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<p class="MsoNormal">Dear SLURM users,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am IT Administrator of a small scientific computing center. We recently installed SLURM as a job scheduler on our Cluster and everything seems to be working fine. I just have a question about how to create temporary directories with SLURM.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">We use some programs for scientific calculation (such as Gromacs, Gaussian, NAMD, etc.). So, the process is the following:
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">When we need to launch a calculation the first step is to copy all the necessary files from the local "$SLURM_SUBMIT_DIR" directory to the "/scratch" of the remote node, second step is to access the "/scratch" of the remote node and then
run the program. Finally, when the program finishes we copy all the output files from the remote node's "/scratch" back to the local "$SLURM_SUBMIT_DIR" directory.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">So, is there any way to automatically generate a temporary directory inside the "/scratch" of the remote node?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">At the moment I am creating that directory manually as follows:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">"export HOMEDIR=$SLURM_SUBMIT_DIR<o:p></o:p></p>
<p class="MsoNormal">export SCRATCHDIR=/scratch/job.$SLURM_JOB_ID.$USER<o:p></o:p></p>
<p class="MsoNormal">export WORKDIR=$SCRATCHDIR<o:p></o:p></p>
<p class="MsoNormal">mkdir -p $WORKDIR<o:p></o:p></p>
<p class="MsoNormal">cp $HOMEDIR/* $WORKDIR<o:p></o:p></p>
<p class="MsoNormal">cd $WORKDIR<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">$NAMD/namd2 +idlepoll +p11 run_eq.namd > run_eq.log<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">wait<o:p></o:p></p>
<p class="MsoNormal">cp $WORKDIR/* $HOMEDIR"<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The main problem when you create the "/scratch" manually is that in case the calculation ends (successfully or unsuccessfully), users have to check the "/scratch" and remove the directory manually. I know I could include a line at the end
of my script to delete that directory when the calculation is done, but I'm sure there must be a better way to do this.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks in advance for the help.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">best regards,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Alain<o:p></o:p></p>
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