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IDProjectCategoryView StatusDate SubmittedLast Update
0002435OpenFOAMBugpublic2017-01-16 15:552017-01-16 17:03
ReporterSalut Assigned Towyldckat  
PrioritynormalSeverityminorReproducibilityalways
Status closedResolutionno change required 
PlatformLinuxOSMintOS Version17.1
Summary0002435: Command not found on the cluster whereas command found in local
DescriptionHello,

my problem is odd. I installed openFOAM-4.0 on a cluster. I ran some tutorials with it on my computer (not the cluster, I used ./Allrun to run scripts).

When I want to run tutorials on the cluster (sub -x ...), I cannot because it says: "./Allrun: line 5: /bin/tools/RunFunctions: No such file or directory"

The line ". $WM_PROJECT_DIR/bin/tools/RunFunctions" is wrong because it cannot find WM_PROJECT_DIR. But when I run this line in the consol, it works fine.

Moreover, when I change $WM_PROJECT_DIR by the good repository, this line runs and I have blockMesh: command not found.

Of course I ran the bashrc file.
TagsNo tags attached.

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Salut

2017-01-16 15:55

reporter  

Allrun (724 bytes)    
#!/bin/sh
cd /work/salmon/OpenFOAM/run/Cas_test #cd ${0%/*} || exit 1    # Run from this directory

# Source tutorial run functions
. $WM_PROJECT_DIR/bin/tools/RunFunctions

# Set application name
application=`getApplication`

runApplication /work/salmon/OpenFOAM/OpenFOAM-dev/bin/foamExec blockMesh
runApplication surfaceFeatureExtract
runApplication snappyHexMesh -overwrite
runApplication createBaffles -overwrite
#transformPoints -scale '(1e-3 1e-3 1e-3)'

#decomposePar -force > log.decomposePar 2>&1

#decomposePar -fields > log.decomposePar 2>&1

#runParallel `getApplication` 
#runApplication reconstructPar -time 0:
#paraFoam -touch


# ----------------------------------------------------------------- end-of-file
Allrun (724 bytes)   

Salut

2017-01-16 16:08

reporter   ~0007647

And the alias in the bashrc file:

alias of4='source /work/salmon/OpenFOAM4/OpenFOAM-4.0/etc/bashrc WM_COMPILER_TYPE=ThirdParty WM_COMPILER=Gcc48 WM_MPLIB=OPENMPI FOAMY_HEX_MESH=yes'

wyldckat

2017-01-16 17:03

updater   ~0007648

I'm guessing that you've followed the unofficial/community instructions from openfoamwiki.net - those instructions are not yet completed and do not fully explain how to use the installation in a cluster environment.


Nonetheless, the solution is simple: you need to use the complete source command at the beginning of your script for the job scheduler, namely:

  source /work/salmon/OpenFOAM4/OpenFOAM-4.0/etc/bashrc WM_COMPILER_TYPE=ThirdParty WM_COMPILER=Gcc48 WM_MPLIB=OPENMPI FOAMY_HEX_MESH=yes


This is (for the most part) already officially explained here: http://openfoam.org/download/4-0-source/#environment-variables - the detail is that using the alias makes it easier to switch between versions, but you cannot disregard the need to source the environment explicitly when using remote machines or job schedulers, because those are not aware of what you're doing in your command line.


I'm closing this as "no change required"...

I don't understand why, but even after stating in several places at openfoamwiki.net that any questions regarding the instructions given there should be asked at the forums at CFD-Online, people still come and ask about it here...

Issue History

Date Modified Username Field Change
2017-01-16 15:55 Salut New Issue
2017-01-16 15:55 Salut File Added: Allrun
2017-01-16 16:08 Salut Note Added: 0007647
2017-01-16 17:03 wyldckat Note Added: 0007648
2017-01-16 17:03 wyldckat Assigned To => wyldckat
2017-01-16 17:03 wyldckat Status new => closed
2017-01-16 17:03 wyldckat Resolution open => no change required