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LTSReactingParcelFoam doesn't work in parallel

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Old   August 2, 2012, 06:41
Default LTSReactingParcelFoam doesn't work in parallel
  #1
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Hi all,

I figured out that the LTSReactingParcelFoam Solver does not run in parrelel.

When I start the simulation I receive the following error message.

Quote:
[1] --> FOAM FATAL ERROR:
[1] read failed
[1]
[1] From function UIPstream::UIPstream(const commsTypes, const int, DynamicList<char>&, streamFormat, versionNumber)
[1] in file UIPread.C at line [2]

[4]
[4] --> FOAM FATAL ERROR:
[4] read failed
[4]
[4] From function UIPstream::UIPstream(const commsTypes, const int, DynamicList<char>&, streamFormat, versionNumber)
[4] in file UIPread.C at line 114.
[4]
FOAM parallel run aborting
[4]
114.
[1]
FOAM parallel run aborting
[1]
[2]
[2] --> FOAM FATAL ERROR:
[2] read failed
[2]
[2] From function UIPstream::UIPstream(const commsTypes, const int, DynamicList<char>&, streamFormat, versionNumber)
[2] in file UIPread.C at line 114.
[2]
FOAM parallel run aborting
[2]
[1] #0 [4] Foam::error::printStack(Foam::Ostream&)#0 Foam::error::printStack(Foam::Ostream&)[2] #0 Foam::error::printStack(Foam::Ostream&) in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[2] #1 Foam::error::abort() in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[4] #1 Foam::error::abort() in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[1] #1 Foam::error::abort() in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[2] #2 Foam::UIPstream::UIPstream(Foam::UPstream::commsTy pes, int, Foam::DynamicList<char, 0u, 2u, 1u>&, int&, int, bool, Foam::IOstream::streamFormat, Foam::IOstream::versionNumber) in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[4] #2 Foam::UIPstream::UIPstream(Foam::UPstream::commsTy pes, int, Foam::DynamicList<char, 0u, 2u, 1u>&, int&, int, bool, Foam::IOstream::streamFormat, Foam::IOstream::versionNumber) in "/usr/local/openfoam/OpenFOAM-2.1.0/plat in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/openmpi-1.5.3/libPstream.so"
[2] #3 Foam::IPstream::IPstream(Foam::UPstream::commsType s, int, int, int, Foam::IOstream::streamFormat, Foam::IOstream::versionNumber)forms/linux64GccDPOpt/lib/libOpenFOAM.so"
[1] #2 Foam::UIPstream::UIPstream(Foam::UPstream::commsTy pes, int, Foam::DynamicList<char, 0u, 2u, 1u>&, int&, int, bool, Foam::IOstream::streamFormat, Foam::IOstream::versionNumber) in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/openmpi-1.5.3/libPstream.so"
[4] #3 Foam::IPstream::IPstream(Foam::UPstream::commsType s, int, int, int, Foam::IOstream::streamFormat, Foam::IOstream::versionNumber) in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[2] #4 in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/openmpi-1.5.3/libPstream.so"
[1] #3 Foam::IPstream::IPstream(Foam::UPstream::commsType s, int, int, int, Foam::IOstream::streamFormat, Foam::IOstream::versionNumber)Foam::IOdictionary:: readFile(bool) in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[4] #4 Foam::IOdictionary::readFile(bool) in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[2] #5 Foam::IOdictionary::IOdictionary(Foam::IOobject const&) in "/usr/local/openfoam/OpenFOA in "/usr/local/openfoMam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[4] #5 Foam::IOdictionary::IOdictionary(Foam::IOobject const&)-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[1] #4 Foam::IOdictionary::readFile(bool) in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[2] #6 Foam::IObasicSourceList::IObasicSourceList(Foam::f vMesh const&) in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[1] #5 Foam::IOdictionary::IOdictionary(Foam::IOobject const&) in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[4] #6 Foam::IObasicSourceList::IObasicSourceList(Foam::f vMesh const&) in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libfiniteVolume.so"
[4] #7 in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libfiniteVolume.so"
[2] #7 in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[1] #6 Foam::IObasicSourceList::IObasicSourceList(Foam::f vMesh const&) in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libfiniteVolume.so"
[1] #7 mainmain in in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/bin/porousExplicitSourceReactingParcelFoam_new"
[4] #8 __libc_start_main"/usr/lmainocal/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/bin/porousExplicitSourceReactingParcelFoam_new"
[2] #8 __libc_start_main in "/lib64/libc.so.6"
[4] #9 in "/usr/local/openfoam/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/bin/porousExplicitSourceReactingParcelFoam_new"
[1] #8 __libc_start_main in "/lib64/libc.so.6"
[2] #9 in "/lib64/libc.so.6"
[1] #9 _start_start at /usr/src/packages/BUILD/glibc-2.9/csu/../sysdeps/x86_64/elf/start.S:116
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 4 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
_start at /usr/src/packages/BUILD/glibc-2.9/csu/../sysdeps/x86_64/elf/start.S:116
at /usr/src/packages/BUILD/glibc-2.9/csu/../sysdeps/x86_64/elf/start.S:116
--------------------------------------------------------------------------
mpirun has exited due to process rank 4 with PID 3790 on
node fe-z0bb9 exiting improperly. There are two reasons this could occur:

1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.

2. this process called "init", but exited without calling "
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"

This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
Have anybody faced the same problem?

What can be the reason for that problem?

Kind regards

Christian
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Old   August 2, 2012, 15:24
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  #2
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Bruno Santos
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Greetings Christian,

This issue is currently being tracked here: http://www.openfoam.org/mantisbt/view.php?id=579

Best regards,
Bruno
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Old   August 5, 2012, 06:19
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Hello Bruno,

thank you for the link!

I tried to implement those recommendations.

After changing the files like described in our link I recompiled /src/Pstream with "Allwmake"

But the solver LTSReactingParcelFoam ist still not running in parallel. Now I receive the following error message:
Quote:
Creating field source list from sourcesProperties

[1]
[1] [2]
[2]
[2] --> FOAM FATAL IO ERROR: [4]
[4]
[4] --> FOAM FATAL IO ERROR:
[4] Istream not OK for reading dictionary
[4]
[4] file: IOstream at line 0.
[4]
[4] From function
[1] --> FOAM FATAL IO ERROR:
[1] Istream not OK for reading dictionary
[1]
[1] file: IOstream at line 0.
[1]
[1] From function dictionary::read(Istream&, bool)
[1] in file
[2] Istream not OK for reading dictionary
[2]
[2] file: IOstream at line 0.
[2]
[2] From function dictionary::read(Istream&, bool)
[2] in file Creating porous zones

dictionary::read(Istream&, bool)
[4] in file db/dictionary/dictionaryIO.C at line 85.
[4]
FOAM parallel run exiting
[4]
db/dictionary/dictionaryIO.C at line 85.
[1]
FOAM parallel run exiting
[1]
db/dictionary/dictionaryIO.C at line 85.
[2]
FOAM parallel run exiting
[2]

Starting time loop

--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun has exited due to process rank 4 with PID 18035 on
node christian-laptop exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[christian-laptop:18030] 2 more processes have sent help message help-mpi-api.txt / mpi-abort
[christian-laptop:18030] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
What was my mistake in implementing the described changes?

Kind regards

Christian
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Old   August 5, 2012, 08:01
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Bruno Santos
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Hi Christian,

Mmm... there might have been other modifications along the way that might be necessary as well. The simplest way would be for you to build the latest OpenFOAM 2.1.x and that way you'll be certain that no changes were missed .

Best regards,
Bruno
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Old   August 6, 2012, 03:08
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Dima Risch
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Hello Christian,

i think you have to recompile src/OpenFOAM/db/dictionary/dictionaryIO.C and the solver too

of course Bruno's way will be the safest, but if you have not done it yet try ...

in /OpenFOAM-2.1.x/src/OpenFOAM/
type: wmake libso (maybe Allwmake in /OpenFOAM-2.1.x/src is necessary)

and in /OpenFOAM-2.1.x/applications/solvers/lagrangian/LTSReactingParcelFoam/
type: wmake (maybe wclean before)

kind regards,
Dima
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