Segfault when loading PVTU

[WEsToMIL]

Hi

I have a particle dataset of ~7Mio particles and 80 visualization timesteps, each split over 64 vtu files connected via one pvtu file per vis-timestep (so 80*64+64 Files). Each vtu File is about 20 MB.

When I try to load all of this into ParaView and apply a 2D glyph visualization of the particles, first everything goes smoothly, but when I jump to the last timestep the application crashes with a segfault. The crash also immediately happens when I only load the pvtu of one of the last steps and nothing else. As far as I can tell, the data files are not corrupt, but it’s kind of hard to manually inspect a 64 20MB files…

ParaView Version: 5.11.1
OS: Ubuntu 20.04.5 LTS x86_64
RAM: 32 GB
GPU: RTX 5000 (16 GB)

Attached is the output when running with paraview -l=output.log,TRACE
output.log (529.7 KB)

Here is the data from the last timestep that crashes for me:

lastTimestep.7z

[ben.boeckel (Ben Boeckel (Kitware))]

@mwestphal ?

[mwestphal (Mathieu Westphal (Kitware))]

Transfer expired

Please reupload @WEsToMIL

[WEsToMIL]

@mwestphal
New Link, same data

[mwestphal (Mathieu Westphal (Kitware))]

@WEsToMIL

The crash also immediately happens when I only load the pvtu of one of the last steps and nothing else.

I can happen the provided file without issue:

[WEsToMIL]

Cool. I can’t. Neither with paraview nor paraview --mesa and neither on the above-mentioned Ubuntu workstation, where I installed ParaView from here, nor on an Arch laptop, with only an IGPU, where I installed ParaView from the repositories.

Any hints on what I can do or where the problem might come from?

[mwestphal (Mathieu Westphal (Kitware))]

That doesn’t make much sense. I’m using the binary release too, same version, on archlinux too.

I cant really help if I do not reproduce, next step would be to run in debug, so you would need to compile ParaView yourself.

[WEsToMIL]

Interesting things are happening… I compiled ParaView on the workstation from the sources linked from the download page, using this archive. My steps to build and run were:

cd Paraview-v5.11.1
mdkir myBuild && cd myBuild
cmake -DCMAKE_BUILD_TYPE=Debug ..
make
bin/paraview -l ${PWD}/output.log,TRACE

With this new version, I too can load and visualize this one timestep. (I was using the Point Gaussian representation without any filter). However, when I jump to another timestep ParaView crashes again.

In this archive, you can find two timesteps. Jumping between them reliably crashes ParaView for me (binary version as well as manually built in debug or release).

This is the log dump I get after a crash.

output.7z (265.7 KB)

As far as I can tell from htop and nvidia-smi neither RAM nor VRAM are at dangerous levels at the time of the crash.

[mwestphal (Mathieu Westphal (Kitware))]

I confirm the segfault. The stacktrace is hard to exploit in order to figure out what is going on.

corrupted size vs. prev_size

Thread 1 "paraview" received signal SIGABRT, Aborted.
0x00007ffff7e3e26c in ?? () from /usr/lib/libc.so.6
(gdb) bt
#0  0x00007ffff7e3e26c in ?? () from /usr/lib/libc.so.6
#1  0x00007ffff7deea08 in raise () from /usr/lib/libc.so.6
#2  0x00007ffff7dd7538 in abort () from /usr/lib/libc.so.6
#3  0x00007ffff7dd82db in ?? () from /usr/lib/libc.so.6
#4  0x00007ffff7e481b7 in ?? () from /usr/lib/libc.so.6
#5  0x00007ffff7e48cce in ?? () from /usr/lib/libc.so.6
#6  0x00007ffff7e48e40 in ?? () from /usr/lib/libc.so.6
#7  0x00007ffff7e4a400 in ?? () from /usr/lib/libc.so.6
#8  0x00007ffff7e4ccb3 in free () from /usr/lib/libc.so.6
#9  0x00007ffff4ea9f25 in vtkXMLDataParserFreeAsciiBuffer<float> (buffer=0x555584edb130) at /home/glow/dev/paraview/pv1/src/VTK/IO/XMLParser/vtkXMLDataParser.cxx:1318
#10 0x00007ffff4ea5aa7 in vtkXMLDataParser::FreeAsciiBuffer (this=0x55555fdfbc20) at /home/glow/dev/paraview/pv1/src/VTK/IO/XMLParser/vtkXMLDataParser.cxx:1327
#11 0x00007ffff4ea043a in vtkXMLDataParser::~vtkXMLDataParser (this=0x55555fdfbc20, __in_chrg=<optimized out>) at /home/glow/dev/paraview/pv1/src/VTK/IO/XMLParser/vtkXMLDataParser.cxx:94
#12 0x00007ffff4ea0462 in vtkXMLDataParser::~vtkXMLDataParser (this=0x55555fdfbc20, __in_chrg=<optimized out>) at /home/glow/dev/paraview/pv1/src/VTK/IO/XMLParser/vtkXMLDataParser.cxx:96
#13 0x00007fffedeb6d19 in vtkObjectBase::UnRegisterInternal (this=0x55555fdfbc20, check=0) at /home/glow/dev/paraview/pv1/src/VTK/Common/Core/vtkObjectBase.cxx:345
#14 0x00007fffedeb466f in vtkObject::UnRegisterInternal (this=0x55555fdfbc20, o=0x0, check=0) at /home/glow/dev/paraview/pv1/src/VTK/Common/Core/vtkObject.cxx:927
#15 0x00007fffedeb6bb3 in vtkObjectBase::UnRegister (this=0x55555fdfbc20, o=0x0) at /home/glow/dev/paraview/pv1/src/VTK/Common/Core/vtkObjectBase.cxx:300
#16 0x00007fffedeb6838 in vtkObjectBase::Delete (this=0x55555fdfbc20) at /home/glow/dev/paraview/pv1/src/VTK/Common/Core/vtkObjectBase.cxx:239
#17 0x00007ffff3f3f98a in vtkXMLReader::DestroyXMLParser (this=0x55555f501930) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLReader.cxx:433
#18 0x00007ffff3eed366 in vtkXMLDataReader::DestroyXMLParser (this=0x55555f501930) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLDataReader.cxx:102
#19 0x00007ffff3eed174 in vtkXMLDataReader::~vtkXMLDataReader (this=0x55555f501930, __in_chrg=<optimized out>) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLDataReader.cxx:69
#20 0x00007ffff3f65f92 in vtkXMLUnstructuredDataReader::~vtkXMLUnstructuredDataReader (this=0x55555f501930, __in_chrg=<optimized out>) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLUnstructuredDataReader.cxx:93
#21 0x00007ffff3f747ae in vtkXMLUnstructuredGridReader::~vtkXMLUnstructuredGridReader (this=0x55555f501930, __in_chrg=<optimized out>) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLUnstructuredGridReader.cxx:49
#22 0x00007ffff3f747ca in vtkXMLUnstructuredGridReader::~vtkXMLUnstructuredGridReader (this=0x55555f501930, __in_chrg=<optimized out>) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLUnstructuredGridReader.cxx:49
#23 0x00007fffedeb6d19 in vtkObjectBase::UnRegisterInternal (this=0x55555f501930, check=0) at /home/glow/dev/paraview/pv1/src/VTK/Common/Core/vtkObjectBase.cxx:345
#24 0x00007fffedeb466f in vtkObject::UnRegisterInternal (this=0x55555f501930, o=0x7fffffffa2f0, check=0) at /home/glow/dev/paraview/pv1/src/VTK/Common/Core/vtkObject.cxx:927
#25 0x00007fffeddebe4b in vtkGarbageCollectorToObjectBaseFriendship::UnRegister (obj=0x55555f501930, from=0x7fffffffa2f0) at /home/glow/dev/paraview/pv1/src/VTK/Common/Core/vtkGarbageCollector.cxx:141
#26 0x00007fffedde9e46 in vtkGarbageCollectorImpl::CollectComponent (this=0x7fffffffa2f0, c=0x55555fdebc20) at /home/glow/dev/paraview/pv1/src/VTK/Common/Core/vtkGarbageCollector.cxx:702
#27 0x00007fffedde8d94 in vtkGarbageCollectorImpl::CollectInternal (this=0x7fffffffa2f0, root=0x55555f501930) at /home/glow/dev/paraview/pv1/src/VTK/Common/Core/vtkGarbageCollector.cxx:480
#28 0x00007fffeddeb3a9 in vtkGarbageCollector::Collect (root=0x55555f501930) at /home/glow/dev/paraview/pv1/src/VTK/Common/Core/vtkGarbageCollector.cxx:899
#29 0x00007fffedeb6d2d in vtkObjectBase::UnRegisterInternal (this=0x55555f501930, check=1) at /home/glow/dev/paraview/pv1/src/VTK/Common/Core/vtkObjectBase.cxx:353
#30 0x00007fffedeb466f in vtkObject::UnRegisterInternal (this=0x55555f501930, o=0x0, check=1) at /home/glow/dev/paraview/pv1/src/VTK/Common/Core/vtkObject.cxx:927
#31 0x00007fffedeb6bb3 in vtkObjectBase::UnRegister (this=0x55555f501930, o=0x0) at /home/glow/dev/paraview/pv1/src/VTK/Common/Core/vtkObjectBase.cxx:300
#32 0x00007fffedeb6838 in vtkObjectBase::Delete (this=0x55555f501930) at /home/glow/dev/paraview/pv1/src/VTK/Common/Core/vtkObjectBase.cxx:239
#33 0x00007ffff3f2417e in vtkXMLPDataReader::DestroyPieces (this=0x5555571eae30) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLPDataReader.cxx:276
#34 0x00007ffff3f22f02 in vtkXMLPDataObjectReader::SetupPieces (this=0x5555571eae30, numPieces=64) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLPDataObjectReader.cxx:161
#35 0x00007ffff3f2404a in vtkXMLPDataReader::SetupPieces (this=0x5555571eae30, numPieces=64) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLPDataReader.cxx:253
#36 0x00007ffff3f23f8c in vtkXMLPDataReader::ReadPrimaryElement (this=0x5555571eae30, ePrimary=0x5555884ff350) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLPDataReader.cxx:233
#37 0x00007ffff3f32dc7 in vtkXMLPUnstructuredDataReader::ReadPrimaryElement (this=0x5555571eae30, ePri=0x5555884ff350) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLPUnstructuredDataReader.cxx:231
#38 0x00007ffff3f429cc in vtkXMLReader::ReadVTKFile (this=0x5555571eae30, eVTKFile=0x555559a8d7e0) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLReader.cxx:1013
#39 0x00007ffff3f401ca in vtkXMLReader::ReadXMLInformation (this=0x5555571eae30) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLReader.cxx:509
#40 0x00007ffff3f22eca in vtkXMLPDataObjectReader::ReadXMLInformation (this=0x5555571eae30) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLPDataObjectReader.cxx:153
#41 0x00007ffff3f4074b in vtkXMLReader::RequestInformation (this=0x5555571eae30, request=0x555586a07340, outputVector=0x555586a07750) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLReader.cxx:570
#42 0x00007ffff3f33f45 in vtkXMLPUnstructuredDataReader::RequestInformation (this=0x5555571eae30, request=0x555586a07340, inputVector=0x0, outputVector=0x555586a07750) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLPUnstructuredDataReader.cxx:394
#43 0x00007ffff3f47dd5 in vtkXMLReader::ProcessRequest (this=0x5555571eae30, request=0x555586a07340, inputVector=0x0, outputVector=0x555586a07750) at /home/glow/dev/paraview/pv1/src/VTK/IO/XML/vtkXMLReader.cxx:2019
#44 0x00007fffee9a0e00 in vtkFileSeriesReader::RequestInformationForInput (this=0x555557ec8ee0, index=1, request=0x0, outputVector=0x0) at /home/glow/dev/paraview/pv1/src/VTKExtensions/IOCore/vtkFileSeriesReader.cxx:788
#45 0x00007fffee9a09ea in vtkFileSeriesReader::RequestUpdateExtent (this=0x555557ec8ee0, request=0x555588495920, outputVector=0x555559825b70) at /home/glow/dev/paraview/pv1/src/VTKExtensions/IOCore/vtkFileSeriesReader.cxx:701
#46 0x00007fffee99fcba in vtkFileSeriesReader::ProcessRequest (this=0x555557ec8ee0, request=0x555588495920, inputVector=0x0, outputVector=0x555559825b70) at /home/glow/dev/paraview/pv1/src/VTKExtensions/IOCore/vtkFileSeriesReader.cxx:548
#47 0x00007ffff088b6d9 in vtkExecutive::CallAlgorithm (this=0x5555578ed320, request=0x555588495920, direction=0, inInfo=0x0, outInfo=0x555559825b70) at /home/glow/dev/paraview/pv1/src/VTK/Common/ExecutionModel/vtkExecutive.cxx:735
#48 0x00007ffff09c9760 in vtkStreamingDemandDrivenPipeline::ProcessRequest (this=0x5555578ed320, request=0x555588495920, inInfoVec=0x0, outInfoVec=0x555559825b70) at /home/glow/dev/paraview/pv1/src/VTK/Common/ExecutionModel/vtkStreamingDemandDrivenPipeline.cxx:320
#49 0x00007ffff0877a43 in vtkCompositeDataPipeline::ForwardUpstream (this=0x555559811210, request=0x555588495920) at /home/glow/dev/paraview/pv1/src/VTK/Common/ExecutionModel/vtkCompositeDataPipeline.cxx:733
#50 0x00007ffff09c9799 in vtkStreamingDemandDrivenPipeline::ProcessRequest (this=0x555559811210, request=0x555588495920, inInfoVec=0x55555f97f200, outInfoVec=0x555557f2bc30) at /home/glow/dev/paraview/pv1/src/VTK/Common/ExecutionModel/vtkStreamingDemandDrivenPipeline.cxx:325
#51 0x00007ffff0877a43 in vtkCompositeDataPipeline::ForwardUpstream (this=0x555557c62b90, request=0x555588495920) at /home/glow/dev/paraview/pv1/src/VTK/Common/ExecutionModel/vtkCompositeDataPipeline.cxx:733
#52 0x00007ffff09c9799 in vtkStreamingDemandDrivenPipeline::ProcessRequest (this=0x555557c62b90, request=0x555588495920, inInfoVec=0x555586a53a00, outInfoVec=0x555555d48290) at /home/glow/dev/paraview/pv1/src/VTK/Common/ExecutionModel/vtkStreamingDemandDrivenPipeline.cxx:325
#53 0x00007ffff0877a43 in vtkCompositeDataPipeline::ForwardUpstream (this=0x55555f9ce3b0, request=0x555588495920) at /home/glow/dev/paraview/pv1/src/VTK/Common/ExecutionModel/vtkCompositeDataPipeline.cxx:733
#54 0x00007ffff09c9799 in vtkStreamingDemandDrivenPipeline::ProcessRequest (this=0x55555f9ce3b0, request=0x555588495920, inInfoVec=0x555555b568b0, outInfoVec=0x555555b03eb0) at /home/glow/dev/paraview/pv1/src/VTK/Common/ExecutionModel/vtkStreamingDemandDrivenPipeline.cxx:325
#55 0x00007ffff0877a43 in vtkCompositeDataPipeline::ForwardUpstream (this=0x5555878dd560, request=0x555588495920) at /home/glow/dev/paraview/pv1/src/VTK/Common/ExecutionModel/vtkCompositeDataPipeline.cxx:733
#56 0x00007fffeac54006 in vtkPVDataRepresentationPipeline::ForwardUpstream (this=0x5555878dd560, request=0x555588495920) at /home/glow/dev/paraview/pv1/src/Remoting/Views/vtkPVDataRepresentationPipeline.cxx:52
#57 0x00007ffff09c9799 in vtkStreamingDemandDrivenPipeline::ProcessRequest (this=0x5555878dd560, request=0x555588495920, inInfoVec=0x555587873110, outInfoVec=0x555587a55260) at /home/glow/dev/paraview/pv1/src/VTK/Common/ExecutionModel/vtkStreamingDemandDrivenPipeline.cxx:325
#58 0x00007fffeac54094 in vtkPVDataRepresentationPipeline::ProcessRequest (this=0x5555878dd560, request=0x555588495920, inInfo=0x555587873110, outInfo=0x555587a55260) at /home/glow/dev/paraview/pv1/src/Remoting/Views/vtkPVDataRepresentationPipeline.cxx:68
#59 0x00007ffff09caefd in vtkStreamingDemandDrivenPipeline::PropagateUpdateExtent (this=0x5555878dd560, outputPort=-1) at /home/glow/dev/paraview/pv1/src/VTK/Common/ExecutionModel/vtkStreamingDemandDrivenPipeline.cxx:710
#60 0x00007ffff09c9be3 in vtkStreamingDemandDrivenPipeline::Update (this=0x5555878dd560, port=-1, requests=0x0) at /home/glow/dev/paraview/pv1/src/VTK/Common/ExecutionModel/vtkStreamingDemandDrivenPipeline.cxx:415
#61 0x00007ffff09c9abb in vtkStreamingDemandDrivenPipeline::Update (this=0x5555878dd560, port=-1) at /home/glow/dev/paraview/pv1/src/VTK/Common/ExecutionModel/vtkStreamingDemandDrivenPipeline.cxx:381
#62 0x00007ffff086974e in vtkAlgorithm::Update (this=0x555586638f80, port=-1) at /home/glow/dev/paraview/pv1/src/VTK/Common/ExecutionModel/vtkAlgorithm.cxx:1492
#63 0x00007ffff0869719 in vtkAlgorithm::Update (this=0x555586638f80) at /home/glow/dev/paraview/pv1/src/VTK/Common/ExecutionModel/vtkAlgorithm.cxx:1486
#64 0x00007fffeac51f83 in vtkPVDataRepresentation::ProcessViewRequest (this=0x555586638f80, request=0x5555556c7ff0) at /home/glow/dev/paraview/pv1/src/Remoting/Views/vtkPVDataRepresentation.cxx:157
#65 0x00007fffeabaca90 in vtkGeometryRepresentation::ProcessViewRequest (this=0x555586638f80, request_type=0x5555556c7ff0, inInfo=0x555557a49e20, outInfo=0x555587cef310) at /home/glow/dev/paraview/pv1/src/Remoting/Views/vtkGeometryRepresentation.cxx:373
#66 0x00007fffeabbfec1 in vtkGeometryRepresentationWithFaces::ProcessViewRequest (this=0x555586638f80, request_type=0x5555556c7ff0, inInfo=0x555557a49e20, outInfo=0x555587cef310) at /home/glow/dev/paraview/pv1/src/Remoting/Views/vtkGeometryRepresentationWithFaces.cxx:62
#67 0x00007fffead44d41 in vtkPVView::CallProcessViewRequest (this=0x555557d87a00, type=0x5555556c7ff0, inInfo=0x555557a49e20, outVec=0x555557d5e150) at /home/glow/dev/paraview/pv1/src/Remoting/Views/vtkPVView.cxx:582
#68 0x00007fffead445af in vtkPVView::Update (this=0x555557d87a00) at /home/glow/dev/paraview/pv1/src/Remoting/Views/vtkPVView.cxx:467
#69 0x00007fffeacee6a5 in vtkPVRenderView::Update (this=0x555557d87a00) at /home/glow/dev/paraview/pv1/src/Remoting/Views/vtkPVRenderView.cxx:1358
#70 0x00007fffeb5d8c3c in vtkPVRenderViewCommand (arlu=0x555555a3fa30, ob=0x555557d87a00, method=0x55558d8e0cf9 "Update", msg=..., resultStream=...) at /home/glow/dev/paraview/pv1/build/CMakeFiles/vtkRemotingViewsCS/vtkPVRenderViewClientServer.cxx:1843
#71 0x00007ffff57b2388 in vtkClientServerInterpreter::CallCommandFunction (this=0x555555a3fa30, cname=0x7fffeaeaa60b "vtkPVRenderView", ptr=0x555557d87a00, method=0x55558d8e0cf9 "Update", msg=..., result=...) at /home/glow/dev/paraview/pv1/src/Remoting/ClientServerStream/vtkClientServerInterpreter.cxx:810
#72 0x00007ffff57b0653 in vtkClientServerInterpreter::ProcessCommandInvoke (this=0x555555a3fa30, css=..., midx=1) at /home/glow/dev/paraview/pv1/src/Remoting/ClientServerStream/vtkClientServerInterpreter.cxx:424
#73 0x00007ffff57afacc in vtkClientServerInterpreter::ProcessOneMessage (this=0x555555a3fa30, css=..., message=1) at /home/glow/dev/paraview/pv1/src/Remoting/ClientServerStream/vtkClientServerInterpreter.cxx:265
#74 0x00007ffff57af92f in vtkClientServerInterpreter::ProcessStream (this=0x555555a3fa30, css=...) at /home/glow/dev/paraview/pv1/src/Remoting/ClientServerStream/vtkClientServerInterpreter.cxx:235
#75 0x00007ffff58fd63a in vtkPVSessionCore::ExecuteStreamInternal (this=0x555555ebe7e0, stream=..., ignore_errors=false) at /home/glow/dev/paraview/pv1/src/Remoting/ServerManager/vtkPVSessionCore.cxx:620
#76 0x00007ffff58fd3d6 in vtkPVSessionCore::ExecuteStream (this=0x555555ebe7e0, location=21, stream=..., ignore_errors=false) at /home/glow/dev/paraview/pv1/src/Remoting/ServerManager/vtkPVSessionCore.cxx:590
#77 0x00007ffff58f8fc4 in vtkPVSessionBase::ExecuteStream (this=0x555555ec78a0, location=21, stream=..., ignore_errors=false) at /home/glow/dev/paraview/pv1/src/Remoting/ServerManager/vtkPVSessionBase.cxx:165
#78 0x00007ffff5a7b6a8 in vtkSMProxy::ExecuteStream (this=0x55555731e0a0, stream=..., ignore_errors=false, location=21) at /home/glow/dev/paraview/pv1/src/Remoting/ServerManager/vtkSMProxy.cxx:2406

The backtrace is not super helpfull but we can clearly see that it is related to the data being ASCII.

You may want to switch to Appended format to work around the issue (and improve reading performance A LOT), and also please open an issue on gitlab:
https://gitlab.kitware.com/paraview/paraview/-/issues

I will take care of uploading the data to a more permanent place one you open the issue.

[WEsToMIL]

Here is the issue on GitLab: https://gitlab.kitware.com/paraview/paraview/-/issues/22155

I’ll have a look at changing the data layout but I fear this is not trivial given that our writers are custom-built and ancient. I’d appreciate it if this could be fixed before I rewrite everything on our side

[mwestphal (Mathieu Westphal (Kitware))]

@WEsToMIL

I’d appreciate it if this could be fixed before I rewrite everything on our side

That would be nice indeed but this will require investigation and hence funding. Do not hesitate to reach out to Kitware if that is something that interest you.

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