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IDProjectCategoryView StatusLast Update
0000879OpenFOAMBugpublic2014-02-21 16:42
Reporteruser656Assigned Touser2 
PriorityhighSeveritycrashReproducibilityalways
Status resolvedResolutionfixed 
PlatformLinuxOSSlackware 64 bitOS Version13.37
Summary0000879: OF crashes using cyclic BC with scotch decomposition
DescriptionIdentical to the issue in 0000302: after decomposing the mesh, a parallel checkMesh crashes with the error reported below. Changing the number of processors from 8 to 7 doesn't trigger the bug anymore. Also replacing cyclic patches with normal patches avoids the crash.

Build : 2.2.x-7e515871f236
Exec : checkMesh -constant -noZero -parallel
Date : Jun 07 2013
Time : 11:26:24
Host : "bombadil"
PID : 20516
Case : /home/gabriele/CRF/CFD_broken
nProcs : 8
Slaves :
7
(
"bombadil.20517"
"bombadil.20518"
"bombadil.20520"
"bombadil.20521"
"bombadil.20522"
"bombadil.20525"
"bombadil.20526"
)

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 : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create polyMesh for time = constant

[2] [0] #0 #Foam::error::printStack(Foam::Ostream&)0 Foam::error::printStack(Foam::Ostream&) in "/opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[2] #1 Foam::sigSegv::sigHandler(int) in "/opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[0] #1 Foam::sigSegv::sigHandler(int) in "/opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[2] #2 in "/opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[0] #2 in "/lib64/libc.so.6"
[2] #3 Foam::processorPolyPatch::updateMesh(Foam::PstreamBuffers&) in "/lib64/libc.so.6"
[0] #3 Foam::processorPolyPatch::updateMesh(Foam::PstreamBuffers&) in "/opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[2] #4 Foam::polyBoundaryMesh::updateMesh() in "/opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[0] #4 Foam::polyBoundaryMesh::updateMesh() in "/opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[2] #5 Foam::polyMesh::polyMesh(Foam::IOobject const&) in "/opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[0] #5 Foam::polyMesh::polyMesh(Foam::IOobject const&) in "/opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[2] #6 in "/opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[0] #6

[2] in "/opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/bin/checkMesh"
[2] #7 __libc_start_main[0] in "/opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/bin/checkMesh"
[0] #7 __libc_start_main in "/lib64/libc.so.6"
[2] #8 in "/lib64/libc.so.6"
[0] #8

[0] at /glibc-tmp-62a75ea9181aa4d700420d624ea76307/glibc-2.13/csu/../sysdeps/x86_64/elf/start.S:116
[bombadil:20516] *** Process received signal ***
[bombadil:20516] Signal: Segmentation fault (11)
[bombadil:20516] Signal code: (-6)
[bombadil:20516] Failing at address: 0x3e900005024
[bombadil:20516] [ 0] /lib64/libc.so.6(+0x340b0) [0x7f2e0ecaf0b0]
[bombadil:20516] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x7f2e0ecaf035]
[bombadil:20516] [ 2] /lib64/libc.so.6(+0x340b0) [0x7f2e0ecaf0b0]
[bombadil:20516] [ 3] /opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam18processorPolyPatch10updateMeshERNS_14PstreamBuffersE+0x23e) [0x7f2e0fdbef8e]
[bombadil:20516] [ 4] /opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam16polyBoundaryMesh10updateMeshEv+0x201) [0x7f2e0fdc5771]
[bombadil:20516] [ 5] /opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam8polyMeshC1ERKNS_8IOobjectE+0xbad) [0x7f2e0fe1a3dd]
[bombadil:20516] [ 6] checkMesh() [0x428566]
[bombadil:20516] [ 7] /lib64/libc.so.6(__libc_start_main+0xfd) [0x7f2e0ec99e5d]
[bombadil:20516] [ 8] checkMesh() [0x409c19]
[bombadil:20516] *** End of error message ***
[2] at /glibc-tmp-62a75ea9181aa4d700420d624ea76307/glibc-2.13/csu/../sysdeps/x86_64/elf/start.S:116
[bombadil:20518] *** Process received signal ***
[bombadil:20518] Signal: Segmentation fault (11)
[bombadil:20518] Signal code: (-6)
[bombadil:20518] Failing at address: 0x3e900005026
[bombadil:20518] [ 0] /lib64/libc.so.6(+0x340b0) [0x7f4bb4a7c0b0]
[bombadil:20518] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x7f4bb4a7c035]
[bombadil:20518] [ 2] /lib64/libc.so.6(+0x340b0) [0x7f4bb4a7c0b0]
[bombadil:20518] [ 3] /opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam18processorPolyPatch10updateMeshERNS_14PstreamBuffersE+0x232) [0x7f4bb5b8bf82]
[bombadil:20518] [ 4] /opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam16polyBoundaryMesh10updateMeshEv+0x201) [0x7f4bb5b92771]
[bombadil:20518] [ 5] /opt/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam8polyMeshC1ERKNS_8IOobjectE+0xbad) [0x7f4bb5be73dd]
[bombadil:20518] [ 6] checkMesh() [0x428566]
[bombadil:20518] [ 7] /lib64/libc.so.6(__libc_start_main+0xfd) [0x7f4bb4a66e5d]
[bombadil:20518] [ 8] checkMesh() [0x409c19]
[bombadil:20518] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 20516 on node bombadil exited on signal 11 (Segmentation fault).
Steps To ReproduceDecompose the mesh with:
decomposePar -force

Run checkMesh with
foamJob -p -s checkMesh -constant -noZero

Checkmesh crashes.
Additional InformationI've a small testcase which shows the problem, but it's too big for attaching it to the bug. However I can send the case by email (it's about 10Mb compressed).
TagsNo tags attached.

Relationships

has duplicate 0000904 resolveduser2 channel395 tutorial fails after increasing resolution 

Activities

user4

2013-06-11 13:00

  ~0002271

Can you cut down the problem in size?

You can try sending it (m.janssens at the usual)

user2

2014-02-21 16:42

  ~0002888

Thanks for the report - fixed by commit 9e38fbd

Issue History

Date Modified Username Field Change
2013-06-07 10:47 user656 New Issue
2013-06-11 13:00 user4 Note Added: 0002271
2013-07-10 09:36 user4 Relationship added has duplicate 0000904
2014-02-21 16:42 user2 Note Added: 0002888
2014-02-21 16:42 user2 Status new => resolved
2014-02-21 16:42 user2 Fixed in Version => 2.3.x
2014-02-21 16:42 user2 Resolution open => fixed
2014-02-21 16:42 user2 Assigned To => user2