[bling]

Hi All,

I am a newbie to openfoam. I was trying to run a DES case using pisofoam on a cluster but ending up with a fatal error message. Can anyone help me slove this problem? Thanks a lot!

Junji

--> FOAM FATAL IO ERROR:
Expected a ')' while reading binaryBlock, found on line 20 an error

file: /lustre/home/junji/test/constant/polyMesh/faces at line 20.

From function Istream::readEnd(const char*)
in file db/IOstreams/IOstreams/Istream.C at line 111.

FOAM exiting



--> FOAM FATAL IO ERROR:
Expected a ')' while reading binaryBlock, found on line 20 an error

file: /lustre/home/junji/test/constant/polyMesh/faces at line 20.

From function Istream::readEnd(const char*)
in file db/IOstreams/IOstreams/Istream.C at line 111.

FOAM exiting

[0]
[0]
[0] --> FOAM FATAL ERROR:
[0] pisoFoam: cannot open case directory "/lustre/home/junji/test/processor0"
[0]
[0]
FOAM parallel run exiting
[0]
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 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 0 with PID 32460 on
node cwrc-c02 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 "finalize".
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).
--------------------------------------------------------------------------

[arsalan.dryi]

Hi Jeremy,

Did you run decomposePar application for using parallel processing?
If yes, attach your case for more information.

Regards,
Arsalan.

[bling]

Originally Posted by arsalan.dryi

Hi Jeremy,

Did you run decomposePar application for using parallel processing?
If yes, attach your case for more information.

Regards,
Arsalan.

Hi Arsalan,

Many thanks to your reply!

Yes, I do the decomposition, but the simulation crashes before I could run decomposePar. I noticed this problem happening because I was writing down the mesh file with binary format. After I change it into ascii, the problem was solved... although I don't the reason...

And moreover... I ran into a different problem... I created my own boundary condition which is time-dependent. After I run pisoFoam I find the max courant number keeps exploding till it reaches an incredibly large number and simulation goes down, leaving the error message below which says
"floating point exception". Does anyone know this problem?

Junji

[0] [1] [2] [3] ##0#0    0  Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)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:          cl1n131 (PID 7568)
  MPI_COMM_WORLD rank: 1

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.
--------------------------------------------------------------------------
 in "/global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libOpenFOAM.so"
[3] #1  Foam::sigFpe::sigHandler(int) in "/global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libOpenFOAM.so"
[2] #1  Foam::sigFpe::sigHandler(int) in "/global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libOpenFOAM.so"
[1] #1  Foam::sigFpe::sigHandler(int) in "/global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libOpenFOAM.so"
[0] #1  Foam::sigFpe::sigHandler(int) addr2line failed
[0] #2  ? in "/global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libOpenFOAM.so"
[3] #2  ? addr2line failed
[0] #3  ? in "/global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libOpenFOAM.so"
[2] #2  ? in "/lib64/libpthread.so.0"
[3] #3  ? in "/global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libOpenFOAM.so"
[1] #2  ? in "/lib64/libpthread.so.0"
[2] #3  ? addr2line failed
[2] #4  Foam::tanh(Foam::Field<double>&, Foam::UList<double> const&) at /export/users/nbtester/efi2linux_nightly/branch-13_0/20121011_000000/libd$
[3] #4  Foam::tanh(Foam::Field<double>&, Foam::UList<double> const&) at /export/users/nbtester/efi2linux_nightly/branch-13_0/20121011_000000/libd$
[0] #4  Foam::tanh(Foam::Field<double>&, Foam::UList<double> const&) in "/lib64/libpthread.so.0"
[1] #3  ? in "/global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libOpenFOAM.so"
[2] #5  Foam::tmp<Foam::GeometricField<double, Foam::volMesh> > Foam::tanh<Foam::fvPatchField, Foam::volMesh>(Foam::tmp<Foam::GeometricField<doub$
[3] #5  Foam::tmp<Foam::GeometricField<double, Foam::volMesh> > Foam::tanh<Foam::fvPatchField, Foam::volMesh>(Foam::tmp<Foam::GeometricField<doub$
[2] #6  Foam::LESModels::SpalartAllmarasDDES<Foam::IncompressibleTurbulenceModel<Foam::transportModel> >::dTilda(Foam::GeometricField<double, Foa$
[1] #4  Foam::tanh(Foam::Field<double>&, Foam::UList<double> const&) addr2line failed
[2] #7  Foam::LESModels::SpalartAllmarasDES<Foam::IncompressibleTurbulenceModel<Foam::transportModel> >::correct() in "/global/software/OpenFOAM/$
[0] #5  Foam::tmp<Foam::GeometricField<double, Foam::volMesh> > Foam::tanh<Foam::fvPatchField, Foam::volMesh>(Foam::tmp<Foam::GeometricField<doub$
[2] #8  main in "/global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libincompressibleTurbulenceModels.so"
[3] #6  Foam::LESModels::SpalartAllmarasDDES<Foam::IncompressibleTurbulenceModel<Foam::transportModel> >::dTilda(Foam::GeometricField<double, Foa$
[2] #9  __libc_start_main in "/global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libincompressibleTurbulenceModels.so"
[0] #6  Foam::LESModels::SpalartAllmarasDDES<Foam::IncompressibleTurbulenceModel<Foam::transportModel> >::dTilda(Foam::GeometricField<double, Foa$
[1] #5  Foam::tmp<Foam::GeometricField<double, Foam::volMesh> > Foam::tanh<Foam::fvPatchField, Foam::volMesh>(Foam::tmp<Foam::GeometricField<doub$
[2] #10   in "/global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libincompressibleTurbulenceModels.so"
[3] #7  Foam::LESModels::SpalartAllmarasDES<Foam::IncompressibleTurbulenceModel<Foam::transportModel> >::correct() in "/global/software/OpenFOAM/$
[0] #7  Foam::LESModels::SpalartAllmarasDES<Foam::IncompressibleTurbulenceModel<Foam::transportModel> >::correct() in "/global/software/OpenFOAM/$
[1] #6  Foam::LESModels::SpalartAllmarasDDES<Foam::IncompressibleTurbulenceModel<Foam::transportModel> >::dTilda(Foam::GeometricField<double, Foa$
[cl1n131:07569] *** Process received signal ***
[cl1n131:07569] Signal: Floating point exception (8)
[cl1n131:07569] Signal code:  (-6)
[cl1n131:07569] Failing at address: 0x2e84db00001d91
[cl1n131:07569] [ 0] /lib64/libpthread.so.0() [0x392ea0f7e0]
[cl1n131:07569] [ 1] /lib64/libpthread.so.0(raise+0x2b) [0x392ea0f6ab]
[cl1n131:07569] [ 2] /lib64/libpthread.so.0() [0x392ea0f7e0]
[cl1n131:07569] [ 3] /global/software/intel/l_ics_2013.0.028/composer_xe_2013.1.117/compiler/lib/intel64/libsvml.so(+0x18e599) [0x2aeb8b854599]
[cl1n131:07569] [ 4] /global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam4tanhERNS_5FieldIdEERKNS_$
[cl1n131:07569] [ 5] /global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libincompressibleTurbulenceModels.so(_ZN4Foam4ta$
[cl1n131:07569] [ 6] /global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libincompressibleTurbulenceModels.so(_ZNK4Foam9L$
[cl1n131:07569] [ 7] /global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libincompressibleTurbulenceModels.so(_ZN4Foam9LE$
[cl1n131:07569] [ 8] pisoFoam(main+0x1a65) [0x41a955]
[cl1n131:07569] [ 9] /lib64/libc.so.6(__libc_start_main+0xfd) [0x392e21ed1d]
[cl1n131:07569] [10] pisoFoam() [0x418e29]
[cl1n131:07569] *** End of error message ***
 in "/global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libincompressibleTurbulenceModels.so"
[3] #8   in "/global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libincompressibleTurbulenceModels.so"
[0] #8   in "/global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libincompressibleTurbulenceModels.so"
[1] #7  Foam::LESModels::SpalartAllmarasDES<Foam::IncompressibleTurbulenceModel<Foam::transportModel> >::correct()main in "/global/software/OpenF$
[3] #9  __libc_start_main in "/lib64/libc.so.6"
[3] #10  ? in "/global/software/OpenFOAM/OpenFOAM-3.0.1/platforms/linux64IccDPInt32Opt/lib/libincompressibleTurbulenceModels.so"
[1] #8  main--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 7569 on node cl1n131 exited on signal 8 (Floating point exception).
--------------------------------------------------------------------------
[cl1n131:07566] 3 more processes have sent help message help-mpi-runtime.txt / mpi_init:warn-fork
[cl1n131:07566] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

[cfd lover]

I solved the problem for my case although it has not converged yet. i changed the values of k and epsilon files (internal values and inlet values).

[Iose]

Hi Guys,
I am facing the same problem:

/*---------------------------------------------------------------------------*\
  =========                 |
  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
   \\    /   O peration     | Website:  https://openfoam.org
    \\  /    A nd           | Version:  6
     \\/     M anipulation  |
\*---------------------------------------------------------------------------*/
Build  : 6-9f9576a0e767
Exec   : checkMesh
Date   : Jan 04 2019
Time   : 11:16:47
Host   : "hwul"
PID    : 20824
I/O    : uncollated
Case   : /home/jdobes/OpenFOAM/Calculation/Audi_H-Tron_FC452_WCAC/Audi_H-Tron_1_CS
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create polyMesh for time = 0



--> FOAM FATAL IO ERROR:
Expected a ')' while reading binaryBlock, found on line 20 the word 'g▒'

file: /home/jdobes/OpenFOAM/Calculation/Audi_H-Tron_FC452_WCAC/Audi_H-Tron_1_CS/constant/polyMesh/faces at line 20.

    From function Foam::Istream& Foam::Istream::readEnd(const char*)
    in file db/IOstreams/IOstreams/Istream.C at line 109.

FOAM exiting

Do you think that convert mesh from binary to ascii solved the problem?

[massive_turbulence]

Are you sure you have the same exact directories on your cluster for where you run your files?

Assuming it's Linux ( or probably windows with "my documents", although spaces in Openfoam are also a pain) If you have your master as

/home/user/run

then all your machines must have the same name "user" and the exact same directories.

[Iose]

Hi massive_turbulence,
yes I am sure about this. But now it works. The main problem was only in binary format of OpenFOAM case, So I used foamFormatConvert, this application wored properly but the constant/polymesh/faces files this application doesn't change. But if I used createBaffles - I need some internal faces where monitoring the pressures; this application changes also the faces files. It is strange to me. But somehow works.