[Paraview] What is the file format of vtkMolecule data type?
Hello, I want to write a vtkMolecule data file using my code (not the API of VTK), but I don't know the format of this kind of data type. I can find detailed file format of Polydata, Structured Grid, etc. but I don't find anything about the vtkMolecule data type in the vtk user guide. I want to know where I can find something introducing the file format of vtkMolecule data type, or could you please send me some examples of this kind of data file? Thanks a lot! -Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
Re: [Paraview] Can I use paraview to visualize molecule dataset?
Thank you very much! That's exactly what I want. -Zhang > -原始邮件- > 发件人: "Cory Quammen" <cory.quam...@kitware.com> > 发送时间: 2017年7月26日 星期三 > 收件人: "张驭洲" <yzhzh...@ipe.ac.cn> > 抄送: ParaView <paraview@paraview.org> > 主题: Re: [Paraview] Can I use paraview to visualize molecule dataset? > > Zhang, > > Yes, you can visualize molecules in ball-and-stick representation in > ParaView (see attached). This representation is used whenever you load > a vtkMolecule data type. If you have a PDB file, for example, it will > be read in as a vtkMolecule data type and displayed with > ball-and-stick representation by default. You can also change the > Molecule "Render Mode" property to "Space Filling" or "Liquorice" > representation. > > HTH, > Cory > > > > On Wed, Jul 26, 2017 at 3:57 AM, 张驭洲 <yzhzh...@ipe.ac.cn> wrote: > > > > > > Hello, > > > > I want to know if I can use paraview to visualize molecule dataset, > > i.e., using ball-and-stick model to represent molecules? Currently I can > > only using point gaussian to represent the "ball", but I don't know how to > > visualize the "stick". I know another visualization tool VMD is designed to > > do works of this kind, but I've not found similar founctions in ParaView. > > > > -Zhang > > > > > > > > > > > > ___ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Please keep messages on-topic and check the ParaView Wiki at: > > http://paraview.org/Wiki/ParaView > > > > Search the list archives at: http://markmail.org/search/?q=ParaView > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/paraview > > > > > > -- > Cory Quammen > Staff R Engineer > Kitware, Inc. ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] Can I use paraview to visualize molecule dataset?
Hello, I want to know if I can use paraview to visualize molecule dataset, i.e., using ball-and-stick model to represent molecules? Currently I can only using point gaussian to represent the "ball", but I don't know how to visualize the "stick". I know another visualization tool VMD is designed to do works of this kind, but I've not found similar founctions in ParaView. -Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] what does gaussian radius represent when "use scale array" is on or off, separately?
Hello, I'm using ParaView 5.2.0 to render some points. I'm using the GUI. I want to render the points as spheres so I select point gaussian. In the data file, there is a data array that defines the radii of the spheres, which range from 1.23e-4 to 2.46e-4. If I set the gaussian radius to 1.23e-4, it looks fine, though it doesn't show the difference of the spheres' radii. When I click use scale array and choose the radius array to be the gaussian scale array, all the spheres disappear. I guess maybe in this situation, the rendered radii are the product of gaussian radius and the values in the radius array, resulting to be at the scale of e-8. Then I set gaussian radius to 1, but it seems that it is still too small and no sphere appear. I keep increasing the value of gaussian radius to 500, and the rendered radii seem to be of the same scale of the beginning. If gaussian radius is the true radius of the spheres defined by the data file when use scale array is off, what it represents when use scale array is on? Why is 500 the proper value? -Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
Re: [Paraview] How to run a simulation with Catalyst and display the result using tiled display?
Hi Andy, Thanks for your reply! Please let me know if there is anything new about this problem. Thank you very much! Sincerely -Zhang -原始邮件- 发件人: "Andy Bauer" <andy.ba...@kitware.com> 发送时间: 2017年4月26日 星期三 收件人: "张驭洲" <yzhzh...@ipe.ac.cn> 抄送: "paraview@paraview.org" <paraview@paraview.org> 主题: Re: [Paraview] How to run a simulation with Catalyst and display the result using tiled display? Hi, I believe that this should be possible but I haven't done it myself so I can't guarantee that it would work. There may be some needed development involved in order to get it working properly. Andy On Tue, Apr 18, 2017 at 9:31 AM, 张驭洲 <yzhzh...@ipe.ac.cn> wrote: Hello, I want to visualize a simulation program in situ and display it using a tiled screen. I can run the simulation with Catalyst and MPI, and I can also configure ParaView for a 3x2 tiled screen. However, if I run paraview with tiled display, the control of the servers' window will be taken by paraview so I can't start the simulation program. I tried to start the simulation through ssh, but after connecting to the simulation using Catalyst, the simulation program crashed with these errors: ERROR: In /root/Desktop/ParaView-v5.2.0/VTK/Common/System/vtkSocket.cxx, line 481 vtkClientSocket (0x1f0bbb0): Socket error in call to connect. Connection refused. ERROR: In /root/Desktop/ParaView-v5.2.0/VTK/Common/System/vtkClientSocket.cxx, line 53 vtkClientSocket (0x1f0bbb0): Failed to connect to server localhost:4 ERROR: In /root/Desktop/ParaView-v5.2.0/VTK/Parallel/Core/vtkSocketCommunicator.cxx, line 714 vtkSocketCommunicator (0x3798ec0): Ca n not connect to localhost on port 4 APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6) Actually the Catalyst connecting port should be 2 and when I click "Catalyst>connect" in the GUI, it is indeed 2. I don't know why the port in the error message is 4. I noticed that if I let Catalyst to output images, there will be windows of the same number of mpi simulation processes on the server, but the windows is of the same size of the view in the GUI on the client, which sames not for tiled display. So, is it possible to display the result of in situ visualization with tiled display? Thanks a lot! -Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] How to run a simulation with Catalyst and display the result using tiled display?
Hello, I want to visualize a simulation program in situ and display it using a tiled screen. I can run the simulation with Catalyst and MPI, and I can also configure ParaView for a 3x2 tiled screen. However, if I run paraview with tiled display, the control of the servers' window will be taken by paraview so I can't start the simulation program. I tried to start the simulation through ssh, but after connecting to the simulation using Catalyst, the simulation program crashed with these errors: ERROR: In /root/Desktop/ParaView-v5.2.0/VTK/Common/System/vtkSocket.cxx, line 481 vtkClientSocket (0x1f0bbb0): Socket error in call to connect. Connection refused. ERROR: In /root/Desktop/ParaView-v5.2.0/VTK/Common/System/vtkClientSocket.cxx, line 53 vtkClientSocket (0x1f0bbb0): Failed to connect to server localhost:4 ERROR: In /root/Desktop/ParaView-v5.2.0/VTK/Parallel/Core/vtkSocketCommunicator.cxx, line 714 vtkSocketCommunicator (0x3798ec0): Can not connect to localhost on port 4 APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6) Actually the Catalyst connecting port should be 2 and when I click "Catalyst>connect" in the GUI, it is indeed 2. I don't know why the port in the error message is 4. I noticed that if I let Catalyst to output images, there will be windows of the same number of mpi simulation processes on the server, but the windows is of the same size of the view in the GUI on the client, which sames not for tiled display. So, is it possible to display the result of in situ visualization with tiled display? Thanks a lot! -Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
Re: [Paraview] How to use tiled display when the server is in off screen rendering mode?
OK, thank you for confirmation. Sincerely -Zhang -原始邮件- 发件人: "Utkarsh Ayachit" <utkarsh.ayac...@kitware.com> 发送时间: 2017年4月17日 星期一 收件人: "张驭洲" <yzhzh...@ipe.ac.cn> 抄送: ParaView <paraview@paraview.org> 主题: Re: [Paraview] How to use tiled display when the server is in off screen rendering mode? I'm using ParaView 5.2.0 in client-server mode and I want to display the rendering result using a 3x5 tiled screen. However, the GPUs of the servers are nvidia Tesla K80 and have no video output port. I can use off screen rendering to get the rendering result on the client, but I don't know how to put the result on the tiled display. I want to know if it is possible to use tiled display when the server is in off sereen rendering mode. I am afraid this use-case is not supported. You'll have to render using the on-screen GPUs i.e. GPUs connected to the tiled screen. ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] How to use tiled display when the server is in off screen rendering mode?
Hello, I'm using ParaView 5.2.0 in client-server mode and I want to display the rendering result using a 3x5 tiled screen. However, the GPUs of the servers are nvidia Tesla K80 and have no video output port. I can use off screen rendering to get the rendering result on the client, but I don't know how to put the result on the tiled display. I want to know if it is possible to use tiled display when the server is in off sereen rendering mode. Thanks a lot! Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
Re: [Paraview] How to configure ParaView 5.2.0 to use off screen rendering?
Thanks for your reply! But I don't know where the KHR/khrplatform.h is used. When I configure paraview using ccmake, the options about EGL are EGL_INCLUDE_DIR, EGL_LIBRARY, EGL_gldispatch_LIBRARY, EGL_opengl_LIBRARY, VTK_EGL_DEVICE_INDEX and VTK_USE_OFFSCREEN_EGL. In the path that I assigned to the EGL_INCLUDE_DIR, there is khrplatform.h file. What's more, I have built ParaView 5.2.0 with EGL used on another machine. That machine use NVIDIA GT 730 GPU, and in the EGL_INCLUDE_DIR path, there is not a khrplatform.h file, but the paraview can be built successfully and works. The khrplatform.h is required by the current EGL (1.5), but my EGL version is 1.4. Maybe it doesn't need that file? Thank you again! -Zhang -原始邮件- 发件人: "Dan Lipsa" <dan.li...@kitware.com> 发送时间: 2017年3月20日 星期一 收件人: "张驭洲" <yzhzh...@ipe.ac.cn> 抄送: paraview <paraview@paraview.org> 主题: Re: [Paraview] How to configure ParaView 5.2.0 to use off screen rendering? It seems you are missing KHR/khrplatform.h You can download it from the EGL website: https://www.khronos.org/registry/EGL/ On Sat, Mar 18, 2017 at 3:51 AM, 张驭洲 <yzhzh...@ipe.ac.cn> wrote: Hello, I'm building ParaView 5.2.0 on a machine that uses NVIDIA Tesla K80 GPUs. The K80 GPUs have no interface for monitor, so I have to use off screen rendering. It's said that EGL is a pretty good choice for this situation, but as I switch VTK_USE_OFFSCREEN and VTK_USE_OFFSCREEN_EGL to "ON" and then make, I get these errors: Built target vtkIOImage [ 16%] Building C object VTK/ThirdParty/glew/vtkglew/CMakeFiles/vtkglew.dir/src/glew.c.o In file included from /pan20/yzzhang/EGL/egl.h:39, from /pan20/yzzhang/ParaView-v5.2.0/VTK/ThirdParty/glew/vtkglew/src/glew.c:38: /pan20/yzzhang/EGL/eglplatform.h:37:29: error: KHR/khrplatform.h: No such file or directory In file included from /pan20/yzzhang/EGL/egl.h:39, from /pan20/yzzhang/ParaView-v5.2.0/VTK/ThirdParty/glew/vtkglew/src/glew.c:38: /pan20/yzzhang/EGL/eglplatform.h:151: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘EGLint’ In file included from /pan20/yzzhang/ParaView-v5.2.0/VTK/ThirdParty/glew/vtkglew/src/glew.c:38: /pan20/yzzhang/EGL/egl.h:121: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘EGLBoolean’ In file included from /pan20/yzzhang/ParaView-v5.2.0/VTK/ThirdParty/glew/vtkglew/src/glew.c:38: /pan20/yzzhang/EGL/egl.h:122: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘EGLBoolean’ /pan20/yzzhang/EGL/egl.h:123: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘EGLContext’ /pan20/yzzhang/EGL/egl.h:124: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘EGLSurface’ /pan20/yzzhang/EGL/egl.h:125: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘EGLSurface’ .. Maybe it is clear that there is something wrong with the EGL header file, but I don't know how to fix it. The operation system is CentOS 6.6. There is an integrated graphics and 6 K80 GPUs. I connect to the machine using ssh and have set headless X server using one of the K80 GPUs. I can run the glxgears test in the off screen mode, but I don'n know how to make sure that EGL is correctly setted. I want to know how to use EGL for off screen rendering. Any help would be highly appreciated! -Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] How to configure ParaView 5.2.0 to use off screen rendering?
Hello, I'm building ParaView 5.2.0 on a machine that uses NVIDIA Tesla K80 GPUs. The K80 GPUs have no interface for monitor, so I have to use off screen rendering. It's said that EGL is a pretty good choice for this situation, but as I switch VTK_USE_OFFSCREEN and VTK_USE_OFFSCREEN_EGL to "ON" and then make, I get these errors: Built target vtkIOImage [ 16%] Building C object VTK/ThirdParty/glew/vtkglew/CMakeFiles/vtkglew.dir/src/glew.c.o In file included from /pan20/yzzhang/EGL/egl.h:39, from /pan20/yzzhang/ParaView-v5.2.0/VTK/ThirdParty/glew/vtkglew/src/glew.c:38: /pan20/yzzhang/EGL/eglplatform.h:37:29: error: KHR/khrplatform.h: No such file or directory In file included from /pan20/yzzhang/EGL/egl.h:39, from /pan20/yzzhang/ParaView-v5.2.0/VTK/ThirdParty/glew/vtkglew/src/glew.c:38: /pan20/yzzhang/EGL/eglplatform.h:151: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘EGLint’ In file included from /pan20/yzzhang/ParaView-v5.2.0/VTK/ThirdParty/glew/vtkglew/src/glew.c:38: /pan20/yzzhang/EGL/egl.h:121: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘EGLBoolean’ In file included from /pan20/yzzhang/ParaView-v5.2.0/VTK/ThirdParty/glew/vtkglew/src/glew.c:38: /pan20/yzzhang/EGL/egl.h:122: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘EGLBoolean’ /pan20/yzzhang/EGL/egl.h:123: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘EGLContext’ /pan20/yzzhang/EGL/egl.h:124: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘EGLSurface’ /pan20/yzzhang/EGL/egl.h:125: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘EGLSurface’ .. Maybe it is clear that there is something wrong with the EGL header file, but I don't know how to fix it. The operation system is CentOS 6.6. There is an integrated graphics and 6 K80 GPUs. I connect to the machine using ssh and have set headless X server using one of the K80 GPUs. I can run the glxgears test in the off screen mode, but I don'n know how to make sure that EGL is correctly setted. I want to know how to use EGL for off screen rendering. Any help would be highly appreciated! -Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] How to save a high-resolution image that contains a selected region of the viewport?
Hello, I'm using paraview 5.2.0 to render a relatively large dataset. In the simulated region, the Z direction is much larger than that of X and Y. I want to save a high-resolution image that contains the whole simulation region, but no other regions. However, by only specifying a relatively high resolution, like 2,000*50,000, in the Save Screenshot Options dialog, I got an image that mainly contains the background, not the simulation region. I wonder if I can select the region that I want to save and specify a high resolution to get the details in the region and then save it as an image? Thanks! -Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] what is the difference between OpenGL rendering backend and OpenGL2 rendering backend when they communicate with the X Window System?
Hello, For a long time I have a problem using ParaView 5.2.0 in the client-server mode. However, at the same time, I can use ParaView 4.4.0 in this mode on the same machine. Recently I have built several different versions of ParaView, including 4.3.1, 4.4.0, 5.1.2, 5.2.0, on the same machine and with almost the same compilation options (the only difference among the buildings is the rendering backend), and I found that when built with OpenGL rendering backend, all the versions, including 5.1.2 and 5.2.0, can work normally, in both standalone mode and client-server mode. But when 5.1.2 and 5.2.0 are built with OpenGL2 rendering backend, they can't work. The machine is a node of a HPC system, so I connect to it via realVNC. If I start the paraview execuble by typing ./paraview, I get this output: Segmentation fault (core dumped) If I connect to the node via ssh, and type ./paraview , then I get: paraview: cannot connect to X server I know this is because I didn't start the X for the paraview, this test is just for comparison. If I connect to the node via ssh, and type ./paraview -display :0 , then I get: X Error: GLXBadContext 144 Extension:135 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x36001bc ERROR: In /root/Desktop/ParaView-v5.2.0/VTK/Rendering/OpenGL2/vtkOpenGLRenderWindow.cxx, line 629 vtkXOpenGLRenderWindow (0x339c550): GLEW could not be initialized. Segmentation fault (core dumped) If I connect to the node via ssh, and type ./pvserver and connect to it from the paraview GUI on my PC, then I get: Display is not accessible on the server side. Remote rendering will be disabled. This means if I dont't use the rendering feature on the node, other features of the ParaView can be used normally. If I connect to the node via ssh, and type ./pvserver -display :0, and connect to it from the paraview GUI on my PC, then I get lots of errors on the client side, like this: ERROR: In /home/buildslave/dashboards/buildbot/paraview-pvbinsdash-linux-shared-release_opengl2_qt4_superbuild/source-paraview/VTK/Common/System/vtkSocket.cxx, line 572 vtkClientSocket (0x1973c70): Socket error in call to send. Broken pipe. And on the server side, the errors are: X Error of failed request: GLXBadContext Major opcode of failed request: 135 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 28 Current serial number in output stream: 28 >From all the tests, I think it's reasonable to guess that the problem lies in >the X Window system and the OpenGL2 rendering backend. The operation system of >the node is CentOS 6.3 and the X Window System was installed using "yum >groupinstall". The GPU on the node is Tesla C2050 and the driver version is >331.67. The output from "glxinfo | grep OpenGL" is as follow: OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: Tesla C2050/PCIe/SSE2 OpenGL version string: 4.4.0 NVIDIA 331.67 OpenGL shading language version string: 4.40 NVIDIA via Cg compiler OpenGL extensions: Is there anything wrong with the setting? Why does ParaView with OpenGL rendering backend work on it but that with OpenGL2 not work? Any help or reply is highly appreciated! -Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] ParaView 5.2.0 client/server connection problem
Hello, I have a problem in using ParaView 5.2.0 in the client-server mode. Could anyone please give me a help? Firstly, the operation system on my rendering server is CentOS 6.3 and on my PC it's CentOS 6.8. I think I have built the ParaView 5.2.0 successfully from the source package from Kitware on my server, because during the processes of configure with CMake and the following make, there was no error. Then I start the pvserver on the rendering server through VNC: [root@V18 bin]# ./pvserver Waiting for client... Connection URL: cs://V18:1 Accepting connection(s): V18:1 Then I connect to the server with the paraview client GUI on my PC, which is also 5.2.0 and is built from the binary installer from Kitware. It seems that the connection is completed, but actually I get output messages from the GUI immediately like this: And the command line reads: ERROR: In /home/buildslave/dashboards/buildbot/paraview-pvbinsdash-linux-shared-release_opengl2_qt4_superbuild/source-paraview/VTK/Common/System/vtkSocket.cxx, line 572 vtkClientSocket (0x1c9aa20): Socket error in call to send. Broken pipe. And this message repeats for dozens of times. Actually they are the same of the output messages on the GUI. Then, 5 or so seconds later, antoher dialog popped up : For clicking No or Yes, the GUI shutdown or save a file that records the state of ParaView and then shutdown, respectively. On the command line of the server, it reads: Client connected. X Error of failed request: GLXBadContext Major opcode of failed request: 135 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 28 Current serial number in output stream: 28 I googled the error messages above and got many answers indicating that it's a problem about OpenGL. When I configured ParaView with Cmake, the options of VTK_RENDER_BACKEND:STRING are OpenGL,OpenGL2 and None. I have tried both OpenGL and OpenGL2 for that variable, but got the same error finally. The OpenGL version on my server is 4.4.0 and on my PC it's 4.5.0. There are GPUs on both the server and my PC so I didn't use OSMesa. Here is the output form "glxinfo | grep OpenGL" on my render server: OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: Tesla C2050/PCIe/SSE2 OpenGL version string: 4.4.0 NVIDIA 331.67 OpenGL shading language version string: 4.40 NVIDIA via Cg compiler OpenGL extensions: and on my PC, the output from "glxinfo | grep OpenGL" is: OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: GeForce GT 730/PCIe/SSE2 OpenGL version string: 4.5.0 NVIDIA 375.20 OpenGL shading language version string: 4.50 NVIDIA OpenGL extensions: Oddly, the ParaView 4.4.0 works perfectly on the same machine after the same process of configure and make. Is that because that the 5.2.0 needs some new dependent libraries that the 4.4.0 dosen't need? If you have any idea about solving this problem, please tell me. Thanks a lot! -Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] Can ParaView Catalyst be used in GPU-based simulation?
Hello, I'm using ParaView Catalyst for in situ visualization of some scientific simulation codes, mainly CFD and DEM. I have implemented a demo in which a small simulation code is interfaced with the ParaView Catalyst libraries. However, our major codes that are in use are based on GPU(written in CUDA) and the data generated by the simulation is in the memory of GPU. As far as I know, ParaView and VTK are CPU codes and in my case, I have to copy the data from memory of GPU to memory of CPU and then use Catalyst. That is not very ideal in respect of efficiency. I know there seems to be some professionals of computer visualization developing GPU-based VTK pipeline using CUDA, but I'm not computer professional and I can't use CUDA. I want to know if there is any open source GPU-based VTK pipeline, or if I do have to copy data from GPU to use Catalyst, is it worth the effort? Thanks a lot! -Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
Re: [Paraview] How to load different data files for multiple pvservers
Hi Mathieu, Thank you very much! You solved my problem perfectly! Sincerely -Zhang -原始邮件- 发件人: "Mathieu Westphal" <mathieu.westp...@kitware.com> 发送时间: 2017年1月10日 星期二 收件人: "张驭洲" <yzhzh...@ipe.ac.cn> 抄送: ParaView <paraview@paraview.org> 主题: Re: Re: [Paraview] How to load different data files for multiple pvservers Hi Sure, take a look into vtkXMLPolyDataWriter Regards Mathieu Westphal On Tue, Jan 10, 2017 at 2:56 PM, 张驭洲 <yzhzh...@ipe.ac.cn> wrote: Hi Mathieu, Thank you for the quick reply! I have some .vtp files and tried the way you told me, and got the result what I want. However, I don't know how to convert my .vtk files to .vtp files. Could you please give me more information about this? And, can I generate .vtp files from a simulation code by using some vtkwriter object? Sincerely -Zhang -原始邮件- 发件人: "Mathieu Westphal" <mathieu.westp...@kitware.com> 发送时间: 2017年1月10日 星期二 收件人: "张驭洲" <yzhzh...@ipe.ac.cn> 抄送: ParaView <paraview@paraview.org> 主题: Re: [Paraview] How to load different data files for multiple pvservers Hi It is quite simple. First convert your file to modern file type, eg .vtu , .vtp or .vti Then manually create a .pvtu/p/i with the correct syntax. Take a look at the attached file file.pvtp Regards Mathieu Westphal On Tue, Jan 10, 2017 at 12:41 PM, 张驭洲 <yzhzh...@ipe.ac.cn> wrote: Hello, I'm using ParaView for parallel visualization. My dataset is polydata, it is not "parallel aware". However, using the D3 filter, as the ParaView User's Guide says, is too expensive, which slow down the whole process significantly. As my data is generated in parallel, I want to assign these data files to multiple pvservers. For example, I have a dataset contains four files: file0.vtk, file1.vtk, file2.vtk and file3.vtk. Note that they are not temporal file series, but each represent a different area of the simulation domain. And, I start four pvservers by mpirun -np 4 ./pvserver. I can connect to the pvserver using paraview GUI on my PC, but I don't how to distribute the four files to each pvserver. I tried to select the four files using the Ctrl key and hit Apply, but it seems that they are all assigned to the process 0. Is there any way I can distribute the data files to each pvserver using the paraview GUI? Thanks a lot! -Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
Re: [Paraview] How to load different data files for multiple pvservers
Hi Mathieu, Thank you for the quick reply! I have some .vtp files and tried the way you told me, and got the result what I want. However, I don't know how to convert my .vtk files to .vtp files. Could you please give me more information about this? And, can I generate .vtp files from a simulation code by using some vtkwriter object? Sincerely -Zhang -原始邮件- 发件人: "Mathieu Westphal" <mathieu.westp...@kitware.com> 发送时间: 2017年1月10日 星期二 收件人: "张驭洲" <yzhzh...@ipe.ac.cn> 抄送: ParaView <paraview@paraview.org> 主题: Re: [Paraview] How to load different data files for multiple pvservers Hi It is quite simple. First convert your file to modern file type, eg .vtu , .vtp or .vti Then manually create a .pvtu/p/i with the correct syntax. Take a look at the attached file file.pvtp Regards Mathieu Westphal On Tue, Jan 10, 2017 at 12:41 PM, 张驭洲 <yzhzh...@ipe.ac.cn> wrote: Hello, I'm using ParaView for parallel visualization. My dataset is polydata, it is not "parallel aware". However, using the D3 filter, as the ParaView User's Guide says, is too expensive, which slow down the whole process significantly. As my data is generated in parallel, I want to assign these data files to multiple pvservers. For example, I have a dataset contains four files: file0.vtk, file1.vtk, file2.vtk and file3.vtk. Note that they are not temporal file series, but each represent a different area of the simulation domain. And, I start four pvservers by mpirun -np 4 ./pvserver. I can connect to the pvserver using paraview GUI on my PC, but I don't how to distribute the four files to each pvserver. I tried to select the four files using the Ctrl key and hit Apply, but it seems that they are all assigned to the process 0. Is there any way I can distribute the data files to each pvserver using the paraview GUI? Thanks a lot! -Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] How to load different data files for multiple pvservers
Hello, I'm using ParaView for parallel visualization. My dataset is polydata, it is not "parallel aware". However, using the D3 filter, as the ParaView User's Guide says, is too expensive, which slow down the whole process significantly. As my data is generated in parallel, I want to assign these data files to multiple pvservers. For example, I have a dataset contains four files: file0.vtk, file1.vtk, file2.vtk and file3.vtk. Note that they are not temporal file series, but each represent a different area of the simulation domain. And, I start four pvservers by mpirun -np 4 ./pvserver. I can connect to the pvserver using paraview GUI on my PC, but I don't how to distribute the four files to each pvserver. I tried to select the four files using the Ctrl key and hit Apply, but it seems that they are all assigned to the process 0. Is there any way I can distribute the data files to each pvserver using the paraview GUI? Thanks a lot! -Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
Re: [Paraview] Still Render in PV5.2.0 takes longer time than in PV4.4.0
Thank you all! I'm using Kitware's binaries and 4.4 is with OpenGL 1 and 5.2 is with OpenGL 2. Now that this option has no impact on OpenGL2 backend, is there any other option (besides those mentioned in the User's Guide) that can improve the performance of PV 5.2? In my case, by turning off the display list, the overall performance of PV 4.4 is similar to that of PV 5.2. -Zhang -原始邮件- 发件人: "Ken Martin" <ken.mar...@kitware.com> 发送时间: 2017年1月3日 星期二 收件人: "Utkarsh Ayachit" <utkarsh.ayac...@kitware.com> 抄送: "David E DeMarle" <dave.dema...@kitware.com>, "张驭洲" <yzhzh...@ipe.ac.cn>, "paraview@paraview.org" <paraview@paraview.org> 主题: Re: [Paraview] Still Render in PV5.2.0 takes longer time than in PV4.4.0 For the new OpenGL2 backend setting ImmediateModeRendering or UseDisplayLists or something similar has no impact. Those concepts are part of the legacy OpenGL API. So you should see no difference in timings with them turned on or off with the new OpenGL backend. On Tue, Jan 3, 2017 at 9:42 AM, Utkarsh Ayachit <utkarsh.ayac...@kitware.com> wrote: On Tue, Jan 3, 2017 at 9:10 AM, David E DeMarle <dave.dema...@kitware.com> wrote: > Is this with OpenGL1 or 2 back end? If you are using Kitware's binaries 4.4 > will be OpenGL1 and 5.2 will be OpenGL2. If you built from source or got it > from a distro then it might be otherwise. A way to tell which type of build you're using is to loo at the title bar. For OpenGL1, the title bar says "Legacy Rendering Backend". Such a suffix is missing for OpenGL2 build. Utkarsh ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview -- Ken Martin PhD Chairman & CFO Kitware Inc. 28 Corporate Drive Clifton Park NY 12065 518 371 3971 This communication, including all attachments, contains confidential and legally privileged information, and it is intended only for the use of the addressee. Access to this email by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken in reliance on it is prohibited and may be unlawful. If you received this communication in error please notify us immediately and destroy the original message. Thank you. ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] some more questions about Catalyst
Hi Andy, Thanks for your reply! Now I can run the CxxFullExample, but I've encountered some more problems about it. 1.The CxxFullExample has a 70x60x44 unstructured grid, and it runs relatively quickly. A truncated sample output of Timer Log is as follows: RenderView::Update, 0.161069 seconds PVTrivialProducer::GatherInformation, 0.051133 seconds vtkSMDataDeliveryManager: Deliver Geome, 0.336371 seconds FullRes Data Migration, 0.336246 seconds Still Render, 0.034509 seconds RenderView::Update, 0.149692 seconds PVTrivialProducer::GatherInformation, 0.051577 seconds vtkSMDataDeliveryManager: Deliver Geome, 0.322268 seconds FullRes Data Migration, 0.322144 seconds Still Render, 0.033618 seconds RenderView::Update, 0.156578 seconds PVTrivialProducer::GatherInformation, 0.051578 seconds vtkSMDataDeliveryManager: Deliver Geome, 0.342933 seconds FullRes Data Migration, 0.342809 seconds Still Render, 0.033976 seconds However, after I modified the grid to a 700x60x44 one and nothing else were modified, it became fairly slow when running. Also, a truncated sample output of Timer Log: RenderView::Update, 1.48987 seconds PVTrivialProducer::GatherInformation, 0.493497 seconds vtkSMRepresentationProxy::GetRepresente, 2.44198 seconds vtkSMDataDeliveryManager: Deliver Geome, 0.480933 seconds FullRes Data Migration, 0.480786 seconds Still Render, 0.116726 seconds OpenGL Dev Render, 0.020361 seconds RenderView::Update, 1.51507 seconds PVTrivialProducer::GatherInformation, 0.493821 seconds vtkSMRepresentationProxy::GetRepresente, 2.47383 seconds vtkSMDataDeliveryManager: Deliver Geome, 0.481844 seconds FullRes Data Migration, 0.481686 seconds Still Render, 0.116896 seconds OpenGL Dev Render, 0.020697 seconds RenderView::Update, 1.50415 seconds PVTrivialProducer::GatherInformation, 0.491896 seconds vtkSMRepresentationProxy::GetRepresente, 2.44277 seconds vtkSMDataDeliveryManager: Deliver Geome, 0.474105 seconds FullRes Data Migration, 0.473959 seconds Still Render, 0.114223 seconds OpenGL Dev Render, 0.020254 seconds Comparing the two outputs, I find that the time spent in some processes became about 10 times longer, as the dataset became 10 times larger, but some other processes didn't take 10 times longer time. The biggest difference is vtkSMRepresentationProxy::GetRepresente, which takes more than 2.4s per frame in the bigger dataset example while in the smaller dataset example it takes less than 0.01s per frame. I don't know what the program does in the vtkSMRepresentationProxy::GetRepresente method. Actually I only know about Still Render. Could you please give me a brief introduction to these items? And, as Catalyst is designed for in situ visualization of very large dataset, is there any method to make the example run faster? 2.When I create Catelyst Python scripts in the ParaView GUI, I have to enable all of the Live Visualization, Output to Cinema and Output rendering components i.e. views options to get live visualization of the simulation in the PV GUI, but under this setting, it generates lots of pictures, which I don't need. If I don't enable either of Output to Cinema or Output rendering components i.e. views, I could not get the live visualization, and of course no picture is generated. But what's the function of the Live Visualization option? All of the above are situations in the PV 4.4.0 in the client-server mode. As for PV 5.2, I have some problems in using it in the client-server mode. Hope you can help me. Thank you again! -Zhang -原始邮件- 发件人: "Andy Bauer" <andy.ba...@kitware.com> 发送时间: 2017年1月2日 星期一 收件人: "张驭洲" <yzhzh...@ipe.ac.cn> 抄送: "paraview@paraview.org" <paraview@paraview.org> 主题: Re: [Paraview] How to start the Catalyst example: CxxFullExample Hi, The Catalyst examples have been moved to the ParaView source repo. I'd recommend using the newest version of ParaView as well as Catalyst since there have been a lot of improvements since PV 4.4. For the CxxFullExample, if you've built it with Catalyst enabled you can run it as you've done as well as pass in Catalyst Python scripts to use through command line arguments. Andy On Fri, Dec 30, 2016 at 10:08 PM, 张驭洲 <yzhzh...@ipe.ac.cn> wrote: Hello everyone, I'm learning the ParaView Catalyst by starting at the CxxFullExample, which is one of the Catalyst examples from https://github.com/Kitware/ParaViewCatalystExampleCode-MOVED-. I have compiled and built it and got the CxxFullExample executable. It is said that it's a full example of a simulation code interfacing with Catalyst, but I don't know how to execute it. I typed "./CxxFullExample" in the command line under the build directory of the example and nothing happened. I read the Chapter 2 of the Catalyst User's Guide and found what's mainly discussed is about creating ParaView Catalyst scripts i
[Paraview] How to start the Catalyst example: CxxFullExample
Hello everyone, I'm learning the ParaView Catalyst by starting at the CxxFullExample, which is one of the Catalyst examples from https://github.com/Kitware/ParaViewCatalystExampleCode-MOVED-. I have compiled and built it and got the CxxFullExample executable. It is said that it's a full example of a simulation code interfacing with Catalyst, but I don't know how to execute it. I typed "./CxxFullExample" in the command line under the build directory of the example and nothing happened. I read the Chapter 2 of the Catalyst User's Guide and found what's mainly discussed is about creating ParaView Catalyst scripts in ParaView. It is said that to create ParaView Catalyst scripts in ParaView, I must have a representative dataset, and the Appendix 7.1.2 of the guide has a script that can be used to create the dataset. I managed to get lots of files named "filename_x_x.vtu" and "filename_x.pvtu"(x is a number) by typing "./CxxFullExample ./pvpython python.py"(python.py is the script from the appendix 7.1.2 of the user's guide) in the command line under the bin directory of ParaView 4.4.0. Then I followed the section 2.2 of the user's guide with one of the file I generated above, only to get another script. Actually, what I want is a condition shown at www.kitware.com/blog/home/post/722, but after read the section 2.3 of the user's guide, I'm still unable to implement it. How should I organize the Catalyst enabled simulation and ParaView? Can it work in the client-server mode? Can I get it to work without much knowledge of Python? Maybe I'm on the wrong way of learning Catalyst, if so, you can ignore my questions and just tell me the right way. Thanks a lot! -Zhang ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] parallel rendering is slower than single process rendering and when using D3 filter it becomes much more slower
Hi everyone, I'm using PavaView rendering a dataset which contains 5,000,000 particles. The output file of each single time step is about 172 MB in size. It takes about 100 seconds to render 9 time steps' data when using a single process,and I think it is large enough to take the advantage of parallel rendering. However, it turns out to take almost the same rendering time of single process rendering when I use "mpirun -np 8 pvserver". The dataset is polydata, so I use D3 filter to redistribute it among the 8 processes. To my disappointment, it takes almost 3 times of the rendering time of single process rendering! I'm sure there are 8 cores in my rendering server, and the remote render threshold is 20 MB. Could you tell me why the parallel rendering is so slow and how I can make it faster? Should'n it be faster than single process rendering? By the way, I'm using ParaView 4.4.0 and the operating system is CentOS 6.3. ___ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
