayachit wrote:

On Wed, Aug 13, 2014 at 10:56 AM, Burlen Loring burlen.lor...@gmail.com wrote:

makes me wonder if the installer could also install python binaries? ;-)

Haha! Me wonders too .. the problem is if the user installed Python in
some location, then he'd need to setup PATH before paraview could run.


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Re: [Paraview] streamlines on 2D plane from 3D data

[Burlen Loring]

Hi Ryan,

Try using Surface Vectors filter to remove the out of surface component 
from the vector field, and make sure your seeds are exactly on the surface.


As far as surface lic, are you sure you selected the right vector field? 
If yes, please share the data and I'll see if I can duplicate the issue.


Burlen

On 08/12/2014 11:29 AM, Ryan Crocker wrote:

Hi,

I'm using paraview 4.1.0-64bit and i'm trying to simply add 
streamlines from a 3D flow to a slice.  This happens automatically if 
i start with 2D data but i cannot seem to make it work with 3D data. 
 I've tried using the surface LIC plugin, but i when i activate it and 
try to use it as a representation nothing happens, the slice looks 
like it does without surface LIC.  I changed all the parameters to 
what should be applicable to my data and still, nothing happens. 
 Paraview is not even asking if i would like to apply the changes.


The second approach i tried was to use this tutorial:

http://www.paraview.org/Wiki/ParaView/Custom_Filters

but i'm not even sure how that is stared, is there a more step by step 
approach where they do this from initial raw data to the final form. I 
cannot get this to work.This seems like something that should be 
pretty straight forward.


The flow i'm trying to visualize is a 3D convective cell.


thanks for the help,

Ryan Crocker
University of Vermont, School of Engineering
Mechanical Engineering Department
rcroc...@uvm.edu mailto:rcroc...@uvm.edu
315-212-7331



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Re: [Paraview] [ParaView] Unofficial ParaView 4.1.0 SDK for Windows 32 and 64-bit

[Burlen Loring]

Ahh, that may be, I wouldn't have noticed it since I have admin on my 
account.


as far as the version of the standard implemented by MS MPI in HPC Pack 
2012 (internal ver 256), it's 2.0. The TestSystemCaps regression test 
has the code to report.


On 8/11/2014 9:53 AM, Utkarsh Ayachit wrote:

Additionally, you need to run the installer as admin since it installs
a daemon (I believe). I think it would make sense to put out two
version of Windows binaries (without MPI and with MS MPI) and then
include the MSMPI installer as a part of the installation process,
esp. since no other Windows MPI is officially supported any more.

Something to think about for 4.3, not sure I want to make the plunge
for 4.2 -- but we'll keep the options open :).

Utkarsh





On Mon, Aug 11, 2014 at 12:46 PM, Burlen Loring blor...@lbl.gov wrote:

Hi Utkarsh,

I think it does implement MPI2. At least my codes make heavy use of MPI 2
and it works fine. However, I'll look into it and report back.

Microsoft's documentation says:

You may also redistribute this MS-MPI installation package with your own
applications, to facilitate having an application that can run on a
stand-alone workstation and easily take advantage of an HPC Pack 2012
R2-based cluster. Please refer to the license agreement for additional
details.


Sounds like if you use an installer it could handle the dependency.

Burlen


On 08/11/2014 08:03 AM, Utkarsh Ayachit wrote:

The ParaView dev team switched from Open-MPI 1.6.2 backwards to 1.4.4,
precisely because the support was dropped.

That is correct. That's  precisely why we've stuck with 1.4.4. I spent
a lot of time trying to packing 1.6.* on Windows to no success and
then decided to just stick with 1.4.4.

Problem is that the source code for the current MS-MPI builds does not seem
to be publicly available,

The problem with using MS-MPI is two fold:
1. I can't remember if its support MPIv2 API. I don't think so, but I
may be wrong.
2. The license (at least when I checked) doesn't allow us to packing
the dlls in our binaries. In other words, we would always have to have
the user manually install using the installer distributed by MS.

Utkarsh



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Re: [Paraview] [ParaView] Unofficial ParaView 4.1.0 SDK for Windows 32 and 64-bit

[Burlen Loring]

Hi Utkarsh,

I think it does implement MPI2. At least my codes make heavy use of MPI 
2 and it works fine. However, I'll look into it and report back.


Microsoft's documentation says:

   You may also redistribute this MS-MPI installation package with your
   own applications, to facilitate having an application that can run
   on a stand-alone workstation and easily take advantage of an HPC
   Pack 2012 R2-based cluster. Please refer to the license agreement
   for additional details. 



Sounds like if you use an installer it could handle the dependency.

Burlen

On 08/11/2014 08:03 AM, Utkarsh Ayachit wrote:

The ParaView dev team switched from Open-MPI 1.6.2 backwards to 1.4.4,
precisely because the support was dropped.

That is correct. That's  precisely why we've stuck with 1.4.4. I spent
a lot of time trying to packing 1.6.* on Windows to no success and
then decided to just stick with 1.4.4.


Problem is that the source code for the current MS-MPI builds does not seem
to be publicly available,

The problem with using MS-MPI is two fold:
1. I can't remember if its support MPIv2 API. I don't think so, but I
may be wrong.
2. The license (at least when I checked) doesn't allow us to packing
the dlls in our binaries. In other words, we would always have to have
the user manually install using the installer distributed by MS.

Utkarsh


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Re: [Paraview] [ParaView] Unofficial ParaView 4.1.0 SDK for Windows 32 and 64-bit

[Burlen Loring]

OpenMPI dropped support for windows some time ago. Would it not make 
sense to use MS MPI?


https://www.open-mpi.org/software/ompi/v1.6/ms-windows.php
http://msdn.microsoft.com/en-us/library/bb524831(v=vs.85).aspx 
http://msdn.microsoft.com/en-us/library/bb524831%28v=vs.85%29.aspx


On 08/08/2014 07:30 AM, Robert Maynard wrote:

This is really cool! We should try to integrate the open mpi changes
as those seem really reasonable.


As far as building Qt, this is required for two reasons. The first is
that the Qt 4.8 series only has 32bit official binaries for windows,
and we would need 32 and 64bit. If we moved to Qt 5.X it would be
possible to use the official binaries, as long as moved to VS
2010/2012.

Now the reason that we currently build with VS 2008 is because of hard
requirements in the python build system. I know that people are
investigating a new build system for python that supports VS 2010 /
VS2012.  So if ParaView is ever able to use the new python build
system, and officially moves over to Qt 5.X we should transition to
use the official Qt binaries for windows.

On Wed, Aug 6, 2014 at 8:59 AM, Bruno Santos
bruno.san...@bluecape.com.pt wrote:

Greetings to all!

We at blueCAPE have made available an unofficial SDK of ParaView 4.1.0 for
Windows 32 and 64-bit, based on the official SuperBuild and respective build
options. It's available here:
https://code.google.com/p/unofficial-paraview-dev-install/wiki/Downloads#ParaView_4.1.0
Instructions on how these packages were built is provided here:
https://code.google.com/p/unofficial-paraview-dev-install/wiki/Notes410

According to our tests, it's possible to use this SDK to build plug-ins and
any other associated applications, which will work with the respective
official ParaView 4.1.0 builds for Windows. A proof of concept we've used is
the vtkPOFFReader plug-in which was successfully built with these SDK
packages:
https://code.google.com/p/unofficial-paraview-dev-install/wiki/vtkPOFFReaderBuilds

Note: We roughly used the same development environment as the original
ParaView 4.1.0 binaries for Windows:
http://www.paraview.org/Wiki/ParaView_Binaries - although we've used MSVC
2008 C++ Express and did not have a respective FORTRAN compiler (which
requires the Professional version either way), which is why we needed to do
some adjustments to build Open-MPI with success.

Furthermore, here's a bit of a back story and the current status of this
endeavour:

Back in January 2012 we at blueCAPE began to try to bring back the
development installers of ParaView for Windows, which was last officially
available for ParaView 3.8.1.
The overall features available in the development installers we created were
still missing important files, because we were still basing ourselves on the
infrastructure that was still remnant from ParaView 3.8.1.
Nonetheless, we made available our findings and builds for ParaView 3.12.0,
3.14.0, 3.14.1 and 3.98.0, where the last release we managed to build was
back in January 2013.
ParaView fortunately kept evolving since then. We missed the versions 3.98.1
and 4.0.1, due to time constraints on our side and a few failed builds.
As far as we can see, ParaView 4.1.0 already has a pretty good SDK structure
which evolved overtime. The official SuperBuild repository also already
provides many of the necessary features for making the SDK releases, at
least for the Unix-like environments.
This Summer 2014 we at blueCAPE finally managed to get around back to trying
and adjust the SuperBuild settings to build and deliver a ParaView 4.1.0 SDK
for Windows and believe we have successfully achieved it. The changes have
been shared and referenced in the following wiki page at our project:
https://code.google.com/p/unofficial-paraview-dev-install/wiki/Notes410
In addition to this, after some reviewing and building tests with the latest
commits on the master branch from the SuperBuild repository, we have adapted
most of the changes we've developed for the SDK build above and have
submitted two commits to Kitware Gerrit, namely:

http://review.source.kitware.com/#/t/4487/
http://review.source.kitware.com/#/t/4488/

We haven't managed to create the NSIS and ZIP packages through CMake/CPack,
but our main concern has mostly been on having a working SDK.

Hopefully this can help bring sooner the ParaView SDK in future versions in
a more official way... so that we won't have to look into generating the
NSIS/ZIP packages ourselves, nor build Qt 4.8.6 ;)

If anyone has any questions, feel free to ask!

Best regards,
Bruno Santos

PS: I haven't sent this email to the ParaView Developers mailing list simply
because previous emails I've sent on this topic have been to this main
mailing list.


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