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

Segmentation fault when running in parallel

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

Reply
 
LinkBack Thread Tools Search this Thread Display Modes
Old   April 1, 2015, 08:31
Default Segmentation fault decomposing in a certain number of CPU (runs fine with other ncpu)
  #1
Pj.
Member
 
Luca
Join Date: Mar 2013
Posts: 68
Rep Power: 13
Pj. is on a distinguished road
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
and this is what i find in the standard error:

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).
--------------------------------------------------------------------------
To run in parallel I do the common practice

Code:
renumberMesh -overwrite
snappyHexMesh -overwrite
potentialFoam -noFunctionObjects
decomposePar
mpirun  pimpleFoam  -parallel
I already run a case almost identical correctly. I just slightly modified the snappyHexMesh dictionary in order to expand a refinement region that was including part of the mesh to include within it the whole mesh.

CheckMesh returns no error, while checkMesh -allGeometry returns this failure:
Code:
***Concave cells (using face planes) found, number of cells: 35616
Before snappyHexMesh the mesh is COMPLETELY structured with a non ortogonality close to the machine error. snappy only refines some areas and only the castellatedMesh step is set to true.

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 09:14.
Pj. is offline   Reply With Quote

Old   April 1, 2015, 09:32
Default
  #2
New Member
 
Jesus Contreras Espada
Join Date: Aug 2011
Location: Switzerland
Posts: 12
Rep Power: 14
jcespada is on a distinguished road
Maybe I'm wrong, but I think you have to indicate the number of processors.
For example:

mpirun -np 8 pimpleFoam -parallel
jcespada is offline   Reply With Quote

Old   April 1, 2015, 09:48
Default
  #3
Pj.
Member
 
Luca
Join Date: Mar 2013
Posts: 68
Rep Power: 13
Pj. is on a distinguished road
Quote:
Originally Posted by jcespada View Post
Maybe I'm wrong, but I think you have to indicate the number of processors.
For example:

mpirun -np 8 pimpleFoam -parallel
It works like this for this particular system. I actually don't know why it's different (i usually do like you say), the sys admin told me to do like this.

It's not the first time I use this system and it always worked without neither np nor the hostfile
Pj. is offline   Reply With Quote

Old   April 8, 2015, 09:12
Default
  #4
Pj.
Member
 
Luca
Join Date: Mar 2013
Posts: 68
Rep Power: 13
Pj. is on a distinguished road
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?
Pj. is offline   Reply With Quote

Reply

Thread Tools Search this Thread
Search this Thread:

Advanced Search
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 Off
Pingbacks are On
Refbacks are On


Similar Threads
Thread Thread Starter Forum Replies Last Post
Error running simpleFoam in parallel Yuby OpenFOAM Running, Solving & CFD 14 October 7, 2021 05:38
Fluent 14.0 file not running in parallel mode in cluster tejakalva FLUENT 0 February 4, 2015 08:02
Running CFX parallel distributed Under linux system with loadleveler queuing system ahmadbakri CFX 1 December 21, 2014 05:19
Segmentation Fault Shawn_A OpenFOAM Running, Solving & CFD 6 October 31, 2011 15:38
Fluent parallel: segmentation fault? hp FLUENT 2 September 6, 2001 15:18


All times are GMT -4. The time now is 22:22.