Hi Arsene.
I did something like that some weeks ago.
I used the lines
Prolog=/home/conf/Prolog.sh
TaskProlog=/home/conf/TaskProlog.sh
Epilog=/home/conf/Epilog.sh
The scripts for prolog and epilog manage the creation (and permissions
assignment) of a directory in local storage (including the job ID, so
that different jobs don't get messed up).
TaskProlog script should export an environment variable but I couldn't
make it work :(
In your case, TaskProlog should copy the dataset to the local storage
and then you should add a TaskEpilog script to copy back the result. I
don't know if the TaskEpilog gets run for aborted jobs.
Moreover, IIRC you shouldn't do slow operations in task prolog or
epilog, so in your case a state machine implemented as a job array could
probably be better suited than TaskProlog/TaskEpilog (you'd need
Prolog/Epilog anyway): the first "job" copies to scratch, the second
does the number crunching and the third copies back the results.
HIH,
Diego
Il 23/05/2022 11:30, Arsene Marian Alain ha scritto:
Dear SLURM users,
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.
We use some programs for scientific calculation (such as Gromacs,
Gaussian, NAMD, etc.). So, the process is the following:
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.
So, is there any way to automatically generate a temporary directory
inside the "/scratch" of the remote node?
At the moment I am creating that directory manually as follows:
"export HOMEDIR=$SLURM_SUBMIT_DIR
export SCRATCHDIR=/scratch/job.$SLURM_JOB_ID.$USER
export WORKDIR=$SCRATCHDIR
mkdir -p $WORKDIR
cp $HOMEDIR/* $WORKDIR
cd $WORKDIR
$NAMD/namd2 +idlepoll +p11 run_eq.namd > run_eq.log
wait
cp $WORKDIR/* $HOMEDIR"
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.
Thanks in advance for the help.
best regards,
Alain
--
Diego Zuccato
DIFA - Dip. di Fisica e Astronomia
Servizi Informatici
Alma Mater Studiorum - Università di Bologna
V.le Berti-Pichat 6/2 - 40127 Bologna - Italy
tel.: +39 051 20 95786
