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April 1, 2015, 07:31 |
Segmentation fault decomposing in a certain number of CPU (runs fine with other ncpu)
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#1 |
Member
Luca
Join Date: Mar 2013
Posts: 68
Rep Power: 13 |
Hi everybody
I have a case I'm trying to solve. The case runs correctly when I launch on one core. However when I launch it on multiple cores this is what i find in the standard output: Code:
/*---------------------------------------------------------------------------*\ | ========= | | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / O peration | Version: 2.3.0 | | \\ / A nd | Web: www.OpenFOAM.org | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ Build : 2.3.0-f5222ca19ce6 Exec : pimpleFoam -parallel Date : Apr 01 2015 Time : 13:27:21 Host : "n08" PID : 14194 Case : /home/amerio/Catherine_blocks_noSpires_narrow2 nProcs : 8 Slaves : 7 ( "n08.14195" "n08.14196" "n08.14197" "n08.14198" "n08.14199" "n08.14200" "n08.14201" ) 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 Code:
[5] #0 Foam::error::printStack(Foam::Ostream&)[0] #0 Foam::error::printStack(Foam::Ost ream&)[1] #0 Foam::error::printStack(Foam::Ostream&)[4] #0 Foam::error::printStack(Foa m::Ostream&) in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libOpenFOAM. so" [5] #1 Foam::sigSegv::sigHandler(int) in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux6 4GccDPOpt/lib/libOpenFOAM.so" [0] #1 Foam::sigSegv::sigHandler(int) in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux6 4GccDPOpt/lib/libOpenFOAM.so" [1] #1 Foam::sigSegv::sigHandler(int) in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux6 4GccDPOpt/lib/libOpenFOAM.so" [4] #1 Foam::sigSegv::sigHandler(int) in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux6 4GccDPOpt/lib/libOpenFOAM.so" [5] #2 in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so" [0] #2 in "/lib/x86_64-linux-gnu/libc.so.6" [5] #3 Foam::processorPolyPatch::updateMesh(Foam::PstreamBuffers&) in "/lib/x86_64-linu x-gnu/libc.so.6" [0] #3 Foam::processorPolyPatch::updateMesh(Foam::PstreamBuffers&) in "/opt/OpenFOAM/Op enFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so" [4] #2 in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so" [1] #2 in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so" [5] #4 Foam::polyBoundaryMesh::updateMesh() in "/lib/x86_64-linux-gnu/libc.so.6" [4] #3 Foam::processorPolyPatch::updateMesh(Foam::PstreamBuffers&) in "/lib/x86_64-linu x-gnu/libc.so.6" [1] #3 Foam::processorPolyPatch::updateMesh(Foam::PstreamBuffers&) in "/opt/OpenFOAM/Op enFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so" [0] #4 Foam::polyBoundaryMesh::updateMesh() in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/ linux64GccDPOpt/lib/libOpenFOAM.so" [5] #5 Foam::polyMesh::polyMesh(Foam::IOobject const&) in "/opt/OpenFOAM/OpenFOAM-2.3.0 /platforms/linux64GccDPOpt/lib/libOpenFOAM.so" [4] #4 Foam::polyBoundaryMesh::updateMesh() in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/ linux64GccDPOpt/lib/libOpenFOAM.so" [1] #4 Foam::polyBoundaryMesh::updateMesh() in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/ linux64GccDPOpt/lib/libOpenFOAM.so" [0] #5 Foam::polyMesh::polyMesh(Foam::IOobject const&) in "/opt/OpenFOAM/OpenFOAM-2.3.0 /platforms/linux64GccDPOpt/lib/libOpenFOAM.so" [4] #5 Foam::polyMesh::polyMesh(Foam::IOobject const&) in "/opt/OpenFOAM/OpenFOAM-2.3.0 /platforms/linux64GccDPOpt/lib/libOpenFOAM.so" [5] #6 Foam::fvMesh::fvMesh(Foam::IOobject const&) in "/opt/OpenFOAM/OpenFOAM-2.3.0/pla tforms/linux64GccDPOpt/lib/libOpenFOAM.so" [1] #5 Foam::polyMesh::polyMesh(Foam::IOobject const&) in "/opt/OpenFOAM/OpenFOAM-2.3.0 /platforms/linux64GccDPOpt/lib/libOpenFOAM.so" [0] #6 Foam::fvMesh::fvMesh(Foam::IOobject const&) in "/opt/OpenFOAM/OpenFOAM-2.3.0/pla tforms/linux64GccDPOpt/lib/libOpenFOAM.so" [4] #6 Foam::fvMesh::fvMesh(Foam::IOobject const&) in "/opt/OpenFOAM/OpenFOAM-2.3.0/pla tforms/linux64GccDPOpt/lib/libOpenFOAM.so" [1] #6 Foam::fvMesh::fvMesh(Foam::IOobject const&) in "/opt/OpenFOAM/OpenFOAM-2.3.0/pla tforms/linux64GccDPOpt/lib/libfiniteVolume.so" [5] #7 in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libfiniteVolume.so" [0] #7 in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libfiniteVolume. so" [4] #7 [5] in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/bin/pimpleFoam" [5] #8 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" [5] #9 in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libfiniteVolume. so" [1] #7 [0] in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/bin/pimpleFoam" [0] #8 __libc_start_main[4] in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt /bin/pimpleFoam" [4] #8 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" [0] #9 in "/lib/x86_64-linux-gnu/libc.so.6" [4] #9 [1] in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/bin/pimpleFoam" [1] #8 __libc_start_main[5] in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt /bin/pimpleFoam" [n08:13738] *** Process received signal *** [n08:13738] Signal: Segmentation fault (11) [n08:13738] Signal code: (-6) [n08:13738] Failing at address: 0x3ed000035aa [n08:13738] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x321e0) [0x7f75652211e0] [n08:13738] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) [0x7f7565221165] [n08:13738] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x321e0) [0x7f75652211e0] [n08:13738] [ 3] /opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libOpenFOAM. so(_ZN4Foam18processorPolyPatch10updateMeshERNS_14PstreamBuffersE+0x2b5) [0x7f75663cfc95 ] [n08:13738] [ 4] /opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libOpenFOAM. so(_ZN4Foam16polyBoundaryMesh10updateMeshEv+0x2b9) [0x7f75663d7729] [n08:13738] [ 5] /opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libOpenFOAM. so(_ZN4Foam8polyMeshC1ERKNS_8IOobjectE+0xd47) [0x7f7566426027] [n08:13738] [ 6] /opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libfiniteVol ume.so(_ZN4Foam6fvMeshC2ERKNS_8IOobjectE+0x19) [0x7f7567e54319] [n08:13738] [ 7] pimpleFoam() [0x428154] [n08:13738] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd) [0x7f756520dead ] [n08:13738] [ 9] pimpleFoam() [0x42b66d] [n08:13738] *** End of error message *** [0] in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/bin/pimpleFoam" [n08:13733] *** Process received signal *** [n08:13733] Signal: Segmentation fault (11) [n08:13733] Signal code: (-6) [n08:13733] Failing at address: 0x3ed000035a5 [n08:13733] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x321e0) [0x7f325085f1e0] [n08:13733] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) [0x7f325085f165] [n08:13733] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x321e0) [0x7f325085f1e0] [n08:13733] [ 3] /opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libOpenFOAM. so(_ZN4Foam18processorPolyPatch10updateMeshERNS_14PstreamBuffersE+0x2bd) [0x7f3251a0dc9d ] [n08:13733] [ 4] /opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libOpenFOAM. so(_ZN4Foam16polyBoundaryMesh10updateMeshEv+0x2b9) [0x7f3251a15729] [n08:13733] [ 5] /opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libOpenFOAM. so(_ZN4Foam8polyMeshC1ERKNS_8IOobjectE+0xd47) [0x7f3251a64027] [n08:13733] [ 6] /opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libfiniteVol ume.so(_ZN4Foam6fvMeshC2ERKNS_8IOobjectE+0x19) [0x7f3253492319] [n08:13733] [ 7] pimpleFoam() [0x428154] [n08:13733] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd) [0x7f325084bead ] [n08:13733] [ 9] pimpleFoam() [0x42b66d] [n08:13733] *** End of error message *** [4] in "/opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/bin/pimpleFoam" [n08:13737] *** Process received signal *** [n08:13737] Signal: Segmentation fault (11) [n08:13737] Signal code: (-6) [n08:13737] Failing at address: 0x3ed000035a9 in "/lib/x86_64-linux-gnu/libc.so.6" [1] #9 [n08:13737] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x321e0) [0x7f956738b1e0] [n08:13737] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) [0x7f956738b165] [n08:13737] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x321e0) [0x7f956738b1e0] [n08:13737] [ 3] /opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libOpenFOAM. so(_ZN4Foam18processorPolyPatch10updateMeshERNS_14PstreamBuffersE+0x2bd) [0x7f9568539c9d ] [n08:13737] [ 4] /opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libOpenFOAM. so(_ZN4Foam16polyBoundaryMesh10updateMeshEv+0x2b9) [0x7f9568541729] [n08:13737] [ 5] /opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libOpenFOAM. so(_ZN4Foam8polyMeshC1ERKNS_8IOobjectE+0xd47) [0x7f9568590027] [n08:13737] [ 6] /opt/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libfiniteVol ume.so(_ZN4Foam6fvMeshC2ERKNS_8IOobjectE+0x19) [0x7f9569fbe319] [n08:13737] [ 7] pimpleFoam() [0x428154] [n08:13737] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd) [0x7f9567377ead ] [n08:13737] [ 9] pimpleFoam() [0x42b66d] [n08:13737] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 5 with PID 13738 on node n08 exited on signal 11 (Segme ntation fault). -------------------------------------------------------------------------- Code:
renumberMesh -overwrite snappyHexMesh -overwrite potentialFoam -noFunctionObjects decomposePar mpirun pimpleFoam -parallel CheckMesh returns no error, while checkMesh -allGeometry returns this failure: Code:
***Concave cells (using face planes) found, number of cells: 35616 What could be the cause of that segmentation fault? The case is running on a unix cluster running SMP Debian 3.2.65-1+deb7u1 x86_64. Last edited by Pj.; April 8, 2015 at 08:14. |
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April 1, 2015, 08:32 |
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#2 |
New Member
Jesus Contreras Espada
Join Date: Aug 2011
Location: Switzerland
Posts: 12
Rep Power: 15 |
Maybe I'm wrong, but I think you have to indicate the number of processors.
For example: mpirun -np 8 pimpleFoam -parallel |
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April 1, 2015, 08:48 |
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#3 | |
Member
Luca
Join Date: Mar 2013
Posts: 68
Rep Power: 13 |
Quote:
It's not the first time I use this system and it always worked without neither np nor the hostfile |
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April 8, 2015, 08:12 |
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#4 |
Member
Luca
Join Date: Mar 2013
Posts: 68
Rep Power: 13 |
Solved decomposing in a different number of processors.
In my opinion this sounds like a bug, but I wait someone more experienced than me to say so. Any opinion? |
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