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-   -   Help Troubleshooting simpleFoam problem on Harpoon made mesh (http://www.cfd-online.com/Forums/openfoam-bugs/62312-help-troubleshooting-simplefoam-problem-harpoon-made-mesh.html)

lhcamilo February 17, 2009 10:26

Hello everyone, Sorry to b
 
Hello everyone,

Sorry to bother everyone with this, but lately I have been a little clueless as to how to troubleshoot this bug I have been having. Long story short I am running a Mesh made on harpoon with the simpleFoam solver for a car model on a fedora 9 32-bit box.

unfortunately whenever I try to run the problem I get the following message

new cannot satisfy memory request.
This does not necessarily mean you have run out of virtual memory.
It could be due to a stack violation caused by e.g. bad use of pointers or an out of date shared library
Aborted


and whenever I try to run it in parallel(2,3 and 4 processors) I get a more elaborate message:

Starting time loop

Time = 1

new cannot satisfy memory request.
This does not necessarily mean you have run out of virtual memory.
It could be due to a stack violation caused by e.g. bad use of pointers or an out of date shared library
[openfoam01:00754] *** Process received signal ***
[openfoam01:00754] Signal: Aborted (6)
[openfoam01:00754] Signal code: (-6)
[openfoam01:00754] [ 0] [0xd8f40c]
[openfoam01:00754] [ 1] /lib/libc.so.6(abort+0x188) [0xa76028]
[openfoam01:00754] [ 2] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libOpenFOAM.so(_ZN4Foam8newErr orEv+0xf8) [0x763fe8]
[openfoam01:00754] [ 3] /usr/lib/libstdc++.so.6(_Znwj+0x3a) [0x2b9417a]
[openfoam01:00754] [ 4] /usr/lib/libstdc++.so.6(_Znaj+0x1d) [0x2b942ad]
[openfoam01:00754] [ 5] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libfiniteVolume.so(_ZN4Foam14G eometricFieldINS_6TensorIdEENS_13fvsPatchFieldENS_ 11surfaceMeshEEC1ERKNS_8IOobje ctERKNS_6fvMeshERKNS_12dimensionSetERKNS_4wordE+0x 18e) [0x1220bbe]
[openfoam01:00754] [ 6] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libfiniteVolume.so(_ZN4Foam26s urfaceInterpolationSchemeINS_6TensorIdEEE11interpo lateERKNS_14GeometricFieldIS2_ NS_12fvPatchFieldENS_7volMeshEEERKNS_3tmpINS4_IdNS _13fvsPatchFieldENS_11surfaceM eshEEEEE+0x3fb) [0x122181b]
[openfoam01:00754] [ 7] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libfiniteVolume.so(_ZNK4Foam26 surfaceInterpolationSchemeINS_6TensorIdEEE11interp olateERKNS_14GeometricFieldIS2 _NS_12fvPatchFieldENS_7volMeshEEE+0x56) [0x12365e6]
[openfoam01:00754] [ 8] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libfiniteVolume.so(_ZN4Foam2fv 14gaussDivSchemeINS_6TensorIdEEE6fvcDivERKNS_14Geo metricFieldIS3_NS_12fvPatchFie ldENS_7volMeshEEE+0x45) [0x1514d85]
[openfoam01:00754] [ 9] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libincompressibleRASModels.so( _ZN4Foam3fvc3divINS_6TensorIdEEEENS_3tmpINS_14Geom etricFieldINS_12innerProductIN S_6VectorIdEET_E4typeENS_12fvPatchFieldENS_7volMes hEEEEERKNS5_IS9_SC_SD_EERKNS_4 wordE+0x79) [0x3809c9]
[openfoam01:00754] [10] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libincompressibleRASModels.so( _ZN4Foam3fvc3divINS_6TensorIdEEEENS_3tmpINS_14Geom etricFieldINS_12innerProductIN S_6VectorIdEET_E4typeENS_12fvPatchFieldENS_7volMes hEEEEERKNS5_IS9_SC_SD_EE+0xbf) [0x38194f]
[openfoam01:00754] [11] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libincompressibleRASModels.so( _ZNK4Foam14incompressible9RASModels15SpalartAllmar as10divDevReffERNS_14Geometric FieldINS_6VectorIdEENS_12fvPatchFieldENS_7volMeshE EE+0x104) [0x3e86c4]
[openfoam01:00754] [12] simpleFoam [0x8059657]
[openfoam01:00754] [13] /lib/libc.so.6(__libc_start_main+0xe6) [0xa605d6]
[openfoam01:00754] [14] simpleFoam(_ZN4Foam11regIOobject14readIfModifiedEv +0x1e9) [0x80589d1]
[openfoam01:00754] *** End of error message ***
new cannot satisfy memory request.
This does not necessarily mean you have run out of virtual memory.
It could be due to a stack violation caused by e.g. bad use of pointers or an out of date shared library
[openfoam01:00756] *** Process received signal ***
[openfoam01:00756] Signal: Aborted (6)
[openfoam01:00756] Signal code: (-6)
[openfoam01:00756] [ 0] [0x5d040c]
[openfoam01:00756] [ 1] /lib/libc.so.6(abort+0x188) [0x358028]
[openfoam01:00756] [ 2] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libOpenFOAM.so(_ZN4Foam8newErr orEv+0xf8) [0x2472fe8]
[openfoam01:00756] [ 3] /usr/lib/libstdc++.so.6(_Znwj+0x3a) [0x2b9417a]
[openfoam01:00756] [ 4] /usr/lib/libstdc++.so.6(_Znaj+0x1d) [0x2b942ad]
[openfoam01:00756] [ 5] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libfiniteVolume.so(_ZN4Foam14G eometricFieldINS_6TensorIdEENS_13fvsPatchFieldENS_ 11surfaceMeshEEC1ERKNS_8IOobje ctERKNS_6fvMeshERKNS_12dimensionSetERKNS_4wordE+0x 18e) [0xe35bbe]
[openfoam01:00756] [ 6] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libfiniteVolume.so(_ZN4Foam26s urfaceInterpolationSchemeINS_6TensorIdEEE11interpo lateERKNS_14GeometricFieldIS2_ NS_12fvPatchFieldENS_7volMeshEEERKNS_3tmpINS4_IdNS _13fvsPatchFieldENS_11surfaceM eshEEEEE+0x3fb) [0xe3681b]
[openfoam01:00756] [ 7] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libfiniteVolume.so(_ZNK4Foam26 surfaceInterpolationSchemeINS_6TensorIdEEE11interp olateERKNS_14GeometricFieldIS2 _NS_12fvPatchFieldENS_7volMeshEEE+0x56) [0xe4b5e6]
[openfoam01:00756] [ 8] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libfiniteVolume.so(_ZN4Foam2fv 14gaussDivSchemeINS_6TensorIdEEE6fvcDivERKNS_14Geo metricFieldIS3_NS_12fvPatchFie ldENS_7volMeshEEE+0x45) [0x1129d85]
[openfoam01:00756] [ 9] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libincompressibleRASModels.so( _ZN4Foam3fvc3divINS_6TensorIdEEEENS_3tmpINS_14Geom etricFieldINS_12innerProductIN S_6VectorIdEET_E4typeENS_12fvPatchFieldENS_7volMes hEEEEERKNS5_IS9_SC_SD_EERKNS_4 wordE+0x79) [0x8209c9]
[openfoam01:00756] [10] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libincompressibleRASModels.so( _ZN4Foam3fvc3divINS_6TensorIdEEEENS_3tmpINS_14Geom etricFieldINS_12innerProductIN S_6VectorIdEET_E4typeENS_12fvPatchFieldENS_7volMes hEEEEERKNS5_IS9_SC_SD_EE+0xbf) [0x82194f]
[openfoam01:00756] [11] /home/leo/OpenFOAM/OpenFOAM-1.5/lib/linuxGccDPOpt/libincompressibleRASModels.so( _ZNK4Foam14incompressible9RASModels15SpalartAllmar as10divDevReffERNS_14Geometric FieldINS_6VectorIdEENS_12fvPatchFieldENS_7volMeshE EE+0x104) [0x8886c4]
[openfoam01:00756] [12] simpleFoam [0x8059657]
[openfoam01:00756] [13] /lib/libc.so.6(__libc_start_main+0xe6) [0x3425d6]
[openfoam01:00756] [14] simpleFoam(_ZN4Foam11regIOobject14readIfModifiedEv +0x1e9) [0x80589d1]
[openfoam01:00756] *** End of error message ***
mpirun noticed that job rank 0 with PID 754 on node openfoam01 exited on signal 6 (Aborted).
2 additional processes aborted (not shown)


So, I thought that maybe the problem would be with the glibc libraries, so I downloaded the rpm packages of the libraries but that didn't do any good. I really am at my wits end on this one, any help would be very much appreciated.

regards

Leo

lhcamilo February 18, 2009 08:11

Problem solved. After spending
 
Problem solved. After spending a few hours banging my head against the keyboard, it turned out hanging nodes were the cause of the problem. Using harpoons option to get rid of the hanging nodes did the trick.

sorry for posting such a novice problem.

anyway problem solved.

happy foaming

leo


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