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Setting the output file name

Scheduled Pinned Locked Moved Running CRYSTAL in Parallel
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  • piquini
    piquini
    piquini
    wrote on last edited by GiacomoAmbrogio
    #1

    I am using the script file below to submit crystal23 jobs in a cluster, and I would like to know a way to set the output filename in this script. Also, I would like to see the temporary content of the output file in my $PBS_O_WORKDIR directory. Is there a simple way to do that?
    In the way it is now, the output is going to the runerr file in the $PBS_O_WORKDIR directory, and only at the end of the calculation.
    The working directory is set to $CRY23_SCRDIR/$PBS_JOBID where the $SCRDIR = /work/ppiquini

    #!/bin/bash
    ### Name of the execution queue ###
    #PBS -q testes
    #PBS -N test33
    #PBS -o runout
    #PBS -e runerr
    #PBS -l nodes=1:ppn=4
    #
    module load openmpi/4.1.1-gcc-9.4.0
    #
    cd $PBS_O_WORKDIR
    echo "-----------------------------------------"
    echo "beginning of the job:" `date`
    echo $PBS_O_WORKDIR
    #
    source $HOME/CRYSTAL23/utils23/cry23.bashrc
    mkdir -p $CRY23_SCRDIR
    cp $PBS_JOBNAME".d12" $CRY23_SCRDIR/INPUT
    cd $CRY23_SCRDIR
    #
    mpirun -np 4 $CRY23_EXEDIR/$VERSION/Pcrystal 
    #
    cd /work/ppiquini
    rm -r ./$PBS_JOBID
    echo "Final do job:" `date`
    echo "-----------------------------------------"
    
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    • GiacomoAmbrogio
      GiacomoAmbrogio
      GiacomoAmbrogio
      Developer
      wrote on last edited by
      #2

      Hi piquini,
      You could try to add this to your mpirun line:

      mpirun -np 4 $CRY23_EXEDIR/$VERSION/Pcrystal |& tee $PBS_O_WORKDIR/${PBS_JOBNAME}.out
      

      Let me know if it works!

      Giacomo Ambrogio, PhD Student
      Department of Chemistry - University of Torino
      V. Giuria 5, 10125 Torino (Italy)

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      • piquini
        piquini
        piquini
        wrote on last edited by
        #3

        Dear Giacomo, it worked fine. Thank you very much!

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