View Issue Details
| ID | Project | Category | View Status | Date Submitted | Last Update |
|---|---|---|---|---|---|
| 0001386 | OpenFOAM | Bug | public | 2014-08-29 20:30 | 2015-10-01 09:20 |
| Reporter | Assigned To | will | |||
| Priority | high | Severity | crash | Reproducibility | always |
| Status | resolved | Resolution | no change required | ||
| Platform | Linux 64 | OS | CentOS | OS Version | 6.3 |
| Summary | 0001386: OF fails after "Create mesh for time = 0" | ||||
| Description | The error log is following for one of the tests: ---------------------------------------------------------------- The following have been reloaded with a version change: 1) mvapich2/1.9a2 => mvapich2/2.0b TACC: Starting up job 3890257 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... /*---------------------------------------------------------------------------*\ | ========= | | | \\ / 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 : /home1/02898/bharat/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPDebug/bin/pisoFoam -parallel Date : Aug 12 2014 Time : 16:23:09 Host : "c405-403.stampede.tacc.utexas.edu" PID : 97078 Case : /work/02898/bharat/OpenFOAM/bharat-2.3.0/rod-airfoil-new-3d-pisoFoam-les-scotch-n256 nProcs : 256 Slaves : 255 ( "c405-403.stampede.tacc.utexas.edu.97079" "c405-403.stampede.tacc.utexas.edu.97080" "c405-403.stampede.tacc.utexas.edu.97081" "c405-403.stampede.tacc.utexas.edu.97082" "c405-403.stampede.tacc.utexas.edu.97083" . . . "c411-903.stampede.tacc.utexas.edu.127990" "c411-903.stampede.tacc.utexas.edu.127991" ) Pstream initialized with: floatTransfer : 0 nProcsSimpleSum : 0 commsType : nonBlocking polling iterations : 0 fileModificationChecking : Monitoring run-time modified files using timeStampMaster allowSystemOperations : Disallowing user-supplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Create mesh for time = 0 [83] [83] [83] --> FOAM FATAL ERROR: [83] index 1 out of range 0 ... 0 [83] [83] From function UList<T>::checkIndex(const label) [83] in file /home1/02898/bharat/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/UListI.H at line 109. [83] FOAM parallel run aborting [83] [27] [27] [137] [27] --> FOAM FATAL ERROR: [27] index 6 out of range 0 ... 5[137] [27] [137] --> FOAM FATAL ERROR: [27] From function [137] index 3 out of range 0 ... 2UList<T>::checkIndex(const label) [27] [137] in file /home1/02898/bharat/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/UListI.H[137] From function at line 109.UList<T>::checkIndex(const label) [27] [137] in file /home1/02898/bharat/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/UListI.H FOAM parallel run aborting [27] at line 109. [137] FOAM parallel run aborting [137] [83] #0 Foam::error::printStack(Foam::Ostream&)[80] [80] [80] --> FOAM FATAL ERROR: [80] index 1 out of range 0 ... 0 [80] [80] From function UList<T>::checkIndex(const label) [80] in file /home1/02898/bharat/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/UListI.H at line 109. [80] FOAM parallel run aborting ---------------------------------------------------------------- This was a debug mode compilation and attempted with 256 processors. The error from one particular process is below: ---------------------------------------------------------------- [83] [83] [83] --> FOAM FATAL ERROR: [83] index 1 out of range 0 ... 0 [83] [83] From function UList<T>::checkIndex(const label) [83] in file /home1/02898/bharat/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/UListI.H at line 109. [83] [83] [83] #0 Foam::error::printStack(Foam::Ostream&)[80] [83] #1 Foam::error::abort() at /work/02898/bharat/OpenFOAM/OpenFOAM-2.3.0-Debug/src/OSspecific/POSIX/printStack.C:221 [83] #2 Foam::Ostream& Foam::operator<< <Foam::error>(Foam::Ostream&, Foam::errorManip<Foam::error>) at /work/02898/bharat/OpenFOAM/OpenFOAM-2.3.0-Debug/src/OpenFOAM/lnInclude/error.C:230 [83] #3 Foam::UList<Foam::face>::checkIndex(int) const at ~/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/errorManip.H:85 [83] #4 Foam::UList<Foam::face>::operator[](int) const at ~/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/UListI.H:111 [83] #5 Foam::processorPolyPatch::updateMesh(Foam::PstreamBuffers&) at ~/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/UListI.H:200 [83] #6 Foam::processorCyclicPolyPatch::updateMesh(Foam::PstreamBuffers&) at /work/02898/bharat/OpenFOAM/OpenFOAM-2.3.0-Debug/src/OpenFOAM/meshes/polyMesh/polyPatches/constraint/processor/processorPolyPatch.C:396 [83] #7 Foam::polyBoundaryMesh::updateMesh() at /work/02898/bharat/OpenFOAM/OpenFOAM-2.3.0-Debug/src/OpenFOAM/meshes/polyMesh/polyPatches/constraint/processorCyclic/processorCyclicPolyPatch.C:282 [83] #8 Foam::polyMesh::polyMesh(Foam::IOobject const&) at /work/02898/bharat/OpenFOAM/OpenFOAM-2.3.0-Debug/src/OpenFOAM/meshes/polyMesh/polyBoundaryMesh/polyBoundaryMesh.C:1095 [83] #9 Foam::polyMesh::polyMesh(Foam::IOobject const&) at /work/02898/bharat/OpenFOAM/OpenFOAM-2.3.0-Debug/src/OpenFOAM/meshes/polyMesh/polyMesh.C:302 [83] #10 Foam::fvMesh::fvMesh(Foam::IOobject const&) at /work/02898/bharat/OpenFOAM/OpenFOAM-2.3.0-Debug/src/finiteVolume/fvMesh/fvMesh.C:236 [83] #11 [83] at ~/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/createMesh.H:11 [83] #12 __libc_start_main[87] at ~/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude/createMesh.H:11 [83] #13 [83] in "/home1/02898/bharat/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64IccDPDebug/bin/pisoFoam" ---------------------------------------------------------------- I noticed the issue "0000879: OF crashes using cyclic BC with scotch decomposition". I see that it is marked resolved but I feel that my issue is similar. | ||||
| Steps To Reproduce | I have attached a set of input files excluding the mesh. My unpartitioned mesh is 7GB which I created in Pointwise. I have put the Pointwise mesh file on http://bharatr.public.iastate.edu/pub/periodic_3D.pw This can be opened in Pointwise to save the full 7GB mesh for OF. Also, the boundary file written by Pointwise is incomplete and the set of input files I provide in tarball contain the complete boundary file inside constant folder. After having the complete setup, I would do decomposePar and then pisoFoam -parallel with 256 processors. | ||||
| Additional Information | The tarball also contains full log files for the crashes when the case was ran in both Opt and Debug modes. | ||||
| Tags | No tags attached. | ||||
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2014-08-29 20:30
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I think I figured this out, how do I mark it resolved? |
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We can mark this as resolved. However, before we do, it would be nice to know what the issue was, and how you fixed it. Could you please post that information? |
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The issue was using periodic boundary conditions with scotch partitioning. I got rid of that error by specifying preservePatches keyword in decomposeParDict for periodic boundaries. |
| Date Modified | Username | Field | Change |
|---|---|---|---|
| 2014-08-29 20:30 |
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New Issue | |
| 2014-08-29 20:30 |
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File Added: bug-report.tar.bz2 | |
| 2014-09-25 15:05 |
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Note Added: 0003238 | |
| 2014-10-15 11:10 | will | Note Added: 0003257 | |
| 2014-11-01 00:38 |
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Note Added: 0003276 | |
| 2014-11-03 09:05 | will | Status | new => resolved |
| 2014-11-03 09:05 | will | Resolution | open => no change required |
| 2014-11-03 09:05 | will | Assigned To | => will |
