| Jonathan |
April 1, 2013 09:33 |
problem with mpirun (runs fine in single thread mode)
hi there,
I am running some SRFSimpleFoam simulations which run fine when i run on just one processor - but when i decomposePar the mesh and run over several threads, i get the following error message:
Code:
Create time
Create mesh for time = 0
[1] #0 Foam::error::printStack(Foam::Ostream&)[0] #0 Foam::error::printStack(Foam::Ostream&) in "/opt/openfoam211/platforms/linux64GccDPOpt/ in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAMlib/libOpenFOAM.so"
.so"
[0] #1 [1] #1 Foam::sigSegv::sigHandler(int)Foam::sigSegv::sigHandler(int) in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libO in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
penFOAM.so"
[0] #2 [1] #2 in "/lib/x86_64-linux-gnu/libc.so.6"
[0] # in "/lib/x86_64-linux-gnu/libc.so.6"
[1] #3 3 Foam::processorPolyPatch::updateMesh(Foam::PstreamBuffers&)Foam::processorPolyPatch::updateMesh(Foam::PstreamBuffers&) in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenF in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
OAM.so"
[1] [0] #4 #4 Foam::polyBoundaryMesh::updateMesh()Foam::polyBoundaryMesh::updateMesh() in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[0] #5 Foam::polyMesh::polyMesh(Foam::IOobject const&) in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[1] #5 Foam::polyMesh::polyMesh(Foam::IOobject const&) in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[0] #6 Foam::fvMesh::fvMesh(Foam::IOobject const&) in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[1] #6 Foam::fvMesh::fvMesh(Foam::IOobject const&) in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libfiniteVolume.so"
[0] #7 in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libfiniteVolume.so"
[1] #7
[0] in "/opt/openfoam211/platforms/linux64GccDPOpt/bin/SRFSimpleFoam"
[0] #8 __libc_start_main[1] in "/opt/openfoam211/platforms/linux64GccDPOpt/bin/SRFSimpleFoam"
[1] #8 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"
[0] #9 in "/lib/x86_64-linux-gnu/libc.so.6"
[1] #9
[0] in "/opt/openfoam211/platforms/linux64GccDPOpt/bin/SRFSimpleFoam"
[bergh01:09105] *** Process received signal ***
[bergh01:09105] Signal: Segmentation fault (11)
[bergh01:09105] Signal code: (-6)
[bergh01:09105] Failing at address: 0x3e800002391
[bergh01:09105] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7f7a131464a0]
[bergh01:09105] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) [0x7f7a13146425]
[bergh01:09105] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7f7a131464a0]
[bergh01:09105] [ 3] /opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam18processorPolyPatch10updateMeshERNS_14PstreamBuffersE+0x251) [0x7f7a141db4d1]
[bergh01:09105] [ 4] /opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam16polyBoundaryMesh10updateMeshEv+0x1a9) [0x7f7a141df449]
[bergh01:09105] [ 5] /opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam8polyMeshC2ERKNS_8IOobjectE+0xd61) [0x7f7a1422b9b1]
[bergh01:09105] [ 6] /opt/openfoam211/platforms/linux64GccDPOpt/lib/libfiniteVolume.so(_ZN4Foam6fvMeshC1ERKNS_8IOobjectE+0x19) [0x7f7a14f2a9a9]
[bergh01:09105] [ 7] SRFSimpleFoam() [0x416623]
[bergh01:09105] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f7a1313176d]
[bergh01:09105] [ 9] SRFSimpleFoam() [0x41951d]
[bergh01:09105] *** End of error message ***
[1] in "/opt/openfoam211/platforms/linux64GccDPOpt/bin/SRFSimpleFoam"
[bergh01:09106] *** Process received signal ***
[bergh01:09106] Signal: Segmentation fault (11)
[bergh01:09106] Signal code: (-6)
[bergh01:09106] Failing at address: 0x3e800002392
[bergh01:09106] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7f1efbc764a0]
[bergh01:09106] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) [0x7f1efbc76425]
[bergh01:09106] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7f1efbc764a0]
[bergh01:09106] [ 3] /opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam18processorPolyPatch10updateMeshERNS_14PstreamBuffersE+0x251) [0x7f1efcd0b4d1]
[bergh01:09106] [ 4] /opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam16polyBoundaryMesh10updateMeshEv+0x1a9) [0x7f1efcd0f449]
[bergh01:09106] [ 5] /opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam8polyMeshC2ERKNS_8IOobjectE+0xd61) [0x7f1efcd5b9b1]
[bergh01:09106] [ 6] /opt/openfoam211/platforms/linux64GccDPOpt/lib/libfiniteVolume.so(_ZN4Foam6fvMeshC1ERKNS_8IOobjectE+0x19) [0x7f1efda5a9a9]
[bergh01:09106] [ 7] SRFSimpleFoam() [0x416623]
[bergh01:09106] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f1efbc6176d]
[bergh01:09106] [ 9] SRFSimpleFoam() [0x41951d]
[bergh01:09106] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 9105 on node bergh01 exited on signal 11 (Segmentation fault).
I can run the tutorial examples without any issues (i.e. mixer tut for SRFSimpleFoam), but when i get onto bigger models it seems to crash. i have a machine with 32GB so i dont think this is a memory problem, and as i said, i can run fine on a single thread as well so i cant really see what the issue is?
the only other thing is that the mesh is imported from using fluent3DMeshtoFoam. i dont know if this is an issue at all ...
does anybody recognise what is going on / has had this same issue as well??
many thanks
jonathan |
