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OpenFoam2.3 project path error in Rocks6.1.1 using qsub |
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December 16, 2015, 12:57 |
OpenFoam2.3 project path error in Rocks6.1.1 using qsub
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#1 |
Senior Member
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Hello everyone,
My qsub scripts are not running on our group's server because the node receiving the job looks for the 0, constant, system directories where it it not supposed to. These scripts used to work some time ago, there has been some updates in this server but our administrators don't see any reason why my scripts are not running any longer. I am pasting the files I use below in case someone can give me some hints: *** run.sh *** #!/bin/bash # #$ -cwd #$ -j y #$ -S /bin/bash #$ -pe * 8 #$ -v MPI_BUFFER_SIZE=200000000 # ACTIVATE OPENFOAM ENVIRONMENT # source /share/apps/centFOAM/OpenFOAM/OpenFOAM-2.1.0/etc/bashrc # or . /share/apps/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc # Shouldn't be necessary, since the OpenFOAM should already have this defined export PATH=$PATH:/opt/openmpi/bin # FORMATO GENERAL: # mpirun -np <nProcs> <foamExec> <otherArgs> -parallel > log & mpirun -np 8 simpleFoam -parallel > log.simpleFoam I use the following command to submit my job: >>> qsub -N hembase -q <computation_node> run.sh And the following error message is received: Cannot read "/<home>/<user>/system/decomposeParDict" When that file is at: /<home>/<user>/OpenFOAM/carlos-2.3.0/run/<project>/system/decomposeParDict Some time ago I had to create a bashrc file in: /<home>/<user>/OpenFOAM/bashrc to overwrite the bashrc file that OpenFOAM installs at the 'etc' directory inside the installation path. Any hints? Thanks!!! |
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December 16, 2015, 17:09 |
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#2 |
Senior Member
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Hi,
Usually I prepend execution of the solver in PBS script with Code:
cd $PBS_O_WORKDIR Code:
mpirun -np 8 simpleFoam -parallel -case $PBS_O_WORKDIR > log.simpleFoam |
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December 17, 2015, 03:39 |
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#3 |
Senior Member
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Dear Alexey,
Thanksfor your reply! The job was 'q'submitted from the project folder, the same way it's done when working on a local computer. The error message tells me that the node receiving the job through 'qsub' doesn't know about the openfoam paths. But, if I 'ssh' to that node and run the case locally on it (from the project folder), it's all fun&games. I am guessing now that the qsub command doesn't "tell" the node to start the job from the folder it was launched. The policy in our cluster is to always use 'qsub', if we 'ssh' to the node we want to use, the administrators lose the ability to manage properly the system. By the way, I get no information if I "echo $PBS_O_WORKDIR". cheers! |
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December 17, 2015, 12:50 |
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#4 |
Senior Member
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Hi,
Did not pay attention to the syntax of configuration comments. So in fact it is SGE and not OpenPBS derivative and variable name should be SGE_O_WORKDIR. Or just use man qsub to figure out name for your job scheduler. Using qsub in fact a question of optimal cluster resources distribution. |
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