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Writing fields with layer information makes snappyHexMesh crash in motorbike tutorial (reopen)

    • Open Issue created by Riccardo Rossi @Ricky-11

    I've just tried to test the issue reported in #1420 (closed) with the v1912 and it's still there:

    Writing fields with layer information: nSurfaceLayers : actual number of layers thickness : overall layer thickness [0] #0 [1] #0 [2] #0 [3] #0 [4] #0 [5] #0 Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&) at at ??:?

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      • Riccardo Rossi changed the description

        changed the description

      • Riccardo Rossi
        Riccardo Rossi @Ricky-11 ·
        Author

        I guess this should be classified as a bug and fixed if replicated on your side.

      • Mattijs Janssens
        Mattijs Janssens @Mattijs ·
        Maintainer

        Is this the incompressible simpleFoam motorBike tutorial? What is your architecture?

      • Mattijs Janssens
        Mattijs Janssens @Mattijs ·
        Maintainer

        I've just run develop (which should be similar to v1912 for snappyHexMesh) and see no problems:

        Build  : 97ff8fee20-20200311 OPENFOAM=2002 patch=200129
Arch   : "LSB;label=32;scalar=64"
Exec   : snappyHexMesh -parallel -decomposeParDict system/decomposeParDict.6 -overwrite
        Writing fields with layer information:
    nSurfaceLayers    : actual number of layers
    thickness         : overall layer thickness
    thicknessFraction : overall layer thickness (fraction of desired thickness)

        Can you

        • run with FOAM_SIGFPE=false to make sure it doesn't crash
        • run with 'writeFormat ascii'
        • check afterwards which of the three fields has NaNs in it.
      • Riccardo Rossi
        Riccardo Rossi @Ricky-11 ·
        Author

        This is the system architecture

        Build  : _f3950763fe-20191219 OPENFOAM=1912
Arch   : "LSB;label=32;scalar=64"
Exec   : snappyHexMesh -parallel -decomposeParDict system/decomposeParDict.6 -overwrite
        Edited by Riccardo Rossi
      • Riccardo Rossi
        Riccardo Rossi @Ricky-11 ·
        Author

        Using FOAM_SIGFPE=false with 'writeFormat ascii I get:

        Writing 27863 added cells to cellSet addedCells
Writing 0 faces inside added layer to faceSet layerFaces

Writing fields with layer information:
    nSurfaceLayers    : actual number of layers
    thickness         : overall layer thickness

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 59575 RUNNING AT r032c02s02
=   EXIT CODE: 8
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
   Intel(R) MPI Library troubleshooting guide:
      https://software.intel.com/node/561764
===================================================================================
        Edited by Riccardo Rossi
      • Riccardo Rossi
        Riccardo Rossi @Ricky-11 ·
        Author

        Using FOAM_SIGFPE=false with 'writeFormat ascii I get:

        Writing fields with layer information:
    nSurfaceLayers    : actual number of layers
    thickness         : overall layer thickness
[0] [1] #0  [2] #0  [3] #0  [4] #0  [5] #0  #0  Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&) at ??:?
[0] #1  Foam::sigFpe::sigHandler(int) at ??:?
[0] #2  ? at ??:?
[0] #3  Foam::snappyLayerDriver::writeLayerData(Foam::fvMesh const&, Foam::List<int> const&, Foam::List<int> const&, Foam::Field<double> const&, Foam::Field<double> const&) const in /lib64/libc.so.6
[0] #4  Foam::snappyLayerDriver::addLayers(Foam::layerParameters const&, Foam::dictionary const&, Foam::List<int> const&, int, Foam::decompositionMethod&, Foam::fvMeshDistribute&) at ??:?
[0] #5  Foam::snappyLayerDriver::doLayers(Foam::dictionary const&, Foam::dictionary const&, Foam::layerParameters const&, Foam::meshRefinement::FaceMergeType, bool, Foam::decompositionMethod&, Foam::fvMeshDistribute&) at ??:?

        Note that I've copied last error messages coming from processor0 only for sake of space.

      • Mattijs Janssens
        Mattijs Janssens @Mattijs ·
        Maintainer

        If still seems to be using floating-point exceptions. Are you running with

        export FOAM_SIGFPE=false

        ?

        1. The issue seems might come from the division

        patchReal[i]/patchWanted[i]

        (is in two places). This is protected with

        patchWanted[i] > VSMALL

        what happens if you replace that VSMALL with ROOTVSMALL (1e-150) or even SMALL (1e-15)?

      • Riccardo Rossi
        Riccardo Rossi @Ricky-11 ·
        Author

        I have edited the Allrun script as follows for testing:

        export FOAM_SIGFPE=true/false

runParallel $decompDict snappyHexMesh -overwrite

        Do I need to recompile snappyHexMesh to change VSMALL or can I set it somewhere/somehow?

        Edited by Riccardo Rossi
      • Mattijs Janssens
        Mattijs Janssens @Mattijs ·
        Maintainer

        We're still trying to figure out why it crashes for you and not for others.

        • you'll have change snappyLayerDriver.C and recompile & rerun
        • can you post your complete log file? Just trying to make sure that sigFpe (floating point error trapping) is switched off
      • Riccardo Rossi
        Riccardo Rossi @Ricky-11 ·
        Author

        I've just tested the v2006 and the bug is still there.

      • Mattijs Janssens
        Mattijs Janssens @Mattijs ·
        Maintainer

        Can you post your log file?

      • Riccardo Rossi
        Riccardo Rossi @Ricky-11 ·
        Author

        log.snappyHexMesh

      • Mattijs Janssens
        Mattijs Janssens @Mattijs ·
        Maintainer

        Can you run with

        unset FOAM_SETNAN
unset FOAM_SIGFPE

        ? I did notice some problem in that they actually need to be unset and not set to e.g. false.

      • Riccardo Rossi
        Riccardo Rossi @Ricky-11 ·
        Author

        Is it sufficient to do it in the terminal where I'll be issuing snappyHexMesh?

      • Mattijs Janssens
        Mattijs Janssens @Mattijs ·
        Maintainer

        sure

      • Riccardo Rossi
        Riccardo Rossi @Ricky-11 ·
        Author

        Just tried adding

        unset FOAM_SETNAN
unset FOAM_SIGFPE

        in the ''Allrun'' script and I get the same error.

      • puneet singh
        puneet singh @puneet336 ·

        getting the same issue at the snappyHexMesh step.

        Writing 27781 added cells to cellSet addedCells
Writing 0 faces inside added layer to faceSet layerFaces

Writing fields with layer information:
    nSurfaceLayers    : actual number of layers
    thickness         : overall layer thickness
[node1:2199184:0:2199184] Caught signal 8 (Floating point exception: floating-point invalid operation)
[node1:2199182:0:2199182] Caught signal 8 (Floating point exception: floating-point invalid operation)
[node1:2199181:0:2199181] Caught signal 8 (Floating point exception: floating-point invalid operation)
[node1:2199180:0:2199180] Caught signal 8 (Floating point exception: floating-point invalid operation)
[node1:2199183:0:2199183] Caught signal 8 (Floating point exception: floating-point invalid operation)
==== backtrace (tid:2199182) ====
 0 0x00000000000532f9 ucs_debug_print_backtrace()  ???:0
 1 0x0000000000037790 .annobin_sigaction.c()  sigaction.c:0
 2 0x000000000007d62f Foam::snappyLayerDriver::writeLayerData()  ???:0
 3 0x000000000006e467 Foam::snappyLayerDriver::addLayers()  ???:0
 4 0x00000000000687df Foam::snappyLayerDriver::doLayers()  ???:0
 5 0x000000000041851b main()  ???:0
 6 0x00000000000236a3 __libc_start_main()  ???:0
 7 0x00000000004150ae _start()  ???:0
=================================
==== backtrace (tid:2199181) ====
 0 0x00000000000532f9 ucs_debug_print_backtrace()  ???:0
 1 0x0000000000037790 .annobin_sigaction.c()  sigaction.c:0
 2 0x000000000007d653 Foam::snappyLayerDriver::writeLayerData()  ???:0
 3 0x000000000006e467 Foam::snappyLayerDriver::addLayers()  ???:0
 4 0x00000000000687df Foam::snappyLayerDriver::doLayers()  ???:0
 5 0x000000000041851b main()  ???:0
 6 0x00000000000236a3 __libc_start_main()  ???:0
 7 0x00000000004150ae _start()  ???:0
=================================
==== backtrace (tid:2199180) ====
 0 0x00000000000532f9 ucs_debug_print_backtrace()  ???:0
 1 0x0000000000037790 .annobin_sigaction.c()  sigaction.c:0
 2 0x000000000007d62f Foam::snappyLayerDriver::writeLayerData()  ???:0
 3 0x000000000006e467 Foam::snappyLayerDriver::addLayers()  ???:0
 4 0x00000000000687df Foam::snappyLayerDriver::doLayers()  ???:0
 5 0x000000000041851b main()  ???:0
 6 0x00000000000236a3 __libc_start_main()  ???:0
 7 0x00000000004150ae _start()  ???:0
=================================
==== backtrace (tid:2199184) ====
 0 0x00000000000532f9 ucs_debug_print_backtrace()  ???:0
 1 0x0000000000037790 .annobin_sigaction.c()  sigaction.c:0
 2 0x000000000007d62f Foam::snappyLayerDriver::writeLayerData()  ???:0
 3 0x000000000006e467 Foam::snappyLayerDriver::addLayers()  ???:0
 4 0x00000000000687df Foam::snappyLayerDriver::doLayers()  ???:0
 5 0x000000000041851b main()  ???:0
 6 0x00000000000236a3 __libc_start_main()  ???:0
 7 0x00000000004150ae _start()  ???:0
=================================
==== backtrace (tid:2199183) ====
 0 0x00000000000532f9 ucs_debug_print_backtrace()  ???:0
 1 0x0000000000037790 .annobin_sigaction.c()  sigaction.c:0
 2 0x000000000007d62f Foam::snappyLayerDriver::writeLayerData()  ???:0
 3 0x000000000006e467 Foam::snappyLayerDriver::addLayers()  ???:0
 4 0x00000000000687df Foam::snappyLayerDriver::doLayers()  ???:0
 5 0x000000000041851b main()  ???:0
 6 0x00000000000236a3 __libc_start_main()  ???:0
 7 0x00000000004150ae _start()  ???:0
=================================
===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 0 PID 2199180 RUNNING AT node1
=   KILLED BY SIGNAL: 8 (Floating point exception)
===================================================================================

        WM_PRECISION_OPTION was set to SP, and FOAM_SIGFPE was set to blank during compilation. compiler is intel 2019 and -march=core-avx2 was the compiler flag. OS- CentOS 8

        could you please suggest the changes in the snappyLayerDriver.C file which could fix this issue?

        Edited by puneet singh
      • Mattijs Janssens
        Mattijs Janssens @Mattijs ·
        Maintainer

        Can you confirm you don't see

        trapFpe: Floating point exception trapping enabled (FOAM_SIGFPE).

        in the log file?

        1. You could check for any division inside writeLayerData, e.g.
        pfld[i] = patchReal[i]/patchWanted[i];

        Maybe patchWanted is larger than VSMALL but still too small to divide against.

      • Mark OLESEN mentioned in commit 23e27b17fe5968863cae14ca15d12c1d860c29f2

        mentioned in commit 23e27b17fe5968863cae14ca15d12c1d860c29f2

      • Mark OLESEN mentioned in commit 08588134

        mentioned in commit 08588134

      • Mark OLESEN mentioned in commit 0c891547

        mentioned in commit 0c891547

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