CFD Online Logo CFD Online URL
www.cfd-online.com
[Sponsors]
Home > Forums > OpenFOAM Running, Solving & CFD

problem with mpirun (runs fine in single thread mode)

Register Blogs Members List Search Today's Posts Mark Forums Read

Like Tree1Likes
  • 1 Post By Jonathan

Reply
 
LinkBack Thread Tools Display Modes
Old   April 1, 2013, 09:33
Default problem with mpirun (runs fine in single thread mode)
  #1
Senior Member
 
Join Date: Mar 2010
Location: Cape Town, SA
Posts: 153
Rep Power: 8
Jonathan is on a distinguished road
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
Jonathan is offline   Reply With Quote

Old   April 1, 2013, 11:56
Default partially soved
  #2
Senior Member
 
Join Date: Mar 2010
Location: Cape Town, SA
Posts: 153
Rep Power: 8
Jonathan is on a distinguished road
hi,

just an update ...

i am using the 'simple' decomposition method for splitting up the mesh, and it seems the problem is related to the 'delta' / Cell skew factor and the shape of the cells in my mesh in the different directions in which the mesh is being decomposed.

does anyone know exactly what the 'Cell skewness factor' for the simpleCoeffs method does, and how this should be changed according to the mesh properties. my domain is a turbine blade passage meshed with hexahedral cells, and so when cutting the mesh in certain of the cartesian planes i seem to get the error when i run in parallel ...

if i have fairly skewed hexa's should i put the tolerance up or down??

best regards
jonathan
codder likes this.
Jonathan is offline   Reply With Quote

Reply

Thread Tools
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are On
Pingbacks are On
Refbacks are On


Similar Threads
Thread Thread Starter Forum Replies Last Post
cfx11 runs on vista with problem huangfuxiaotao CFX 2 April 28, 2007 06:15
UDF problem on single computer with two procesor Dmitry FLUENT 3 May 18, 2005 12:44
Steady problem and unsteady mode mini FLUENT 6 April 3, 2005 20:28
parallel mode - small problem? co2 FLUENT 2 June 1, 2004 23:47
problem with fluent in batch mode Pat FLUENT 2 February 13, 2003 14:14


All times are GMT -4. The time now is 05:05.