0000865: Agglomeration fails in parallel - OpenFOAM Issue Tracking

ID	Project	Category	View Status	Date Submitted	Last Update

0000865	OpenFOAM	Bug	public	2013-05-22 14:15	2013-05-23 09:43

Reporter	~~user591~~	Assigned To	~~user21~~
Priority	normal	Severity	major	Reproducibility	always
Status	resolved	Resolution	fixed
Platform	amd64	OS	Ubuntu	OS Version	12.10

Summary	0000865: Agglomeration fails in parallel
Description	faceAgglomeration often fails in parallel. At that, it works fine for some number of processes and does not work for others. There is also dependence of the decomposition methods and its parameters. If one decomposition method used it works but for another it may fail. For example, standard tutorial OpenFOAM-2.2.x\tutorials\heatTransfer\chtMultiRegionSimpleFoam\multiRegionHeaterRadiation works with 4, 8 processors, but fails with 16. (scotch decomposition method)
Steps To Reproduce	Run multiRegionHeaterRadiation tutorial decomposed for 16 processors
Tags	No tags attached.

~~user591~~ 2013-05-22 14:15	log.faceAgglomerate.bottomAir (4,100 bytes)

~~user650~~ 2013-05-22 15:35 ~0002234	Dear Dimoon I obtain the same problem on different meshes and different solvers, on a nava scale machine with a redhat and a own compilation of gcc 4.7.3 but with same meshes, faceAgglomerate works on a ubuntu 13.04! Yours

~~user650~~ 2013-05-23 04:10 ~0002235	My output with FOAM_ABORT=1 $ /programs/OpenFoam/ThirdParty-2.2.0/platforms/linux64Gcc/openmpi-1.6.3/bin/mpirun -np 4 faceAgglomerate -dict constant/faceAgglomerateDict -parallel /---------------------------------------------------------------------------\ \| ========= \| \| \| \\ / F ield \| OpenFOAM: The Open Source CFD Toolbox \| \| \\ / O peration \| Version: 2.2.x \| \| \\ / A nd \| Web: www.OpenFOAM.org \| \| \\/ M anipulation \| \| \---------------------------------------------------------------------------/ Build : 2.2.x-29ce554b9686 Exec : faceAgglomerate -dict constant/faceAgglomerateDict -parallel Date : May 23 2013 Time : 07:08:56 Host : "titan1" PID : 29370 Case : /worktmp/users/abastide/test_radiatif nProcs : 4 Slaves : 3 ( "titan1.29371" "titan1.29372" "titan1.29373" ) 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 Agglomerating patch : ENTREE Agglomerating patch : SORTIE Agglomerating patch : HOT [2] [2] [2] --> FOAM FATAL IO ERROR: [2] error in IOstream "IOstream" for operation operator>>(Istream&, List<T>&) : reading first token [2] [2] file: IOstream at line 0. [2] [2] From function IOstream::fatalCheck(const char) const [2] in file db/IOstreams/IOstreams/IOstream.C at line 114. [2] FOAM aborting (FOAM_ABORT set) [2] [2] #0 Foam::error::printStack(Foam::Ostream&)-------------------------------------------------------------------------- An MPI process has executed an operation involving a call to the "fork()" system call to create a child process. Open MPI is currently operating in a condition that could result in memory corruption or other system errors; your MPI job may hang, crash, or produce silent data corruption. The use of fork() (or system() or other calls that create child processes) is strongly discouraged. The process that invoked fork was: Local host: titan1 (PID 29372) MPI_COMM_WORLD rank: 2 If you are absolutely sure* that your application will successfully and correctly survive a call to fork(), you may disable this warning by setting the mpi_warn_on_fork MCA parameter to 0. -------------------------------------------------------------------------- at ??:? [2] #1 Foam::IOerror::abort() at ??:? [2] #2 Foam::IOerror::exit(int) at ??:? [2] #3 Foam::Istream& Foam::operator>><Foam::List<int> >(Foam::Istream&, Foam::List<Foam::List<int> >&) at ??:? [2] #4 void Foam::Pstream::combineGather<Foam::List<Foam::List<int> >, Foam::UPstream::listEq>(Foam::List<Foam::UPstream::commsStruct> const&, Foam::List<Foam::List<int> >&, Foam::UPstream::listEq const&, int) at ??:? [2] #5 void Foam::Pstream::exchange<Foam::DynamicList<char, 0u, 2u, 1u>, char>(Foam::List<Foam::DynamicList<char, 0u, 2u, 1u> > const&, Foam::List<Foam::DynamicList<char, 0u, 2u, 1u> >&, Foam::List<Foam::List<int> >&, int, bool) at ??:? [2] #6 Foam::PstreamBuffers::finishedSends(bool) at ??:? [2] #7 void Foam::syncTools::syncBoundaryFaceList<int, Foam::eqOp<int>, Foam::mapDistribute::transform>(Foam::polyMesh const&, Foam::UList<int>&, Foam::eqOp<int> const&, Foam::mapDistribute::transform const&) at ??:? [2] #8 main at ??:? [2] #9 __libc_start_main at ??:? [2] #10 _start at ??:? [titan1:29372] * Process received signal * [titan1:29372] Signal: Aborted (6) [titan1:29372] Signal code: (-6) [titan1:29372] [ 0] /lib64/libc.so.6 [0x38a4c302d0] [titan1:29372] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x38a4c30265] [titan1:29372] [ 2] /lib64/libc.so.6(abort+0x110) [0x38a4c31d10] [titan1:29372] [ 3] /labos/piment/abastide/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam7IOerror5abortEv+0xe6) [0x2addd43d28c6] [titan1:29372] [ 4] /labos/piment/abastide/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam7IOerror4exitEi+0x150) [0x2addd43d2b60] [titan1:29372] [ 5] faceAgglomerate(_ZN4FoamrsINS_4ListIiEEEERNS_7IstreamES4_RNS1_IT_EE+0x49) [0x418109] [titan1:29372] [ 6] /labos/piment/abastide/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam7Pstream13combineGatherINS_4ListINS2_IiEEEENS_8UPstream6listEqEEEvRKNS2_INS5_11commsStructEEERT_RKT0_i+0xdb) [0x2addd446982b] [titan1:29372] [ 7] /labos/piment/abastide/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam7Pstream8exchangeINS_11DynamicListIcLj0ELj2ELj1EEEcEEvRKNS_4ListIT_EERS6_RNS4_INS4_IiEEEEib+0x1a2) [0x2addd446a0a2] [titan1:29372] [ 8] /labos/piment/abastide/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam14PstreamBuffers13finishedSendsEb+0x3b) [0x2addd44676cb] [titan1:29372] [ 9] faceAgglomerate(_ZN4Foam9syncTools20syncBoundaryFaceListIiNS_4eqOpIiEENS_13mapDistribute9transformEEEvRKNS_8polyMeshERNS_5UListIT_EERKT0_RKT1_+0x702) [0x41ad02] [titan1:29372] [10] faceAgglomerate [0x40c586] [titan1:29372] [11] /lib64/libc.so.6(__libc_start_main+0xf4) [0x38a4c1d994] [titan1:29372] [12] faceAgglomerate [0x40d151] [titan1:29372] * End of error message * -------------------------------------------------------------------------- mpirun noticed that process rank 2 with PID 29372 on node titan1 exited on signal 6 (Aborted). --------------------------------------------------------------------------

~~user21~~ 2013-05-23 09:43 ~0002237	It is fixed in commit 61aa86dfaf40266401c52a5aad8fb655950c02fa Thanks

Date Modified	Username	Field	Change
2013-05-22 14:15	~~user591~~	New Issue
2013-05-22 14:15	~~user591~~	File Added: log.faceAgglomerate.bottomAir
2013-05-22 15:35	~~user650~~	Note Added: 0002234
2013-05-23 04:10	~~user650~~	Note Added: 0002235
2013-05-23 09:43	~~user21~~	Note Added: 0002237
2013-05-23 09:43	~~user21~~	Status	new => resolved
2013-05-23 09:43	~~user21~~	Resolution	open => fixed
2013-05-23 09:43	~~user21~~	Assigned To	=> user21