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-   -   OpenFOAM can't be run in parallel in cluster (https://www.cfd-online.com/Forums/openfoam-solving/184032-openfoam-cant-run-parallel-cluster.html)

sibo February 20, 2017 21:26

OpenFOAM can't be run in parallel in cluster
 
Hello All,

I am trying to run an airfoil case using simpleFoam in parallel with 4 processors in cluster. I can load mpi successfully using "module load openmpi-x86_64 " and the domain is decomposed successfully. But when I type: "mpirun -np 4 simpleFoam -parallel > case.log",
I run into trouble.

Code:

[0]
[0]
[0] --> FOAM FATAL IO ERROR:
[0] wrong token type - expected word, found on line 22 the punctuation token '['
[0]
[0] file: /mnt/store1/home/sli218/try1/processor0/../constant/transportProperties::nu at line 22.
[0]
[0]    From function operator>>(Istream&, word&)
[0]    in file primitives/strings/word/wordIO.C at line 74.
[0]
FOAM parallel run exiting
[0]
[1]
[1]
[1] --> FOAM FATAL IO ERROR:
[1] wrong token type - expected word, found on line 0 the punctuation token '['
[1]
[1] file: IOstream::nu at line 0.
[1]
[1]    From function operator>>(Istream&, word&)
[1]    in file primitives/strings/word/wordIO.C at line 74.
[1]
FOAM parallel run exiting
[1]
[2]
[2]
[2] --> FOAM FATAL IO ERROR:
[2] wrong token type - expected word, found on line 0 the punctuation token '['
[2]
[2] file: IOstream::nu at line 0.
[2]
[2]    From function operator>>(Istream&, word&)
[2]    in file primitives/strings/word/wordIO.C at line 74.
[2]
FOAM parallel run exiting
[2]
[3]
[3]
[3] --> FOAM FATAL IO ERROR:
[3] wrong token type - expected word, found on line 0 the punctuation token '['
[3]
[3] file: IOstream::nu at line 0.
[3]
[3]    From function operator>>(Istream&, word&)
[3]    in file primitives/strings/word/wordIO.C at line 74.
[3]
FOAM parallel run exiting
[3]
--------------------------------------------------------------------------
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 2 with PID 21185 on
node login-1.extreme.uic.edu 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).
--------------------------------------------------------------------------
[login-1.extreme.uic.edu:21179] 3 more processes have sent help message help-mpi-api.txt / mpi-abort
[login-1.extreme.uic.edu:21179] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

And I tried to run this case in parallel with 4 processors in my own laptop, it works fine.


Can someone suggest how I can fix this? Thanks a lot!!!
Sibo

sibo February 20, 2017 21:28

turbulenceProperties
 
Code:

/*--------------------------------*- C++ -*----------------------------------*\
| =========                |                                                |
| \\      /  F ield        | OpenFOAM: The Open Source CFD Toolbox          |
|  \\    /  O peration    | Version:  3.0.1                                |
|  \\  /    A nd          | Web:      www.OpenFOAM.org                      |
|    \\/    M anipulation  |                                                |
\*---------------------------------------------------------------------------*/
FoamFile
{
    version    2.0;
    format      ascii;
    class      dictionary;
    location    "constant";
    object      transportProperties;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

transportModel  Newtonian;

rho            [1 -3 0 0 0 0 0] 1.2;

nu              [0 2 -1 0 0 0 0] 1.7e-05;

CrossPowerLawCoeffs
{
nu0    nu0 [ 0 2 -1 0 0 0 0 ] 1e-06;
nuInf    nuInf [ 0 2 -1 0 0 0 0 ] 1e-06;
m      m [ 0 0 1 0 0 0 0 ] 1;
n      n [ 0 0 0 0 0 0 0 ] 1;
}

BirdCarreauCoeffs
{
nu0    nu0 [ 0 2 -1 0 0 0 0 ] 1e-06;
nuInf    nuInf [ 0 2 -1 0 0 0 0 ] 1e-06;
k      k [ 0 0 1 0 0 0 0 ] 0;
n      n [ 0 0 0 0 0 0 0 ] 1;
}

// ************************************************************************* //


Antimony February 21, 2017 02:07

Hi,

Are the two versions of OF the same (the one on your laptop and the one in cluster)?

From your error message:

Code:

wrong token type - expected word, found on line 0 the punctuation token '['
It would seem that the two versions are not the same. The quick fix would be to do what the error message expects of you. So in the transportProperties file, change this

Code:

nu [0 2 -1 0 0 0 0] 1.7E-05;
To this:

Code:

nu nu [0 2 -1 0 0 0 0] 1.7E-05;
Hope this helps.

Cheers,
Antimony

babakflame February 21, 2017 15:57

Hey sibo

What Antimony said, is correct.

You need to be careful about these stuff. Are u using same versions of OpenFoam on the cluster and your laptop. It seems that you are facing a template error due to version conflicts.

Regards

sibo February 21, 2017 16:29

Hi Antimony and Babak,

Thanks for your reply!
It really enlightened me. I will see if it works now.


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