Snakemake workflow that checks the scalability of LAMMPS run on a cluster

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scalability_check
scalability_check
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General

The workflow separated to core and node scalability checks. Core scalability checks scalibility on same node. Node scalability checks scalability in multi node configurtartion.

Edit the file config.yaml to set the pa

Code Snippets

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shell:
    """
    set -x
    origdir=`pwd`
    cat {input} > timings
    mv timings {params.rundir}
    cd {params.rundir} 
    python ${{origdir}}/scripts/analyze_efficiency.py
    mv core_scalability.png ${{origdir}}/{output} 
    """
SnakeMake From line 22 of master/Snakefile 
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shell:
    """
    origdir=`pwd`
    cat {input} > timings
    mv timings {params.rundir}
    cd {params.rundir} 
    python ${{origdir}}/scripts/analyze_efficiency_multinode.py
    mv core_scalability.png ${{origdir}}/{output} 
    """
SnakeMake From line 44 of master/Snakefile 
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shell:
    """
    set -x
    module load gcc/gcc-12.1
    #module load openmpi/openmpi-4.1.5
    BASE_MPI=/usr/mpi/gcc/openmpi-4.1.5a1/
    export PATH="${{BASE_MPI}}/bin:$PATH"
    export LD_LIBRARY_PATH="${{BASE_MPI}}/lib:$LD_LIBRARY_PATH"
    ORIGDIR=`pwd`

    COMP=GNU
    RUNDIR={params.rundir}

    #send job
    cd $RUNDIR
    cat $PBS_NODEFILE
    mpirun -n {params.threads} --bind-to none --hostfile ${{PBS_NODEFILE}} {params.lmp} -in ${{ORIGDIR}}/{input[0]} -screen none -log ${{ORIGDIR}}/{log}
    cd ${{ORIGDIR}}
    grep Loop {log} >& {output}
    """
SnakeMake From line 69 of master/Snakefile 
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shell:
    """
    set -x
    module load gcc/gcc-12.1.0
    BASE_MPI=/usr/mpi/gcc/openmpi-4.1.5a1/
    export PATH="${{BASE_MPI}}/bin:$PATH"
    export LD_LIBRARY_PATH="${{BASE_MPI}}/lib:$LD_LIBRARY_PATH"
    ORIGDIR=`pwd`

    COMP=GNU
    RUNDIR={params.rundir}

    #send job
    cd $RUNDIR
    cat $PBS_NODEFILE
    mpirun -n {params.total_procs} --hostfile ${{PBS_NODEFILE}} {params.lmp} -in ${{ORIGDIR}}/{input[0]} -screen none -log ${{ORIGDIR}}/{log}
    cd ${{ORIGDIR}}
    grep Loop {log} >& {output}
    """
SnakeMake From line 103 of master/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/pipeandflow/scalability_check
Name: scalability_check
Version: 1
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Copyright: Public Domain
License: None
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