0000879: OF crashes using cyclic BC with scotch decomposition - OpenFOAM Issue Tracking

ID	Project	Category	View Status	Date Submitted	Last Update

0000879	OpenFOAM	Bug	public	2013-06-07 10:47	2014-02-21 16:42

Reporter	~~user656~~	Assigned To	~~user2~~
Priority	high	Severity	crash	Reproducibility	always
Status	resolved	Resolution	fixed
Platform	Linux	OS	Slackware 64 bit	OS Version	13.37

Summary	0000879: OF crashes using cyclic BC with scotch decomposition
Description	Identical 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 Reproduce	Decompose the mesh with: decomposePar -force Run checkMesh with foamJob -p -s checkMesh -constant -noZero Checkmesh crashes.
Additional Information	I'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).
Tags	No tags attached.

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