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big difference between clockTime and executionTime

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Old   February 19, 2014, 08:20
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Join Date: Dec 2009
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katakgoreng is on a distinguished road
Hi Bruno,

I managed to get OpenFOAM running on the cluster for 2 nodes using the method that you proposed.

This time, I don't copy the case folder to the cluster node temporary folder and run openfoam application by using the "-case" statement.

PBS job script that I use:

Code:
#!/bin/bash
#
# --- SET THE PBS DIRECTIVES
#PBS -l walltime=2:00:00
#PBS -l select=2:ncpus=16:mpiprocs=16:mem=4000mb 
#PBS -e ehk112_err		
#PBS -o ehk112_out		
#PBS -m ae
#PBS -M erwanhafizi@hotmail.com
#PBS -V

echo "============================================="
echo "FOLDER LOCATION AND NAME"
echo "============================================="
CASEFOLDER="damBreak32"
CASELOCATION="$WORK/CASEFOLDER/"
echo $CASEFOLDER
echo $CASELOCATION

echo "============================================="
echo "SOURCING SYSTEM BASHRC"
echo "============================================="
. $HOME/.bash_profile

echo "============================================="
echo "SOURCING OPENFOAM 2.2.x BASHRC"
echo "============================================="
. /home/ehk112/OpenFOAM/OpenFOAM-2.2.x/etc/bashrc

echo "============================================="
echo "CD TO CASE FOLDER"
echo "============================================="
cd $CASELOCATION/$CASEFOLDER

echo "============================================="
echo "RUNNING OPENFOAM BATCH SCRIPT"
echo "============================================="
./Allrun
OpenFOAM batch script
Code:
#!/bin/bash

# ===============================
# PREPARE CASES
# ===============================
rm log.*
cp -rf 0/backup/* 0/

# ===============================
# MESHING
# ===============================
blockMesh -case /work/ehk112/CASEFOLDER/damBreak32 > log.blockMesh 2>&1

# ===============================
# SET FIELD
# ===============================
setFields -case /work/ehk112/CASEFOLDER/damBreak32 > log.setField 2>&1

# ===============================
# DECOMPOSE DOMAIN
# ===============================
decomposePar -case /work/ehk112/CASEFOLDER/damBreak32 > log.decomposePar 2>&1

# ===============================
# RENUMBER MESH                 
# ===============================
renumberMesh -overwrite -case /work/ehk112/CASEFOLDER/damBreak32 > log.renumberMesh 2>&1

# ===============================
# RUN APPLICATION
# ===============================
mpirun -hostfile $PBS_NODEFILE -np 32 interFoam -parallel -case /work/ehk112/CASEFOLDER/damBreak32 >  log.interFoam 2>&1
The log file:

Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.2.x                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.2.x-0ee7dc546f1b
Exec   : interFoam -parallel -case /work/ehk112/CASEFOLDER/damBreak32
Date   : Feb 19 2014
Time   : 10:31:39
Host   : "cx1-9-17-2.cx1.hpc.ic.ac.uk"
PID    : 28546
Case   : /work/ehk112/CASEFOLDER/damBreak32
nProcs : 32
Slaves : 
31
(
"cx1-9-17-2.cx1.hpc.ic.ac.uk.28547"
"cx1-9-17-2.cx1.hpc.ic.ac.uk.28548"
"cx1-9-17-2.cx1.hpc.ic.ac.uk.28549"
"cx1-9-17-2.cx1.hpc.ic.ac.uk.28550"
"cx1-9-17-2.cx1.hpc.ic.ac.uk.28551"
"cx1-9-17-2.cx1.hpc.ic.ac.uk.28552"
"cx1-9-17-2.cx1.hpc.ic.ac.uk.28553"
"cx1-9-17-2.cx1.hpc.ic.ac.uk.28554"
"cx1-9-17-2.cx1.hpc.ic.ac.uk.28555"
"cx1-9-17-2.cx1.hpc.ic.ac.uk.28556"
"cx1-9-17-2.cx1.hpc.ic.ac.uk.28557"
"cx1-9-17-2.cx1.hpc.ic.ac.uk.28558"
"cx1-9-17-2.cx1.hpc.ic.ac.uk.28559"
"cx1-9-17-2.cx1.hpc.ic.ac.uk.28560"
"cx1-9-17-2.cx1.hpc.ic.ac.uk.28561"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30201"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30202"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30203"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30204"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30205"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30206"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30207"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30208"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30209"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30210"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30211"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30212"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30213"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30214"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30215"
"cx1-9-17-4.cx1.hpc.ic.ac.uk.30216"
)

Pstream initialized with:
    floatTransfer      : 0
    nProcsSimpleSum    : 0
    commsType          : nonBlocking
    polling iterations : 0
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations

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

Create mesh for time = 0


PIMPLE: Operating solver in PISO mode

Reading field p_rgh

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

No finite volume options present

time step continuity errors : sum local = 0, global = 0, cumulative = 0
DICPCG:  Solving for pcorr, Initial residual = 0, Final residual = 0, No Iterations 0
time step continuity errors : sum local = 0, global = 0, cumulative = 0
Courant Number mean: 0 max: 0

Starting time loop

Courant Number mean: 0 max: 0
Interface Courant Number mean: 0 max: 0
deltaT = 0.00119048
Time = 0.00119048

MULES: Solving for alpha1
Phase-1 volume fraction = 0.130194  Min(alpha1) = 0  Max(alpha1) = 1
MULES: Solving for alpha1
Phase-1 volume fraction = 0.130194  Min(alpha1) = 0  Max(alpha1) = 1
DICPCG:  Solving for p_rgh, Initial residual = 1, Final residual = 0.0039953, No Iterations 1
time step continuity errors : sum local = 0.00110536, global = 0, cumulative = 0
DICPCG:  Solving for p_rgh, Initial residual = 0.00192022, Final residual = 6.91678e-05, No Iterations 17
time step continuity errors : sum local = 3.98241e-05, global = -9.70428e-06, cumulative = -9.70428e-06
DICPCG:  Solving for p_rgh, Initial residual = 5.5586e-05, Final residual = 9.36665e-08, No Iterations 62
time step continuity errors : sum local = 6.72902e-08, global = 7.69607e-09, cumulative = -9.69659e-06
ExecutionTime = 0.18 s  ClockTime = 0 s
At last, it works !!
Thank you so much Bruno.

Kind regards,
katakgoreng
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