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[PyFoam] running pyFoam(Plot)Runner.py in parallel |
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April 10, 2013, 03:44 |
running pyFoam(Plot)Runner.py in parallel
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#1 |
New Member
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Location: Germany
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Hello everybody!
I have troubles starting a case in parallel (only local on one machine with multiple cores). If I type Code:
pyFoamRunner.py --procnr=2 simpleFoam Code:
PyFoam WARNING on line 144 of file /home/fem/OpenFOAM/PyFOAM-0.6.0/lib/python2.7/site-packages/PyFoam/Execution/ParallelExecution.py : which can not find a match for simpleFoam . Hoping for the best [M21556:06485] Warning: could not find environment variable "FOAM_MPI_LIBBIN" [M21556:06485] Warning: could not find environment variable "MPI_B" -------------------------------------------------------------------------- mpirun was unable to launch the specified application as it could not find an executable: Executable: UFFER_SIZE Node: M21556 while attempting to start process rank 0. -------------------------------------------------------------------------- 2 total processes failed to start Killing PID 6485 The weird thing is: Without the parallel options (thus on a single core) pyFoamRunner.py works properly! And on top: If I start a parallel run "manually" with Code:
mpirun -np 2 simpleFoam -parallel Does anyone know, what to do? I really like pyFoam an would like to use it furthermore. Thanks an advance. Regards Sebastian |
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April 10, 2013, 04:45 |
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#2 | |
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Bernhard Gschaider
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I think there is something problematic with the settings: http://openfoamwiki.net/index.php/Co...yFoam#Settings Check with pyFoamDumpConfiguration.py and look for the [MPI]-section. It should look somehow like this: Code:
options_openmpi_post: ["-x","PATH","-x","LD_LIBRARY_PATH","-x","WM_PROJECT_DIR","-x","PYTHONPATH","-x","FOAM_MPI_LIBBIN","-x","MPI_BUFFER_SIZE","-x","MPI_ARCH_PATH"] openmpi_add_prefix: False options_openmpi_pre: ["--mca","pls","rsh","--mca","pls_rsh_agent","rsh"] To check which call to mpirun is actually used you can add this configuration option (will also print a lot of other things): Code:
[Debug] ParallelExecution: True
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April 10, 2013, 06:59 |
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#3 |
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Jose Rey
Join Date: Oct 2012
Posts: 134
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This is working for me with OF-2.2 and PyFoam-0.6.0:
Code:
pyFoamPlotRunner.py mpirun -np 12 simpleFoam -parallel | tee log/simpleFoam.log |
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April 10, 2013, 07:39 |
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#4 | |
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Bernhard Gschaider
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April 10, 2013, 09:18 |
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#5 |
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Hello gschaider!
Direct hit with first shot! Yesterday I have edited the pyfoamrc file to get things working on different machines over network. I deleted the changes again and now it works. There are two warnings again (see appending log), but the solver starts nonetheless. I've read about the deprecated parameter on the openMPI homepage, but as long as it is working, this won't be any of my concerns. The same applies to the FOAM_MPI_LIBBIN. Of course any suggestions for improvement are very welcome nevertheless! Thanks a lot for helping me with this issue! Reminding me of parallel computing with different machines: Is it necessary to distibute the according data on every node (with copying data on every node or via NFS)? I've read about MPI, that it can't "push" the data itself to every node automatically... Regard Sebastian Code:
PyFoam WARNING on line 144 of file /home/fem/OpenFOAM/PyFOAM-0.6.0/lib/python2.7/site-packages/PyFoam/Execution/ParallelExecution.py : which can not find a match for simpleFoam . Hoping for the best -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- [M21556:04881] Warning: could not find environment variable "FOAM_MPI_LIBBIN" -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- /*---------------------------------------------------------------------------*\ | ========= | | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / O peration | Version: 2.1.1 | | \\ / A nd | Web: www.OpenFOAM.org | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ Build : 2.1.1-221db2718bbb Exec : simpleFoam -parallel Date : Apr 10 2013 Time : 14:55:32 Host : "M21556" PID : 4884 Case : /home/fem/Berechnung/tetraMesh/tetraMesh10pyF nProcs : 2 Slaves : 1 ( "M21556.4885" ) Pstream initialized with: floatTransfer : 0 nProcsSimpleSum : 0 commsType : nonBlocking sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE). fileModificationChecking : Monitoring run-time modified files using timeStampMaster allowSystemOperations : Disallowing user-supplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Create mesh for time = 0 Reading field p Reading field U Reading/calculating face flux field phi Selecting incompressible transport model powerLaw Selecting RAS turbulence model laminar No field sources present Starting time loop |
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April 10, 2013, 12:20 |
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#6 | ||
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Bernhard Gschaider
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Quote:
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March 31, 2014, 14:15 |
which can't find my solver
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#7 |
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Ripudaman Manchanda
Join Date: May 2013
Posts: 55
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I have created my own solver which is based on solidDisplacementFoam in 2.3.x. I get the first warning that has been shown above:
Code:
PyFoam WARNING on line 144 of file /usr/local/lib/python2.7/dist-packages/PyFoam/Execution/ParallelExecution.py : which can not find a match for convergeFracWidthFoam . Hoping for the best Thanks in advance. |
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March 31, 2014, 19:51 |
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#8 | |
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Bernhard Gschaider
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March 31, 2014, 22:56 |
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#9 |
Member
Ripudaman Manchanda
Join Date: May 2013
Posts: 55
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The code is able to find my solver. However, it does not run as it should. I tried replacing my modified solver (convergeFracWidthFoam) with solidDisplacementFoam and the code worked using this command:
Code:
run=BasicRunner(argv=["solidDisplacementFoam","-case",work.name],lam=machine) run.start() Code:
run=AnalyzedRunner(CONVERGED,silent=True,argv=["solidDisplacementFoam","-case",work.name],lam=machine) run.start() However when I replace solidDisplacementFoam with convergeFracWidthFoam in either of the above options, the code does not go through the iterations. In fact for the BasicRunner case it gives me the following error: Code:
PyFoam WARNING on line 144 of file /usr/local/lib/python2.7/dist-packages/PyFoam/Execution/ParallelExecution.py : which can not find a match for convergeFracWidthFoam . Hoping for the best -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- [ubuntu:08918] Warning: could not find environment variable "PYTHONPATH" [ubuntu:08918] Warning: could not find environment variable "FOAM_MPI_LIBBIN" -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- /*---------------------------------------------------------------------------*\ | ========= | | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / O peration | Version: 2.3.x | | \\ / A nd | Web: www.OpenFOAM.org | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ Build : 2.3.x-e0d5f5a218ab Exec : convergeFracWidthFoam -case /home/ripuvm/OpenFOAM/ripuvm-2.3.x/multiFrac/cases/noFracTraj/try2 -parallel Date : Mar 31 2014 Time : 21:47:12 Host : "ubuntu" PID : 8921 Case : /home/ripuvm/OpenFOAM/ripuvm-2.3.x/multiFrac/cases/noFracTraj/try2 nProcs : 4 Slaves : 3 ( "ubuntu.8922" "ubuntu.8923" "ubuntu.8924" ) Pstream initialized with: floatTransfer : 0 nProcsSimpleSum : 0 commsType : nonBlocking polling iterations : 0 sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE). fileModificationChecking : Monitoring run-time modified files using timeStampMaster allowSystemOperations : Disallowing user-supplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Create mesh for time = 0 Reading mechanical properties Normalising E : E/rho Calculating Lame's coefficients Plane Strain Reading thermal properties Reading field D Calculating stress field sigmaDex Calculating stress field sigmaD Calculating explicit part of div(sigma) divSigmaExp Calculating displacement field Iteration: 1 Time = 1 One = 0 Two = 0 One = 0 Two = 0 One = 0 Two = 0 [1] #0 [2] #0 Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)[3] #0 Foam::error::printStack(Foam::Ostream&) in "/opt/OpenFOAM/OpenFOAM-2.3.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so" [1] #1 Foam::sigFpe::sigHandler(int) in "/opt/OpenFOAM/OpenFOAM-2.3.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so" [2] #1 Foam::sigFpe::sigHandler(int) in "/opt/OpenFOAM/OpenFOAM-2.3.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so" [3] #1 Foam::sigFpe::sigHandler(int) in "/opt/OpenFOAM/OpenFOAM-2.3.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so" [1] # in "/opt/OpenFOAM/OpenFOAM-2.3.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so" [3] #2 2 in "/opt/OpenFOAM/OpenFOAM-2.3.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so" [2] #2 in "/lib/x86_64-linux-gnu/libc.so.6" [1] #3 in "/lib/x86_64-linux-gnu/libc.so.6" [3] #3 in "/lib/x86_64-linux-gnu/libc.so.6" [2] #3 [3] in "/home/ripuvm/OpenFOAM/ripuvm-2.3.x/platforms/linux64GccDPOpt/bin/convergeFracWidthFoam" [3] #4 __libc_start_main[1] in "/home/ripuvm/OpenFOAM/ripuvm-2.3.x/platforms/linux64GccDPOpt/bin/convergeFracWidthFoam" [1] #4 __libc_start_main[2] in "/home/ripuvm/OpenFOAM/ripuvm-2.3.x/platforms/linux64GccDPOpt/bin/convergeFracWidthFoam" [2] #4 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" [3] #5 in "/lib/x86_64-linux-gnu/libc.so.6" [2] #5 in "/lib/x86_64-linux-gnu/libc.so.6" [1] #5 [1] [3] in "/home/ripuvm/OpenFOAM/ripuvm-2.3.x/platforms/linux64GccDPOpt/bin/convergeFracWidthFoam" [ubuntu:08924] *** Process received signal *** [ubuntu:08924] Signal: Floating point exception (8) [ubuntu:08924] Signal code: (-6) [ubuntu:08924] Failing at address: 0x3e8000022dc in "/home/ripuvm/OpenFOAM/ripuvm-2.3.x/platforms/linux64GccDPOpt/bin/convergeFr[ubuntu:08924] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7f5ee6fb44a0] [ubuntu:08924] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) [0x7f5ee6fb4425] [ubuntu:08924] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7f5ee6fb44a0] [ubuntu:08924] [ 3] convergeFracWidthFoam() [0x42b989] [ubuntu:08924] [ 4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f5ee6f9f76d] [ubuntu:08924] [ 5] convergeFracWidthFoam() [0x43523d] [ubuntu:08924] *** End of error message *** acWidthFoam" [ubuntu:08922] *** Process received signal *** [ubuntu:08922] Signal: Floating point exception (8) [ubuntu:08922] Signal code: (-6) [ubuntu:08922] Failing at address: 0x3e8000022da [ubuntu:08922] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7f7c0749b4a0] [ubuntu:08922] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) [0x7f7c0749b425] [ubuntu:08922] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7f7c0749b4a0] [ubuntu:08922] [ 3] convergeFracWidthFoam() [0x42b989] [ubuntu:08922] [ 4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f7c0748676d] [ubuntu:08922] [ 5] convergeFracWidthFoam() [0x43523d] [ubuntu:08922] *** End of error message *** [2] in "/home/ripuvm/OpenFOAM/ripuvm-2.3.x/platforms/linux64GccDPOpt/bin/convergeFracWidthFoam" [ubuntu:08923] *** Process received signal *** [ubuntu:08923] Signal: Floating point exception (8) [ubuntu:08923] Signal code: (-6) [ubuntu:08923] Failing at address: 0x3e8000022db [ubuntu:08923] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7f04fcf574a0] [ubuntu:08923] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) [0x7f04fcf57425] [ubuntu:08923] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7f04fcf574a0] [ubuntu:08923] [ 3] convergeFracWidthFoam() [0x42b989] [ubuntu:08923] [ 4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f04fcf4276d] [ubuntu:08923] [ 5] convergeFracWidthFoam() [0x43523d] [ubuntu:08923] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 8922 on node ubuntu exited on signal 8 (Floating point exception). -------------------------------------------------------------------------- 3 total processes killed (some possibly by mpirun during cleanup) I understand that this is a problem of creating a solver that can run in parallel. Can you help me out here? |
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April 1, 2014, 04:29 |
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#10 | |
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Bernhard Gschaider
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Quote:
My guess is that it is the common DidASumCalculationAndDividedByItWhichFailsInParall elBecauseOnOneProcessorTheSumIsZeroAndIDidntDoARed uce-bug. But it is hard to tell from your output because it is from a Release-version: before you do anything else compile yourself a Debug version. Stack-traces are much clearer (they even include the line numbers of where the problem occurred) and a lot of common errors are uncovered because of the bound-checking
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September 6, 2015, 16:38 |
similar error message
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#11 |
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Eric Bryant
Join Date: Sep 2013
Location: Texas
Posts: 44
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Hi I use PyFoam for parametric evaluation (it's an amazing tool I'm only just figuring out).
So I have scripted a series of templated cases for my custom solver. The output I get everytime throws a "hoping for the best" warning error: Code:
PyFoam WARNING on line 144 of file /usr/local/lib/python2.7/dist-packages/PyFoam/Execution/ParallelExecution.py : which can not find a match for apfSolidFoam . Hoping for the best ^C Interrupted by the Keyboard Killing PID 5965 New case1 Code:
-------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- [namaste:05967] Warning: could not find environment variable "PYTHONPATH" -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- -------------------------------------------------------------------------- A deprecated MCA parameter value was specified in the environment or on the command line. Deprecated MCA parameters should be avoided; they may disappear in future releases. Deprecated parameter: pls_rsh_agent -------------------------------------------------------------------------- /*---------------------------------------------------------------------------*\ | ========= | | | \\ / F ield | foam-extend: Open Source CFD | | \\ / O peration | Version: 3.1 | | \\ / A nd | Web: http://www.extend-project.de | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ Build : 3.1-f77b4801a214 Exec : apfSolidFoam -case /home/eric/sharma/geomechanics/tutorials/apfSolidFoam/paper/caseTens0 -parallel Date : Sep 05 2015 Time : 17:50:43 Host : namaste PID : 5971 CtrlDict : /home/eric/foam/foam-extend-3.1/etc/controlDict Case : /home/eric/sharma/geomechanics/tutorials/apfSolidFoam/paper/caseTens0 nProcs : 12 Slaves : 11 ( namaste.5972 namaste.5973 namaste.5974 namaste.5975 namaste.5976 namaste.5977 namaste.5978 namaste.5979 namaste.5980 namaste.5981 namaste.5982 ) Pstream initialized with: floatTransfer : 0 nProcsSimpleSum : 0 commsType : blocking SigFpe : Enabling floating point exception trapping (FOAM_SIGFPE). // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Code:
End Finalising parallel run [namaste:05971] *** Process received signal *** [namaste:05971] Signal: Segmentation fault (11) [namaste:05971] Signal code: Invalid permissions (2) [namaste:05971] Failing at address: 0x7f9c851eae50 So like is there any option I through to PlotRunner to just continue through into the next case after that seg fault? Because the seg fault is at the end of the run so I dont care. That would be hecca useful. (I am worried that it'd be default behavoir, but somehow it doesn't happen for me. Like the story of my life). Thanks, Eric PS I use this config: Code:
print("Running solver") machine = LAMMachine(nr=procnrs[i]) PlotRunner(args=["--proc=%d"%procnrs[i], "--progress", "--no-continuity", "--hardcopy", "--non-persist", "apfSolidFoam", "-case",work.name]) |
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