date:20200826

Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-26 Thread Matthias Maier



On Wed, Aug 26, 2020, at 13:01 CDT, Aaditya Lakshmanan  
wrote:

> Hi, 
>   zlib(version 1.2.11) was already loaded as a module in all my previous 
> compilation attempts. I will try it by setting DEAL_II_WITH_ZLIB=OFF but I 
> am not sure why the path to zlib libraries is picked up from /usr . Thanks 
> for the suggestion.

This is probably simply a faulty zlib module shipped with zlib. In order
to force cmake to pick up the correct library it might be easiest to use
"CMAKE_PREFIX_PATH" like so:

  -DCMAKE_PREFIX_PATH=/path/to/the/zlib/module/

If that doesn't help then you can specify zlib by hand:

  -DDEAL_II_WITH_ZLIB=ON -DZLIB_INCLUDE_DIRS=/[...]/include 
-DZLIB_LIBRARIES=/[...]/libz.so

Best,
Matthias

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-26 Thread Aaditya Lakshmanan

Hi, 
  zlib(version 1.2.11) was already loaded as a module in all my previous 
compilation attempts. I will try it by setting DEAL_II_WITH_ZLIB=OFF but I 
am not sure why the path to zlib libraries is picked up from /usr . Thanks 
for the suggestion.

Best,
Aaditya

On Wednesday, August 26, 2020 at 1:46:10 PM UTC-4 jpbla...@lbl.gov wrote:

> HI Matthias,
>
> thanks for your input -- you might be onto something RE ld
>
> We use a wrapper script for ld:
> ```
> blaschke@cori06:~> which ld
> /global/common/cori/software/altd/2.0/bin/ld
> ```
> which is managed by the ALTD module (Automatic Library Tracking Database). 
> Using the system linker (which is what cmake is picking up) isn't usually a 
> problem, but in this case it might be. I checked Aaditya's loaded modules 
> and ALTD is in there, so CMake should be picking it up. How does CMake 
> detect the linker? Is it just a question of adding `-DCMAKE_LINKER=$(which 
> ld)`?
>
> RE zlib: we have a zlib module. So maybe it's just a question of loading 
> that. Does CMake just detect zlib in the PATH? If so, doing a `module load 
> zlib` should be enough. Otherwise, is there a way to point CMake to the 
> zlib module directory?
>
> Cheers,
> Johannes
>
>
> On Wednesday, August 26, 2020 at 8:43:42 AM UTC-7 Matthias Maier wrote:
>
>> Thanks. 
>>
>> This looks mostly good. 
>>
>> In particular, the Lapack CMake module seems to pick up "AtpSigHandler" 
>> and "AtpSigHCommData": 
>>
>> 55 # DEAL_II_WITH_LAPACK set up with external dependencies 
>> 56 # LAPACK_WITH_64BIT_BLAS_INDICES = OFF 
>> 57 # LAPACK_LINKER_FLAGS = 
>> 58 # LAPACK_INCLUDE_DIRS = 
>> 59 # LAPACK_USER_INCLUDE_DIRS = 
>> 60 # LAPACK_LIBRARIES = 
>> /opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_intel_lp64.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel6
>>  
>> 4/libmkl_intel_thread.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_core.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64/libiom
>>  
>> p5.so;-lm;-ldl;hugetlbfs;AtpSigHandler;AtpSigHCommData;z;hdf5_hl;hdf5;hdf5hl_fortran;hdf5_fortran;mpich_intel;mpichf90_intel;ifport;ifcoremt;imf;m;ipgo;irc;pthread;svml;gcc;gcc_s;irc_s;dl
>>  
>> ;c 
>>
>> One thing is peculiar: 
>>
>> 108 # DEAL_II_WITH_ZLIB set up with external dependencies 
>> 109 # ZLIB_VERSION = 1.2.11 
>> 110 # ZLIB_INCLUDE_DIRS = /usr/include 
>> 111 # ZLIB_LIBRARIES = /usr/lib64/libz.so 
>>
>> This library does not reside under /global and I doubt it has the right 
>> architecture. Would you mind disabling zlib support for the time being 
>> (-DDEAL_II_WITH_ZLIB=OFF)? Or reconfigure such that the correct zlib 
>> library is picked up? 
>>
>> Maybe this explains why the system linker /usr/bin/ld is used instead of 
>> one from the toolchain under /opt/cray/pe/craype/2.6.2/bin ... 
>>
>> Best, 
>> Matthias 
>>
>

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-26 Thread Matthias Maier

Thanks.

This looks mostly good.

In particular, the Lapack CMake module seems to pick up "AtpSigHandler"
and "AtpSigHCommData":

 55 #DEAL_II_WITH_LAPACK set up with external dependencies  
 
 56 #LAPACK_WITH_64BIT_BLAS_INDICES = OFF   
 
 57 #LAPACK_LINKER_FLAGS =  
 
 58 #LAPACK_INCLUDE_DIRS =  
 
 59 #LAPACK_USER_INCLUDE_DIRS = 
 
 60 #LAPACK_LIBRARIES = 
/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_intel_lp64.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel6

4/libmkl_intel_thread.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_core.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64/libiom

p5.so;-lm;-ldl;hugetlbfs;AtpSigHandler;AtpSigHCommData;z;hdf5_hl;hdf5;hdf5hl_fortran;hdf5_fortran;mpich_intel;mpichf90_intel;ifport;ifcoremt;imf;m;ipgo;irc;pthread;svml;gcc;gcc_s;irc_s;dl
;c

One thing is peculiar: 

108 #DEAL_II_WITH_ZLIB set up with external dependencies
 
109 #ZLIB_VERSION = 1.2.11  
 
110 #ZLIB_INCLUDE_DIRS = /usr/include   
 
111 #ZLIB_LIBRARIES = /usr/lib64/libz.so 

This library does not reside under /global and I doubt it has the right
architecture. Would you mind disabling zlib support for the time being
(-DDEAL_II_WITH_ZLIB=OFF)? Or reconfigure such that the correct zlib
library is picked up?

Maybe this explains why the system linker /usr/bin/ld is used instead of
one from the toolchain under /opt/cray/pe/craype/2.6.2/bin ...

Best,
Matthias

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[deal.II] step-1 Error

2020-08-26 Thread Scott Ziegler

Hello,

I tried running the first tutorial on my machine and I am getting an error 
message I don't understand. The "cmake step-1.cc ." and "make step-1.cc" 
commands ran fine, but when I try "make run step-1.cc" I get the following 
error:

*Scanning dependencies of target step-1*

[ 33%] Building CXX object CMakeFiles/step-1.dir/step-1.cc.o

[ 66%] *Linking CXX executable step-1*

[ 66%] Built target step-1

*Scanning dependencies of target run*

[100%] *Run step-1 with Debug configuration*

dyld: Library not loaded: libiomp5.dylib

  Referenced from: 
/Applications/deal.II-9.0.0.app/Contents/Resources/spack/opt/spack/darwin-highsierra-x86_64/clang-6.0.0/assimp-4.0.1-pdlrx32676yct2pztierxgvynk5gx277/lib/libassimp.4.dylib

  Reason: image not found

make[3]: *** [CMakeFiles/run] Abort trap: 6

make[2]: *** [CMakeFiles/run.dir/all] Error 2

make[1]: *** [CMakeFiles/run.dir/rule] Error 2

make: *** [run] Error 2


I am running an older version of deal.ii (deal.ii.9.0.0) because the latest 
version wasn't compatible with my laptop. I have a 2012 MacBook Pro running 
macOS 10.13.6. Any help would be greatly appreciated, thank you.

-- 
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Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-26 Thread Johannes Blaschke

HI Matthias,

thanks for your input -- you might be onto something RE ld

We use a wrapper script for ld:
```
blaschke@cori06:~> which ld
/global/common/cori/software/altd/2.0/bin/ld
```
which is managed by the ALTD module (Automatic Library Tracking Database). 
Using the system linker (which is what cmake is picking up) isn't usually a 
problem, but in this case it might be. I checked Aaditya's loaded modules 
and ALTD is in there, so CMake should be picking it up. How does CMake 
detect the linker? Is it just a question of adding `-DCMAKE_LINKER=$(which 
ld)`?

RE zlib: we have a zlib module. So maybe it's just a question of loading 
that. Does CMake just detect zlib in the PATH? If so, doing a `module load 
zlib` should be enough. Otherwise, is there a way to point CMake to the 
zlib module directory?

Cheers,
Johannes


On Wednesday, August 26, 2020 at 8:43:42 AM UTC-7 Matthias Maier wrote:

> Thanks.
>
> This looks mostly good.
>
> In particular, the Lapack CMake module seems to pick up "AtpSigHandler"
> and "AtpSigHCommData":
>
> 55 # DEAL_II_WITH_LAPACK set up with external dependencies 
> 56 # LAPACK_WITH_64BIT_BLAS_INDICES = OFF 
> 57 # LAPACK_LINKER_FLAGS = 
> 58 # LAPACK_INCLUDE_DIRS = 
> 59 # LAPACK_USER_INCLUDE_DIRS = 
> 60 # LAPACK_LIBRARIES = 
> /opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_intel_lp64.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel6
>  
> 4/libmkl_intel_thread.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_core.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64/libiom
>  
> p5.so;-lm;-ldl;hugetlbfs;AtpSigHandler;AtpSigHCommData;z;hdf5_hl;hdf5;hdf5hl_fortran;hdf5_fortran;mpich_intel;mpichf90_intel;ifport;ifcoremt;imf;m;ipgo;irc;pthread;svml;gcc;gcc_s;irc_s;dl
>  
> ;c
>
> One thing is peculiar: 
>
> 108 # DEAL_II_WITH_ZLIB set up with external dependencies 
> 109 # ZLIB_VERSION = 1.2.11 
> 110 # ZLIB_INCLUDE_DIRS = /usr/include 
> 111 # ZLIB_LIBRARIES = /usr/lib64/libz.so 
>
> This library does not reside under /global and I doubt it has the right
> architecture. Would you mind disabling zlib support for the time being
> (-DDEAL_II_WITH_ZLIB=OFF)? Or reconfigure such that the correct zlib
> library is picked up?
>
> Maybe this explains why the system linker /usr/bin/ld is used instead of
> one from the toolchain under /opt/cray/pe/craype/2.6.2/bin ...
>
> Best,
> Matthias
>

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Re: [deal.II] step-1 Error

2020-08-26 Thread Luca Heltai

The 9.0.0 image contains a spack installation. Can you run "module load
dealii" before trying to run?

Luca.

Il giorno mer 26 ago 2020 alle 19:51 Scott Ziegler <
scott...@rams.colostate.edu> ha scritto:

> Hello,
>
> I tried running the first tutorial on my machine and I am getting an error
> message I don't understand. The "cmake step-1.cc ." and "make step-1.cc"
> commands ran fine, but when I try "make run step-1.cc" I get the following
> error:
>
> *Scanning dependencies of target step-1*
>
> [ 33%] Building CXX object CMakeFiles/step-1.dir/step-1.cc.o
>
> [ 66%] *Linking CXX executable step-1*
>
> [ 66%] Built target step-1
>
> *Scanning dependencies of target run*
>
> [100%] *Run step-1 with Debug configuration*
>
> dyld: Library not loaded: libiomp5.dylib
>
>   Referenced from:
> /Applications/deal.II-9.0.0.app/Contents/Resources/spack/opt/spack/darwin-highsierra-x86_64/clang-6.0.0/assimp-4.0.1-pdlrx32676yct2pztierxgvynk5gx277/lib/libassimp.4.dylib
>
>   Reason: image not found
>
> make[3]: *** [CMakeFiles/run] Abort trap: 6
>
> make[2]: *** [CMakeFiles/run.dir/all] Error 2
>
> make[1]: *** [CMakeFiles/run.dir/rule] Error 2
>
> make: *** [run] Error 2
>
>
> I am running an older version of deal.ii (deal.ii.9.0.0) because the
> latest version wasn't compatible with my laptop. I have a 2012 MacBook Pro
> running macOS 10.13.6. Any help would be greatly appreciated, thank you.
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see
> https://groups.google.com/d/forum/dealii?hl=en
> ---
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> "deal.II User Group" group.
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> 
> .
>

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-26 Thread Matthias Maier



On Wed, Aug 26, 2020, at 12:46 CDT, Johannes Blaschke  
wrote:

> HI Matthias,
>
> thanks for your input -- you might be onto something RE ld
>
> We use a wrapper script for ld:
> ```
> blaschke@cori06:~> which ld
> /global/common/cori/software/altd/2.0/bin/ld
> ```
> which is managed by the ALTD module (Automatic Library Tracking Database). 
> Using the system linker (which is what cmake is picking up) isn't usually a 
> problem, but in this case it might be. I checked Aaditya's loaded modules 
> and ALTD is in there, so CMake should be picking it up. How does CMake 
> detect the linker? Is it just a question of adding `-DCMAKE_LINKER=$(which 
> ld)`?

Yes, setting CMAKE_LINKER would be an option. But typically CMake just
invokes the compiler wrapper which should do the right thing...

Best,
Matthias

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Re: [deal.II] Problems with the two-phase flow problem calculated on a hyperball (Step.21)

2020-08-26 Thread Wolfgang Bangerth


On 8/26/20 7:05 AM, 'simon doersam' via deal.II User Group wrote:
In Step.21 (The two phase flow problem) I replaced the domain "Hyper_cube" 
with "Hyper_ball".
The numerical solution is unrealistic and appears to be numerical problems at 
all points,
where the boundary intersects with one of the following planes: E1: = {x \ in 
R ^ 3, x1 = x2}, E2: = {x \ in R ^ 3, x1 = x3}, E3: = {x \ in R ^ 3, x2 = x3}.


The pressure and the viscosity are partially negative at these points.

Can someone help me and explain why this is happening?


You also need to change the definition of boundary values:

  template 
  class SaturationBoundaryValues : public Function
  {
  public:
SaturationBoundaryValues()
  : Function(1)
{}

virtual double value(const Point ,
 const unsigned int /*component*/ = 0) const override
{
  if (p[0] == 0)
return 1;
  else
return 0;
}
  };

This simply doesn't make any sense with the geometry you are now using.

Best
 W.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-26 Thread Aaditya Lakshmanan

Hi,
  Compiling deal.ii with DEAL_II_WITH_ZLIB=OFF and subsequently make -j 32 
install gives the same error as earlier :

[100%] Building CXX object source/CMakeFiles/deal_II.dir/dummy.cc.o
[100%] Linking CXX shared library ../lib/libdeal_II.so
/usr/bin/ld: cannot find -lAtpSigHandler
/usr/bin/ld: cannot find -lAtpSigHCommData
make[2]: *** [source/CMakeFiles/deal_II.dir/build.make:1274: 
lib/libdeal_II.so] Error 1
make[1]: *** [CMakeFiles/Makefile2:2879: source/CMakeFiles/deal_II.dir/all] 
Error 2
make[1]: *** Waiting for unfinished jobs

So I will try with another zlib module than the one originally used. I have 
attached the 'detalied.log' file for my most recent attempt.

Best,
Aaditya

On Wednesday, August 26, 2020 at 3:07:24 PM UTC-4 Matthias Maier wrote:

>
> On Wed, Aug 26, 2020, at 12:46 CDT, Johannes Blaschke  
> wrote:
>
> > HI Matthias,
> >
> > thanks for your input -- you might be onto something RE ld
> >
> > We use a wrapper script for ld:
> > ```
> > blaschke@cori06:~> which ld
> > /global/common/cori/software/altd/2.0/bin/ld
> > ```
> > which is managed by the ALTD module (Automatic Library Tracking 
> Database). 
> > Using the system linker (which is what cmake is picking up) isn't 
> usually a 
> > problem, but in this case it might be. I checked Aaditya's loaded 
> modules 
> > and ALTD is in there, so CMake should be picking it up. How does CMake 
> > detect the linker? Is it just a question of adding 
> `-DCMAKE_LINKER=$(which 
> > ld)`?
>
> Yes, setting CMAKE_LINKER would be an option. But typically CMake just
> invokes the compiler wrapper which should do the right thing...
>
> Best,
> Matthias
>

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###
#
#  deal.II configuration:
#CMAKE_BUILD_TYPE:   DebugRelease
#BUILD_SHARED_LIBS:  ON
#CMAKE_INSTALL_PREFIX:   
/global/project/projectdirs/m2360/packagesCPFE/dealii_trial
#CMAKE_SOURCE_DIR:   
/global/project/projectdirs/m2360/packagesCPFE/dealii
#(version 9.1.1, shortrev 777cf92a41)
#CMAKE_BINARY_DIR:   
/global/project/projectdirs/m2360/packagesCPFE/build
#CMAKE_CXX_COMPILER: Intel 19.0.0.20190206 on platform 
CrayLinuxEnvironment x86_64
#/opt/cray/pe/craype/2.6.2/bin/CC
#CMAKE_C_COMPILER:   /opt/cray/pe/craype/2.6.2/bin/cc
#CMAKE_Fortran_COMPILER: /opt/cray/pe/craype/2.6.2/bin/ftn
#CMAKE_GENERATOR:Unix Makefiles
#
#CROSSCOMPILING!
#
#  Base configuration (prior to feature configuration):
#DEAL_II_CXX_FLAGS:-fpic -ansi -w2 -diag-disable=remark 
-wd21 -wd68 -wd135 -wd175 -wd177 -wd191 -wd193 -wd279 -wd327 -wd383 -wd981 
-wd1418 -wd1478 -wd1572 -wd2259 -wd2536 -wd2651 -wd3415 -wd15531 -wd111 -wd128 
-wd185 -wd186 -wd280 -std=c++17
#DEAL_II_CXX_FLAGS_RELEASE:-O2 -no-ansi-alias -ip -funroll-loops
#DEAL_II_CXX_FLAGS_DEBUG:  -O0 -g -gdwarf-2 -grecord-gcc-switches
#DEAL_II_LINKER_FLAGS: -Wl,--as-needed -shared-intel -rdynamic
#DEAL_II_LINKER_FLAGS_RELEASE:
#DEAL_II_LINKER_FLAGS_DEBUG:
#DEAL_II_DEFINITIONS:
#DEAL_II_DEFINITIONS_RELEASE:
#DEAL_II_DEFINITIONS_DEBUG:DEBUG
#DEAL_II_USER_DEFINITIONS:
#DEAL_II_USER_DEFINITIONS_REL:
#DEAL_II_USER_DEFINITIONS_DEB: DEBUG
#DEAL_II_INCLUDE_DIRS
#DEAL_II_USER_INCLUDE_DIRS:
#DEAL_II_BUNDLED_INCLUDE_DIRS:
#DEAL_II_LIBRARIES:
#DEAL_II_LIBRARIES_RELEASE:
#DEAL_II_LIBRARIES_DEBUG:
#DEAL_II_COMPILER_VECTORIZATION_LEVEL: 0
#
#  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION 
= ON):
#  ( DEAL_II_WITH_64BIT_INDICES = OFF )
#  ( DEAL_II_WITH_ADOLC = OFF )
#  ( DEAL_II_WITH_ARPACK = OFF )
#  ( DEAL_II_WITH_ASSIMP = OFF )
#DEAL_II_WITH_BOOST set up with bundled packages
#BOOST_BUNDLED_INCLUDE_DIRS = 
/global/project/projectdirs/m2360/packagesCPFE/dealii/bundled/boost-1.62.0/include
#BOOST_LIBRARIES = rt
#DEAL_II_WITH_COMPLEX_VALUES = ON
#  ( DEAL_II_WITH_CUDA = OFF )
#DEAL_II_WITH_CXX14 = ON
#DEAL_II_WITH_CXX17 = ON
#  ( DEAL_II_WITH_GINKGO = OFF )
#  ( DEAL_II_WITH_GMSH = OFF )
#  ( DEAL_II_WITH_GSL = OFF )
#  ( DEAL_II_WITH_HDF5 = OFF )
#DEAL_II_WITH_LAPACK set up with external dependencies
#LAPACK_WITH_64BIT_BLAS_INDICES = OFF
#LAPACK_LINKER_FLAGS

Re: [deal.II] deal.ii Installation : expand_instantiations Error

Re: [deal.II] deal.ii Installation : expand_instantiations Error

Re: [deal.II] deal.ii Installation : expand_instantiations Error

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

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