[Paraview] .vtp file not readable
Hi everybody, I have a problem in opening a .vtp file. When I opened from ParaView GUI, I managed to open it by choosing Legacy VTK Files (but this file is not marked as vtkImageData to be used with my filter) But when I used Python Shell and JavaScript Terminal then my .vtp file is marked File not readable. No reader found for '/myfile.vtp'. I wondered if anybody have any idea what happened? Thank you in advance. ___ 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] Parallel Streamtracer
Hello Leo, ok, I took the disk_out_ref.ex2 example data set and did some time measurements. Remember, my machine has 4 Cores + HyperThreading. My first observation is that PV seems to have a problem with distributing the data when the Multi-Core option (GUI) is enabled. When PV is started with builtin Multi-Core I was not able to apply a stream tracer with more than 1000 seed points (PV is freezing and never comes back). Otherwise, when pvserver processes has been started manually I was able to set up to 100.000 seed points. Is it a bug? Now let's have a look on the scaling performance. As you suggested, I've used the D3 filter for distributing the data along the processes. The stream tracer execution time for 10.000 seed points: ## Bulitin: 10.063 seconds ## 1 MPI-Process (no D3): 10.162 seconds ## 4 MPI-Processes: 15.615 seconds ## 8 MPI-Processes: 14.103 seconds and 100.000 seed points: ## Bulitin: 100.603 seconds ## 1 MPI-Process (no D3): 100.967 seconds ## 4 MPI-Processes: 168.1 seconds ## 8 MPI-Processes: 171.325 seconds I cannot see any positive scaling behavior here. Maybe is this example not appropriate for scaling measurements? One more thing: I've visualized the vtkProcessId and saw that the whole vector field is partitioned. I thought, that each streamline is integrated in its own process. But it seems that this is not the case. This could explain my scaling issues: In cases of small vector fields the overhead of synchronization becomes too large and decreases the overall performance. My suggestion is to have a parallel StreamTracer which is built for a single machine with several threads. Could be worth to randomly distribute the seeds over all available (local) processes? Of course, each process have access on the whole vector field. Cheers, Stephan Von: Yuanxin Liu [mailto:leo@kitware.com] Gesendet: Freitag, 1. Juni 2012 16:13 An: Stephan Rogge Cc: Andy Bauer; paraview@paraview.org Betreff: Re: [Paraview] Parallel Streamtracer Hi, Stephan, I did measure the performance at some point and was able to get fairly decent speed up with more processors. So I am surprised you are seeing huge latency. Of course, the performance is sensitive to the input. It is also sensitive to how readers distribute data. So, one thing you might want to try is to attach the D3 filter to the reader. If that doesn't help, I will be happy to get your data and take a look. Leo On Fri, Jun 1, 2012 at 1:54 AM, Stephan Rogge stephan.ro...@tu-cottbus.de wrote: Leo, As I mentioned in my initial post of this thread: I used the up-to-date master branch of ParaView. Which means I have already used your implementation. I can imagine, to parallelize this algorithm can be very tough. And I can see that distribute the calculation over 8 processes does not lead to a nice scaling. But I don't understand this huge amount of latency when using the StreamTracer in a Cave-Mode with two view ports and two pvserver processes on the same machine (extra machine for the client). I guess the tracer filter is applied for each viewport separately? This would be ok as long as both filter executions run parallel. And I doubt that this is the case. Can you help to clarify my problem? Regards, Stephan Von: Yuanxin Liu [mailto:leo@kitware.com] Gesendet: Donnerstag, 31. Mai 2012 21:33 An: Stephan Rogge Cc: Andy Bauer; paraview@paraview.org Betreff: Re: [Paraview] Parallel Streamtracer It is in the current VTK and ParaView master. The class is vtkPStreamTracer. Leo On Thu, May 31, 2012 at 3:31 PM, Stephan Rogge stephan.ro...@tu-cottbus.de wrote: Hi, Andy and Leo, thanks for your replies. Is it possible to get this new implementation? I would to give it a try. Regards, Stephan Am 31.05.2012 um 17:48 schrieb Yuanxin Liu leo@kitware.com: Hi, Stephan, The previous implementation only has serial performance: It traces the streamlines one at a time and never starts a new streamline until the previous one finishes. With communication overhead, it is not surprising it got slower. My new implementation is able to let the processes working on different streamlines simultaneously and should scale much better. Leo On Thu, May 31, 2012 at 11:27 AM, Andy Bauer andy.ba...@kitware.com wrote: Hi Stephan, The parallel stream tracer uses the partitioning of the grid to determine which process does the integration. When the streamline exits the subdomain of a process there is a search to see if it enters a subdomain assigned to any other processes before figuring it whether it has left the entire domain. Leo, copied here, has been improving the streamline implementation inside of VTK so you may want to get his newer version. It is a pretty tough algorithm to parallelize efficiently without making any assumptions on the flow or partitioning. Andy On Thu, May 31, 2012 at 4:16 AM, Stephan Rogge stephan.ro...@tu-cottbus.de wrote: Hello, I have a question related to the parallelism of
Re: [Paraview] Thresholding an image
On Thu, May 31, 2012 at 4:08 PM, David Doria daviddo...@gmail.com wrote: I am trying to look for the pixels in an image whose magnitude are above a certain value. I loaded the image, then tried to use the Threshold filter. The tooltip says Requires an attribute array with 1 component. Question 1) Would it make sense to allow this filter to operate on one of the channels of the image instead of having to extract it manually? To generate this attribute array, I used the Calculator filter to make an array called AbsX with abs(MetaImage_X). Then I applied a Threshold filter to this new array. The values in this array are in [0 512]. When I leave the Lower Threshold all the way down and the Upper Threshold all the way up, I can view the image just fine. In the Display tab, the Color By is set to AbsX, like I want. However, as soon as I move the Lower Threshold slider, the image disappears. When I look in the Display tab, the only option for Color By is now Solid Color. Question 2) Why would the Color By options change based on the threshold that is set? (I'd also ask why the image is disappearing, but I think it might have to do with the coloring). If I then try to glyph the output of the threshold filter (to draw spheres or something at the location of the pixels that remain), the Scalars option of the glyphs shows my AbsX array, but it is not enabled. The only choice is under Vectors, and it is my MetaImage array. Question 3) Why can I not glyph the AbsX array? Sorry for the long winded question, but hopefully someone can shed some light on these issues! Thanks, David Any thoughts on this? Is it just impossible, or am I missing something? David ___ 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] .vtp file not readable
On Mon, Jun 4, 2012 at 4:09 AM, Tuan Ha Tran tuan-ha.t...@insa-lyon.frwrote: Hi everybody, I have a problem in opening a .vtp file. When I opened from ParaView GUI, I managed to open it by choosing Legacy VTK Files (but this file is not marked as vtkImageData to be used with my filter) But when I used Python Shell and JavaScript Terminal then my .vtp file is marked File not readable. No reader found for '/myfile.vtp'. I wondered if anybody have any idea what happened? Thank you in advance Sounds like the contents of the file are not actually in vtp format (i.e. written with vtkXMLPolyDataWriter). Maybe you used vtkPolyDataWriter to write a .vtp instead of .vtk? Or if you are storing vtkImageData, you should have probably used vtkXMLImageDataWriter to write a .vti. David ___ 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] .vtp file not readable
Maybe this is not the cause, but /myfile.vtp is not a correct path, it should read ../myfile.vtp or ../../myfile.vtp You might check your script. Best regards / Cordialmente, William-Fernando Oquendo -- Este correo puede carecer de tildes o eñes debido al teclado. On Mon, Jun 4, 2012 at 6:52 AM, David Doria daviddo...@gmail.com wrote: On Mon, Jun 4, 2012 at 4:09 AM, Tuan Ha Tran tuan-ha.t...@insa-lyon.frwrote: Hi everybody, I have a problem in opening a .vtp file. When I opened from ParaView GUI, I managed to open it by choosing Legacy VTK Files (but this file is not marked as vtkImageData to be used with my filter) But when I used Python Shell and JavaScript Terminal then my .vtp file is marked File not readable. No reader found for '/myfile.vtp'. I wondered if anybody have any idea what happened? Thank you in advance Sounds like the contents of the file are not actually in vtp format (i.e. written with vtkXMLPolyDataWriter). Maybe you used vtkPolyDataWriter to write a .vtp instead of .vtk? Or if you are storing vtkImageData, you should have probably used vtkXMLImageDataWriter to write a .vti. David ___ 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] .vtp file not readable
Thank you all for your reply. I don't quite understand where the problem is from. The .vtp file is readable, but I have to choose the vtkReader for it (there is a window of readers' list appears and I chose Legacy VTK files), so, for me, this is perhaps the problem of paraView or something like that. Because with .vtp file, it can't find the right reader to use. So why there is that error No reader found for /home/thtran/myfile.vtp with python shell and JavaScript Terminal (I'm sorry, I didn't mention that I used the full path to the file) '- Original Message - From: William Oquendo woque...@gmail.com To: David Doria daviddo...@gmail.com Cc: Tuan Ha Tran tuan-ha.t...@insa-lyon.fr, paraview@paraview.org Sent: Mon, 04 Jun 2012 15:15:18 +0200 (CEST) Subject: Re: [Paraview] .vtp file not readable Maybe this is not the cause, but /myfile.vtp is not a correct path, it should read ../myfile.vtp or ../../myfile.vtp You might check your script. Best regards / Cordialmente, William-Fernando Oquendo--Este correo puede carecer de tildes o eñes debido al teclado. On Mon, Jun 4, 2012 at 6:52 AM, David Doria daviddo...@gmail.com wrote: On Mon, Jun 4, 2012 at 4:09 AM, Tuan Ha Tran tuan-ha.t...@insa-lyon.fr wrote: Hi everybody, I have a problem in opening a .vtp file. When I opened from ParaView GUI, I managed to open it by choosing Legacy VTK Files (but this file is not marked as vtkImageData to be used with my filter) But when I used Python Shell and JavaScript Terminal then my .vtp file is marked File not readable. No reader found for '/myfile.vtp'. I wondered if anybody have any idea what happened? Thank you in advance Sounds like the contents of the file are not actually in vtp format (i.e. written with vtkXMLPolyDataWriter). Maybe you used vtkPolyDataWriter to write a .vtp instead of .vtk? Or if you are storing vtkImageData, you should have probably used vtkXMLImageDataWriter to write a .vti. David ___ 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] .vtp file not readable
On Mon, Jun 4, 2012 at 9:41 AM, Tuan Ha Tran tuan-ha.t...@insa-lyon.frwrote: Thank you all for your reply. I don't quite understand where the problem is from. The .vtp file is readable, but I have to choose the vtkReader for it (there is a window of readers' list appears and I chose Legacy VTK files), so, for me, this is perhaps the problem of paraView or something like that. Because with .vtp file, it can't find the right reader to use. So why there is that error No reader found for /home/thtran/myfile.vtp with python shell and JavaScript Terminal (I'm sorry, I didn't mention that I used the full path to the file) I believe if the file data does not match the file extension, Paraview gives you the option to tell it what the file actually contains. Like I said, if you choose Legacy VTK and it works, then the file should have actually been named .vtk instead of .vtp. David ___ 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] .xyz file loading very slow
Hey, I use the .xyz format to have my atoms from Molecular Dynamics plotted. The Point Spirit extension works fast and responsive but loading takes for ever. Trying different file sizes, I figured out that the loading time (i.e. after hitting the Apply button until I get a first representation) scales beautifully with t[sec]=37e-9*numAtoms^2 on my CPU for numAtoms=2..20. I wonder, why is there *quadratic* scaling in *loading*? (which really is a bummer in MD simulations which typically use more than 1e6. My small test run with 2e5 atoms, I had to wait 1/2 hour.) Thanks a lot for your insight. Steffen P.S. Coincidentally, printing an Excel chart took also 1/2 hour on a 286 twenty years ago. Perhaps 1/2hour is a global constant for waiting duration. ;-) ___ 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] .vtp file not readable
Yeah, that is exactly what you said. I changed the .vtp into .vtk and that works Thank you. - Original Message - From: David Doria daviddo...@gmail.com To: Tuan Ha Tran tuan-ha.t...@insa-lyon.fr Cc: paraview@paraview.org Sent: Mon, 04 Jun 2012 15:43:55 +0200 (CEST) Subject: Re: [Paraview] .vtp file not readable On Mon, Jun 4, 2012 at 9:41 AM, Tuan Ha Tran tuan-ha.t...@insa-lyon.fr wrote: Thank you all for your reply. I don't quite understand where the problem is from. The .vtp file is readable, but I have to choose the vtkReader for it (there is a window of readers' list appears and I chose Legacy VTK files), so, for me, this is perhaps the problem of paraView or something like that. Because with .vtp file, it can't find the right reader to use. So why there is that error No reader found for /home/thtran/myfile.vtp with python shell and JavaScript Terminal (I'm sorry, I didn't mention that I used the full path to the file) I believe if the file data does not match the file extension, Paraview gives you the option to tell it what the file actually contains. Like I said, if you choose Legacy VTK and it works, then the file should have actually been named .vtk instead of .vtp. David ___ 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] vtkXOpenGLRenderWindow Error
Hi all, I've been trying to solve the problem. I found an important setting about it. Our ParaView is running on shared Linux cluster, so we operate ParaView with VNC Client. My VNC setting is very simple as below: vncviewer -geometry [width]x[height] But other users' settings are little different: vncviewer -geometry [width]x[height] -depth 32 The -depth option is critical. Maybe this option influences OpenGL setting of VNC, and ParaView gets into GLX errors. I suggested removing -depth option and restarting VNC server, then our ParaView executed perfectly. Magician On 2012/06/01, at 12:58, Magician wrote: Hi all, I was trying to build ParaView on CentOS. It looked OK, but today other users on our machine tried to run ParaView, they got errors as below: ERROR: In /home/magician/ParaView-3.14.1-Source/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 404 vtkXOpenGLRenderWindow (0x2d2e410): Could not find a decent visual ERROR: In /home/magician/ParaView-3.14.1-Source/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 404 vtkXOpenGLRenderWindow (0x2d2e410): Could not find a decent visual X Error: BadValue (integer parameter out of range for operation) 2 Extension:146 (Uknown extension) Minor opcode: 3 (Unknown request) Resource id: 0x22 ERROR: In /home/magician/ParaView-3.14.1-Source/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 629 vtkXOpenGLRenderWindow (0x2d2e410): Cannot create GLX context. Aborting. Maybe our ParaView tried to access my home directory from other users, these errors are dumped. I checked my CMakeCache again, and I found these parameters: VTK_GLEXT_FILE: /home/magician/ParaView-3.14.1-Source/VTK/Utilities/ParseOGLExt/headers/glext.h VTK_GLXEXT_FILE: /home/magician/ParaView-3.14.1-Source/VTK/Utilities/ParseOGLExt/headers/glxext.h VTK_MATERIAL_DIRS: /home/magician/ParaView-bin/VTK/Utilities/MaterialLibrary/Repository VTK_WGLEXT_FILE: /home/magician/ParaView-3.14.1-Source/VTK/Utilities/ParseOGLExt/headers/wglext.h VTK_WRAP_HINTS: /home/magician/ParaView-3.14.1-Source/VTK/Wrapping/hints Maybe our ParaView's build setting depends on original source data on my home directory, but it's not good for using many users. Which is the best way to change our GL settings? Magician ___ 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] Save Data with Python
Hi all, I'm trying to save transient sources with Python scripts. I'd like to save with these formats: - VTK MultiBlock Formats (*.vtm) - ASCII-XML Formats - Save all timesteps I tried Trace tool, but it couldn't catch Save Data processes. How can I save data with Python scripts? Magician ___ 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] Parallel Streamtracer
Hi, Stephan, I will look into the multi-core issue as well as the performance issue. Some quick answers: - Yes, the whole vector fields are partitioned and the streamlines are passed from one process to another. This is why the performance can be highly sensitive to how data are distributed and how the streamlines travel between data partitions. - Your suggestion makes sense if the data is small enough to be run on a single machine. This is definitely something we would like to do in the future. Right now, the implementation is more targeted towards handling large data that have to be distributed across multiple machines. Leo On Mon, Jun 4, 2012 at 5:21 AM, Stephan Rogge stephan.ro...@tu-cottbus.dewrote: Hello Leo, ok, I took the disk_out_ref.ex2 example data set and did some time measurements. Remember, my machine has 4 Cores + HyperThreading. My first observation is that PV seems to have a problem with distributing the data when the Multi-Core option (GUI) is enabled. When PV is started with builtin Multi-Core I was not able to apply a stream tracer with more than 1000 seed points (PV is freezing and never comes back). Otherwise, when pvserver processes has been started manually I was able to set up to 100.000 seed points. Is it a bug? Now let's have a look on the scaling performance. As you suggested, I've used the D3 filter for distributing the data along the processes. The stream tracer execution time for 10.000 seed points: ## Bulitin: 10.063 seconds ## 1 MPI-Process (no D3): 10.162 seconds ## 4 MPI-Processes: 15.615 seconds ## 8 MPI-Processes: 14.103 seconds and 100.000 seed points: ## Bulitin: 100.603 seconds ## 1 MPI-Process (no D3): 100.967 seconds ## 4 MPI-Processes: 168.1 seconds ## 8 MPI-Processes: 171.325 seconds I cannot see any positive scaling behavior here. Maybe is this example not appropriate for scaling measurements? One more thing: I've visualized the vtkProcessId and saw that the whole vector field is partitioned. I thought, that each streamline is integrated in its own process. But it seems that this is not the case. This could explain my scaling issues: In cases of small vector fields the overhead of synchronization becomes too large and decreases the overall performance. My suggestion is to have a parallel StreamTracer which is built for a single machine with several threads. Could be worth to randomly distribute the seeds over all available (local) processes? Of course, each process have access on the whole vector field. Cheers, Stephan Von: Yuanxin Liu [mailto:leo@kitware.com] Gesendet: Freitag, 1. Juni 2012 16:13 An: Stephan Rogge Cc: Andy Bauer; paraview@paraview.org Betreff: Re: [Paraview] Parallel Streamtracer Hi, Stephan, I did measure the performance at some point and was able to get fairly decent speed up with more processors. So I am surprised you are seeing huge latency. Of course, the performance is sensitive to the input. It is also sensitive to how readers distribute data. So, one thing you might want to try is to attach the D3 filter to the reader. If that doesn't help, I will be happy to get your data and take a look. Leo On Fri, Jun 1, 2012 at 1:54 AM, Stephan Rogge stephan.ro...@tu-cottbus.de wrote: Leo, As I mentioned in my initial post of this thread: I used the up-to-date master branch of ParaView. Which means I have already used your implementation. I can imagine, to parallelize this algorithm can be very tough. And I can see that distribute the calculation over 8 processes does not lead to a nice scaling. But I don't understand this huge amount of latency when using the StreamTracer in a Cave-Mode with two view ports and two pvserver processes on the same machine (extra machine for the client). I guess the tracer filter is applied for each viewport separately? This would be ok as long as both filter executions run parallel. And I doubt that this is the case. Can you help to clarify my problem? Regards, Stephan Von: Yuanxin Liu [mailto:leo@kitware.com] Gesendet: Donnerstag, 31. Mai 2012 21:33 An: Stephan Rogge Cc: Andy Bauer; paraview@paraview.org Betreff: Re: [Paraview] Parallel Streamtracer It is in the current VTK and ParaView master. The class is vtkPStreamTracer. Leo On Thu, May 31, 2012 at 3:31 PM, Stephan Rogge stephan.ro...@tu-cottbus.de wrote: Hi, Andy and Leo, thanks for your replies. Is it possible to get this new implementation? I would to give it a try. Regards, Stephan Am 31.05.2012 um 17:48 schrieb Yuanxin Liu leo@kitware.com: Hi, Stephan, The previous implementation only has serial performance: It traces the streamlines one at a time and never starts a new streamline until the previous one finishes. With communication overhead, it is not surprising it got slower. My new implementation is able to let the processes working on different streamlines
