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running OpenFoam on a HPC

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Old   May 25, 2016, 19:21
Default running OpenFoam on a HPC
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Zhifang Hu
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Hi there,

I am new to HPC, so forgive me if the question sounds a bit naive/ or I dont provide enough information.

I have a user directory in the HPC, for example a directory which is /home/myusername/ and after some try I've succeed in complying foam-extend 3.1 there. I can do simple run as my linux machine, with command like blockMesh setField etc.

However when I tried to submit a job through pbs to a computational node, things stopped working and I have no idea why till now.

the error message shows as below

Code:
########################### Execution Started #############################
JobId:5545
UserName:uqzhu5
GroupName:qris-uq
ExecutionHost:eura24
###############################################################################
No Modulefiles Currently Loaded.
blockMesh: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /home/uqzhu5/foam/foam-extend-3.1/lib/linux64GccDPOpt/libfoam.so)
setFields: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /home/uqzhu5/foam/foam-extend-3.1/lib/linux64GccDPOpt/libfiniteVolume.so)
setFields: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /home/uqzhu5/foam/foam-extend-3.1/lib/linux64GccDPOpt/libfoam.so)
olaFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /home/uqzhu5/foam/foam-extend-3.1/lib/linux64GccDPOpt/libfiniteVolume.so)
olaFoam: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /home/uqzhu5/foam/foam-extend-3.1/lib/linux64GccDPOpt/libfoam.so)
########################### Job Execution History #############################
JobId:5545
UserName:uqzhu5
GroupName:qris-uq
JobName:baseWaveFlume
SessionId:17059
ResourcesRequested:mem=4096mb,neednodes=1:ppn=1:amd,nodes=1:ppn=1:amd,vmem=4096mb,walltime=01:00:00
ResourcesUsed:cput=00:00:00,energy_used=0,mem=0kb,vmem=0kb,walltime=00:00:10
QueueUsed:ShortWallTime
AccountString:UQ-EAIT-Civil
ExitStatus:0
###############################################################################

and my job pbs looks like

Code:
#!/bin/bash
#PBS -N baseWaveFlume
#PBS -l nodes=1:ppn=1:amd,mem=4GB
#PBS -l walltime=01:00:00
#PBS -A UQ-EAIT-Civil


cp -r /home/uqzhu5/baseWaveFlume $TMPDIR/.

cd $TMPDIR/baseWaveFlume

cp -r 0.org 0

# load Euramoo modules
./loadmodule.sh

module list

cd /home/uqzhu5/foam/foam-extend-3.1

source etc/bashrc

echo blockMesh Meshing..
blockMesh

echo Setting the fields...
setFields

echo Running...
olaFoam

#copy all the results onto 30days directory
cp -r $TMPDIR/baseWaveFlume /30days/uqzhu5/.

echo Simulation complete.
the loadmodule is just loading module required for the run.

Anyone have any suggestions?
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Old   May 27, 2016, 11:12
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  #2
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Avdeev Evgeniy
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Hello.
What is your
Code:
$ foamInstallationTest
output?
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Old   May 29, 2016, 19:38
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Zhifang Hu
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Quote:
Executing /home/uqzhu5/foam/foam-extend-3.1/bin/foamInstallationTest:


Checking basic setup...
-------------------------------------------------------------------------------
Shell: bash
Host: euramoo3.qld.nectar.org.au
OS: Linux version 2.6.32-573.3.1.el6.x86_64
-------------------------------------------------------------------------------


Checking main foam-extend env variables...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Crit
-------------------------------------------------------------------------------
$WM_PROJECT_INST_DIR /home/uqzhu5/foam yes yes
$WM_PROJECT_USER_DIR /home/uqzhu5/foam/uqzhu5-3.1 yes no
$WM_THIRD_PARTY_DIR ...zhu5/foam/foam-extend-3.1/ThirdParty yes yes
-------------------------------------------------------------------------------


Checking the foam-extend env variables set on the PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Path Crit
-------------------------------------------------------------------------------
$WM_PROJECT_DIR /home/uqzhu5/foam/foam-extend-3.1 yes yes yes

$FOAM_APPBIN ...3.1/applications/bin/linux64GccDPOpt yes yes yes
$FOAM_SITE_APPBIN ...u5/foam/site/3.1/bin/linux64GccDPOpt no no
$FOAM_USER_APPBIN ...3.1/applications/bin/linux64GccDPOpt yes yes no
$WM_DIR /home/uqzhu5/foam/foam-extend-3.1/wmake yes yes yes
-------------------------------------------------------------------------------


Checking the foam-extend env variables set on the LD_LIBRARY_PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Path Crit
-------------------------------------------------------------------------------
$FOAM_LIBBIN .../foam-extend-3.1/lib/linux64GccDPOpt yes yes yes
$FOAM_SITE_LIBBIN ...u5/foam/site/3.1/lib/linux64GccDPOpt no no
$FOAM_USER_LIBBIN .../foam/uqzhu5-3.1/lib/linux64GccDPOpt yes yes no
$MPI_ARCH_PATH ...nmpi-1.6.5/platforms/linux64GccDPOpt yes yes yes
-------------------------------------------------------------------------------


Third party software
-------------------------------------------------------------------------------
Software Version Location
-------------------------------------------------------------------------------
WARNING: gcc version does not match gcc supplied with this release of foam-extend
Supplied version: 4.3.3
User version : 4.4.7
Minimum required: 4.3.1

gcc 4.4.7
WARNING: Conflicting installations:
foam-extend settings : /bin/gcc
current path : /usr/bin/gcc
CRITICAL ERROR

gzip 1.3.12 /bin/gzip
tar 1.23 /bin/tar
icoFoam ...am-extend-3.1/applications/bin/linux64GccDPOpt/icoFoam
-------------------------------------------------------------------------------


Summary
-------------------------------------------------------------------------------
Base configuration ok.

The foam installation contains 1 critical error(s).

Review the output for warning messages and consult
the installation guide for trouble shooting.

done.
This is what it shows. Seems have errors.
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