[Paraview] Paraview hangs when using changing geometries and binary ensight gold format
Hello, I have problems when I try to visualize my results in Paraview which include changing geometries. I can load the first time step but when I switch to the next step (in which 4 points are added), paraview freezes and htop shows 100% load for this process. Surprisingly, this only happens when I use binary ensight gold format. The same results written in ascii ensight gold format work. The ens_checker tells me for both cases that I have valid output files. Attached are the binary and ascii version of the result. It would be nice to use binary output for my results. I work on a 64 bit Linux system and I have checked out the latest repository version of Paraview (but I have also tried older versions: 3.14 and 3.6) giving me the same result. Thanks in advance for your help. Cheers, Georg -- Dipl.-Ing. Georg Hammerl Lehrstuhl für Numerische Mechanik Technische Universität München Boltzmannstrasse 15, D-85747 Garching b. München phone +49 89 289 15237 fax +49 89 289 15301 hamm...@lnm.mw.tum.de http://www.lnm.mw.tum.de BEGIN TIME STEP description part 2 coordinates 0.0e+00 0.0e+00 0.0e+00 0.0e+00 1.95437e+01 1.95437e+01 END TIME STEP BEGIN TIME STEP description part 2 coordinates 1.23048e-01 1.23048e-01 1.23048e-01 1.23048e-01 1.23048e-01 1.23048e-01 1.23048e-01 1.23048e-01 1.23048e-01 1.23048e-01 1.23048e-01 1.23048e-01 1.96667e+01 1.96667e+01 1.96667e+01 1.96667e+01 1.96667e+01 1.96667e+01 END TIME STEP # created using post_drt_ensight FORMAT type: ensight gold GEOMETRY model: 1 1 xxx_ascii_particle.geo VARIABLE vector per node:1 2 acceleration xxx_ascii_particle.acceleration scalar per node:1 3 radius xxx_ascii_particle.radius TIME time set: 1 number of steps:2 time values: 5e-05 0.0001 FILE file set: 1 number of steps:2 file set: 2 number of steps:2 file set: 3 number of steps:2 xxx_ascii_particle.geo Description: application/vnd.dynageo BEGIN TIME STEP description part 2 coordinates 1.0e-02 1.0e-02 END TIME STEP BEGIN TIME STEP description part 2 coordinates 1.0e-02 1.0e-02 1.0e-02 1.0e-02 1.0e-02 1.0e-02 END TIME STEP xxx_binary_particle.acceleration Description: Binary data # created using post_drt_ensight FORMAT type: ensight gold GEOMETRY model: 1 1 xxx_binary_particle.geo VARIABLE vector per node:1 2 acceleration xxx_binary_particle.acceleration scalar per node:1 3 radius xxx_binary_particle.radius TIME time set: 1 number of steps:2 time values: 5e-05 0.0001 FILE file set: 1 number of steps:2 file set: 2 number of steps:2 file set: 3 number of steps:2 xxx_binary_particle.geo Description: application/vnd.dynageo xxx_binary_particle.radius Description: Binary data ___ 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] Paraview hangs when using changing geometries and binary ensight gold format
Hello again,
In the meantime I have found the problem with the binary ensight gold
reader.
Whenever the variable-files are read for a time steps greater than 1,
Paraview has to jump in the binary file to the desired timestep. This is
done by partially parsing and skipping blocks until the correct "BEGIN
TIME STEP" is found. In order to skip the correct block length, Paraview
uses the number of points (numPts) from the current geometry step. This
breaks with a varying number of points per timestep.
As an example my first step contains 2 points and the second step 6
points, therefore when Paraview skips the first time step, it skips a
block length equivalent to 6 points. The correct number would be 2
points. It therefore skips past the next "BEGIN TIME STEP".
In order to verify my theory I have implemented a little hack which
looks for the next "BEGIN TIME STEP" by brute force. In case someone
wants to try this I have attached a patch which can be used in
conjunction with the examples in my previous mail.
A clean solution would be to skip the correct number of points for every
given timestep. Unfortunately I do not have enough insight into the
Paraview/VTK ensight reader to implement this and would appreciate any
help in finding a clean solution to this.
Cheers,
Georg
On 27/02/13 08:17, Georg Hammerl wrote:
Hello,
I have problems when I try to visualize my results in Paraview which
include changing geometries. I can load the first time step but when I
switch to the next step (in which 4 points are added), paraview
freezes and htop shows 100% load for this process. Surprisingly, this
only happens when I use binary ensight gold format. The same results
written in ascii ensight gold format work. The ens_checker tells me
for both cases that I have valid output files. Attached are the binary
and ascii version of the result. It would be nice to use binary output
for my results.
I work on a 64 bit Linux system and I have checked out the latest
repository version of Paraview (but I have also tried older versions:
3.14 and 3.6) giving me the same result.
Thanks in advance for your help.
Cheers,
Georg
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--
Dipl.-Ing. Georg Hammerl
Lehrstuhl für Numerische Mechanik
Technische Universität München
Boltzmannstrasse 15, D-85747 Garching b. München
phone +49 89 289 15237
fax +49 89 289 15301
hamm...@lnm.mw.tum.de
http://www.lnm.mw.tum.de
diff --git a/IO/EnSight/vtkEnSightGoldBinaryReader.cxx b/IO/EnSight/vtkEnSightGoldBinaryReader.cxx
index 81cfdd0..a58d9a5 100644
--- a/IO/EnSight/vtkEnSightGoldBinaryReader.cxx
+++ b/IO/EnSight/vtkEnSightGoldBinaryReader.cxx
@@ -1317,36 +1317,19 @@ int vtkEnSightGoldBinaryReader::ReadScalarsPerNode(
}
this->ReadLine(line); // skip the description line
- if (measured)
-{
-output = static_cast(
- this->GetDataSetFromBlock(compositeOutput, this->NumberOfGeometryParts));
-numPts = output->GetNumberOfPoints();
-if (numPts)
- {
- this->ReadLine(line);
- // Skip sclalars
- this->IFile->seekg(sizeof(float)*numPts, ios::cur);
- }
-}
-
- while (this->ReadLine(line) &&
-strncmp(line, "part", 4) == 0)
-{
-this->ReadPartId(&partId);
-partId--; // EnSight starts #ing with 1.
-realId = this->InsertNewPartId(partId);
-output = static_cast(
- this->GetDataSetFromBlock(compositeOutput, realId));
-numPts = output->GetNumberOfPoints();
-if (numPts)
- {
- this->ReadLine(line); // "coordinates" or "block"
- // Skip sclalars
- this->IFile->seekg(sizeof(float)*numPts, ios::cur);
- }
-}
-}
+ std::streampos position = this->IFile->tellg();
+ char tmp[16];
+ this->IFile->readsome(tmp, 16);
+ tmp[15] = '\0';
+ while (strncmp(tmp, "BEGIN TIME STEP", 15) != 0)
+{
+position = position+1;
+this->IFile->seekg(position);
+this->IFile->readsome(tmp, 16);
+tmp[15] = '\0';
+}
+ this->IFile->seekg(position);
+ }
this->ReadLine(line);
while (strncmp(line, "BEGIN TIME STEP", 15) != 0)
{
@@ -1518,36 +1501,19 @@ int vtkEnSightGoldBinaryReader::ReadVectorsPerNode(
}
this->ReadLine(line); // skip the description line
- if (measured)
[Paraview] Parallel paraview crashes when opening files
Hello, I have compiled paraview from the git repo with MPI support on my Linux 64-bit machine (openmpi 1.5.4). I can start Paraview with multiple processors, but when I try to open one of my result files I get the following error and Paraview is closed automatically: ERROR: In /home/hammerl/programs_local/paraview_git/VTK/Parallel/Core/vtkSocketCommunicator.cxx, line 812 vtkSocketCommunicator (0x2090510): Could not receive tag. 188969 Attached is a file that can be used to reproduce the error. I appreciate any help to solve the problem. Cheers, Georg -- Dipl.-Ing. Georg Hammerl Lehrstuhl für Numerische Mechanik Technische Universität München Boltzmannstrasse 15, D-85747 Garching b. München phone +49 89 289 15237 fax +49 89 289 15301 hamm...@lnm.mw.tum.de http://www.lnm.mw.tum.de # created using post_drt_ensight FORMAT type: ensight gold GEOMETRY model: 1 1 zzz_structure.geo VARIABLE scalar per element: 1 2 Owner zzz_structure.Owner vector per node:1 3 displacement zzz_structure.displacement TIME time set: 1 number of steps:1 time values: 1 FILE file set: 1 number of steps:1 file set: 2 number of steps:1 file set: 3 number of steps:1 zzz_structure.displacement Description: Binary data zzz_structure.geo Description: application/vnd.dynageo zzz_structure.Owner Description: Binary data ___ 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] [EXTERNAL] Parallel paraview crashes when opening files
ew-boun...@paraview.org [mailto:paraview-boun...@paraview.org] On Behalf Of Georg Hammerl Sent: Friday, April 05, 2013 4:12 AM To: paraview@paraview.org Subject: [EXTERNAL] [Paraview] Parallel paraview crashes when opening files Hello, I have compiled paraview from the git repo with MPI support on my Linux 64-bit machine (openmpi 1.5.4). I can start Paraview with multiple processors, but when I try to open one of my result files I get the following error and Paraview is closed automatically: ERROR: In /home/hammerl/programs_local/paraview_git/VTK/Parallel/Core/vtkSocketCommunicator.cxx, line 812 vtkSocketCommunicator (0x2090510): Could not receive tag. 188969 Attached is a file that can be used to reproduce the error. I appreciate any help to solve the problem. Cheers, Georg -- Dipl.-Ing. Georg Hammerl Lehrstuhl für Numerische Mechanik Technische Universität München Boltzmannstrasse 15, D-85747 Garching b. München phone +49 89 289 15237 fax +49 89 289 15301 hamm...@lnm.mw.tum.de http://www.lnm.mw.tum.de -- Dipl.-Ing. Georg Hammerl Lehrstuhl für Numerische Mechanik Technische Universität München Boltzmannstrasse 15, D-85747 Garching b. München phone +49 89 289 15237 fax +49 89 289 15301 hamm...@lnm.mw.tum.de http://www.lnm.mw.tum.de ___ 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] [EXTERNAL] Parallel paraview crashes when opening files
Hello Alan,
attached are the files to reproduce the crashing of paraview.
Thanks in advance for your help.
Georg
On 13/08/13 18:50, Scott, W Alan wrote:
Georg,
I don't know if I can figure it out, but send me the file again and I will try
opening it up.
Alan
-Original Message-
From: Georg Hammerl [mailto:hamm...@lnm.mw.tum.de]
Sent: Tuesday, August 13, 2013 3:35 AM
To: paraview@paraview.org
Cc: Scott, W Alan
Subject: Re: [Paraview] [EXTERNAL] Parallel paraview crashes when opening files
Hello Alan,
I know it is been a while but I ran into this issue again today and I had a
look into the problem again. It seems to be related to the time steps. I use
the ensight gold transient single-file format. When I remove all time stepping
information (i.e. BEGIN TIME STEP and END TIME STEP and everything related to
it in the case file) and only visualize one single time step everything works
fine. I simply cannot figure out what is going wrong. I appreciate any help in
solving this issue.
Georg
On 08/04/13 08:33, Georg Hammerl wrote:
Alan,
now I have compiled a debug version and I have attached with gdb to
the server to find out where the segfault occurs.
Here is the stacktrace:
Program received signal SIGSEGV, Segmentation fault.
0x7f95c93bad40 in vtkIdList::GetId (this=0x0, i=0) at
/home/hammerl/programs_local/paraview_git/VTK/Common/Core/vtkIdList.h:43
43vtkIdType GetId(const vtkIdType i) {return this->Ids[i];};
(gdb) bt
#0 0x7f95c93bad40 in vtkIdList::GetId (this=0x0, i=0) at
/home/hammerl/programs_local/paraview_git/VTK/Common/Core/vtkIdList.h:43
#1 0x7f95c94a199a in vtkPEnSightReader::ReadVariableFiles
(this=0x1b66d60, output=0x1b86050)
at
/home/hammerl/programs_local/paraview_git/ParaViewCore/VTKExtensions/Default/vtkPEnSightReader.cxx:1617
#2 0x7f95c9498fb2 in vtkPEnSightReader::RequestData
(this=0x1b66d60, outputVector=0x1b6ab10)
at
/home/hammerl/programs_local/paraview_git/ParaViewCore/VTKExtensions/Default/vtkPEnSightReader.cxx:446
#3 0x7f95cfc2ee0f in
vtkMultiBlockDataSetAlgorithm::ProcessRequest (this=0x1b66d60,
request=0x1b86c40, inputVector=0x0, outputVector=0x1b6ab10)
at
/home/hammerl/programs_local/paraview_git/VTK/Common/ExecutionModel/vtkMultiBlockDataSetAlgorithm.cxx:88
#4 0x7f95cfc1b73f in vtkExecutive::CallAlgorithm (this=0x1b68c00,
request=0x1b86c40, direction=1, inInfo=0x0, outInfo=0x1b6ab10)
at
/home/hammerl/programs_local/paraview_git/VTK/Common/ExecutionModel/vtkExecutive.cxx:744
#5 0x7f95cfc08ea7 in vtkDemandDrivenPipeline::ExecuteData
(this=0x1b68c00, request=0x1b86c40, inInfo=0x0, outInfo=0x1b6ab10)
at
/home/hammerl/programs_local/paraview_git/VTK/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:498
#6 0x7f95cfbfe943 in vtkCompositeDataPipeline::ExecuteData
(this=0x1b68c00, request=0x1b86c40, inInfoVec=0x0, outInfoVec=0x1b6ab10)
at
/home/hammerl/programs_local/paraview_git/VTK/Common/ExecutionModel/vtkCompositeDataPipeline.cxx:208
#7 0x7f95cfc085e7 in vtkDemandDrivenPipeline::ProcessRequest
(this=0x1b68c00, request=0x1b86c40, inInfoVec=0x0, outInfoVec=0x1b6ab10)
at
/home/hammerl/programs_local/paraview_git/VTK/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:279
#8 0x7f95cfc3b188 in
vtkStreamingDemandDrivenPipeline::ProcessRequest (this=0x1b68c00,
request=0x1b86c40, inInfoVec=0x0, outInfoVec=0x1b6ab10)
at
/home/hammerl/programs_local/paraview_git/VTK/Common/ExecutionModel/vtkStreamingDemandDrivenPipeline.cxx:346
#9 0x7f95cfc08cf0 in vtkDemandDrivenPipeline::UpdateData
(this=0x1b68c00, outputPort=0) at
/home/hammerl/programs_local/paraview_git/VTK/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:449
#10 0x7f95cfc3b3ea in vtkStreamingDemandDrivenPipeline::Update
(this=0x1b68c00, port=0)
at
/home/hammerl/programs_local/paraview_git/VTK/Common/ExecutionModel/vtkStreamingDemandDrivenPipeline.cxx:399
#11 0x7f95cfbf70a6 in vtkAlgorithm::Update (this=0x1b66d60,
port=0) at
/home/hammerl/programs_local/paraview_git/VTK/Common/ExecutionModel/vtkAlgorithm.cxx:1420
#12 0x7f95cfbf7071 in vtkAlgorithm::Update (this=0x1b66d60) at
/home/hammerl/programs_local/paraview_git/VTK/Common/ExecutionModel/vtkAlgorithm.cxx:1414
#13 0x7f95c8da0a44 in vtkGenericEnSightReader::RequestData
(this=0x17e6a30, outputVector=0x1b67220) at
/home/hammerl/programs_local/paraview_git/VTK/IO/EnSight/vtkGenericEnSightReader.cxx:229
#14 0x7f95cfc2ee0f in
vtkMultiBlockDataSetAlgorithm::ProcessRequest (this=0x17e6a30,
request=0x1b85730, inputVector=0x0, outputVector=0x1b67220)
at
/home/hammerl/programs_local/paraview_git/VTK/Common/ExecutionModel/vtkMultiBlockDataSetAlgorithm.cxx:88
#15 0x7f95cfc1b73f in vtkExecutive::CallAlgorithm (this=0x1b67110,
request=0x1b85730, direction=1, inInfo=0x0, outInfo=0x1b67220)
at
/home/hammerl/programs_local/paraview_git/VTK/Common/ExecutionModel/vtkExecutive.cxx:744
#16 0x7f95cfc08ea7 in vtkDemandDriven
