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Old   September 14, 2011, 11:41
Default error using Grid Engine
  #1
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Andrea Ferrari
Join Date: Dec 2010
Posts: 275
Rep Power: 7
Andrea_85 is on a distinguished road
Hi foamers,
I'm trying to use Grid Engine to launch my simulation in parallel on a cluster. Up to now I used the classic "mpirun -np whatever whatever -parallel > log &" for parallel simulation and everything was fine, but i need to use Grid Engine.
So i wrote a small script and i submitted my job using qsub.
I get this error using interFoam:
Code:
Starting openFoam with GridEngine...
(Follow execution details in file "qsub_start_openFoam.sh.o[JobID]".)

--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 11 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.
--------------------------------------------------------------------------
[11]
[11]
[11] --> FOAM FATAL IO ERROR:
[11] error in IOstream "IOstream" for operation operator>>(Istream&, List<T>&)
[11]
[11] file: IOstream at line 0.
[11]
[11]     From function IOstream::fatalCheck(const char*) const
[11]     in file db/IOstreams/IOstreams/IOstream.C at line 108.
[11]
FOAM parallel run exiting
[11]
[8]
[8]
[8] --> FOAM FATAL IO ERROR:
[8] error in IOstream "IOstream" for operation operator>>(Istream&, List<T>&)
[8]
[8] file: IOstream at line 0.
[8]
[8]     From function IOstream::fatalCheck(const char*) const
[8]     in file db/IOstreams/IOstreams/IOstream.C at line 108.
[8]
FOAM parallel run exiting
[8]
[10]
[10]
[10] --> FOAM FATAL IO ERROR:
[10] error in IOstream "IOstream" for operation operator>>(Istream&, List<T>&)
[10]
[10] file: IOstream at line 0.
[10]
[10]     From function IOstream::fatalCheck(const char*) const
[10]     in file db/IOstreams/IOstreams/IOstream.C at line 108.
[10]
FOAM parallel run exiting
[10]
[9]
[9]
[9] --> FOAM FATAL IO ERROR:
[9] wrong token type - expected int found on line 0 the word 'Y'
[9]
[9] file: IOstream at line 0.
[9]
[9]     From function operator>>(Istream&, int&)
[9]     in file primitives/ints/int/intIO.C at line 68.
[9]
FOAM parallel run exiting
[9]
--------------------------------------------------------------------------
mpirun has exited due to process rank 11 with PID 23274 on
node node12.cluster exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[node11.cluster:17619] 3 more processes have sent help message help-mpi-api.txt / mpi-abort
[node11.cluster:17619] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
    
Simulation terminated.
The strange thing is that if i use simpleFoam on the same case (just for try) everything is ok and the simulation runs without any problem.

This is my log file:

Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  1.7.1                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 1.7.1-03e7e056c215
Exec   : interFoam -parallel
Date   : Sep 14 2011
Time   : 17:17:08
Host   : node11.cluster
PID    : 17623
Case   : /home/aferrari/Simulation/OstacoliPerturbati/BigGeometry/Case2_616_side06/provaNuova2e-2alpha150/36proc
nProcs : 16
Slaves :
15
(
node11.cluster.17624
node11.cluster.17625
node11.cluster.17626
node11.cluster.17627
node11.cluster.17628
node11.cluster.17629
node11.cluster.17630
node12.cluster.23271
node12.cluster.23272
node12.cluster.23273
node12.cluster.23274
node12.cluster.23275
node12.cluster.23276
node12.cluster.23277
node12.cluster.23278
)

Pstream initialized with:
    floatTransfer     : 0
    nProcsSimpleSum   : 0
    commsType         : nonBlocking
SigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).

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

Create mesh for time = 0

Reading field p_rgh

Reading field alpha1

Reading field U

Reading/calculating face flux field phi

Reading transportProperties

Selecting incompressible transport model Newtonian
Selecting incompressible transport model Newtonian

Selecting turbulence model type laminar

Reading g
Calculating field g.h
The simulation stops right at the point where the gravity field is calculated (i checked), at this line:

volScalarField gh("gh", g & mesh.C());
surfaceScalarField ghf("ghf", g & mesh.Cf());


I really can not figure out what could be the problem. If i launch the same case using mpirun everything is ok.

Any idea?

thanks

andrea
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Old   September 15, 2011, 04:14
Default
  #2
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Andrea Ferrari
Join Date: Dec 2010
Posts: 275
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Andrea_85 is on a distinguished road
This is the script i wrote:

#!/bin/bash
#$ -S /bin/bash
#$ -e $JOB_NAME.e$JOB_ID
#$ -o $JOB_NAME.o$JOB_ID
#$ -cwd
#$ -j y
#$ -pe orte 36
echo ""
echo "Starting openFoam with GridEngine..."
echo "(Follow execution details in file \"qsub_start_openFoam.sh.o[JobID]\".)"
echo ""
mpirun interFoam -parallel > log
echo ""
echo "Simulation terminated."
echo ""

Then i launch the simulation using "qsub script.sh".
Does anyone known why it works with simpleFoam and not with interFoam?

Any help is appreciated!!

best

andrea
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