Differenze

Queste sono le differenze tra la revisione selezionata e la versione attuale della pagina.

--- calcoloscientifico:userguide:schrodinger [31/08/2024 16:03] – fabio.spataro
+++ calcoloscientifico:userguide:schrodinger [02/09/2024 18:41] (versione attuale) – fabio.spataro
@@ Linea 1: / Linea 1: @@
 ==== Schrodinger ====
+<note>
+The environment variable ''SCHRODINGER_TMPDIR'' is set by ''schrodinger'' module.
+</note>
 === Job Desmond GPU ===
@@ Linea 6: / Linea 10: @@
 <code bash desmond-md-gpu.sh>
-#!/bin/sh
+#!/bin/bash --login
 #SBATCH --job-name=desmond_md_gpu
 #SBATCH --output=%x.o%j
@@ Linea 16: / Linea 20: @@
 #SBATCH --mem=10G
 #SBATCH --partition=gpu
+#SBATCH --qos=gpu
 #
 # Charge resources to account
 #SBATCH --account=<account>
-test -n "$SLURM_NODELIST" || exit
+shopt -q login_shell || exit 1
+test -n "$SLURM_NODELIST" || exit 1
 module load cuda
 module load schrodinger
-SCHRODINGER_TMPDIR=$(dirname "${LOCAL_SCRATCH:-$SCRATCH}")
-export SCHRODINGER_TMPDIR
 cd "$SLURM_SUBMIT_DIR"
-test -n "$STAGE" || STAGE=1
+multisim \
+    -WAIT \
-test $STAGE -eq 1 && \
+    -JOBNAME "$SLURM_JOB_NAME" \
-    multisim \
+    -m "${SLURM_JOB_NAME}.msj" \
-        -WAIT \
+    -c "${SLURM_JOB_NAME}.cfg" \
-        -JOBNAME "$SLURM_JOB_NAME" \
+    "${SLURM_JOB_NAME}.cms" \
-        -m "${SLURM_JOB_NAME}-in.msj" \
+    -o "${SLURM_JOB_NAME}-out.cms" \
-        -o "${SLURM_JOB_NAME}-out.cms" \
+    -maxjob $SLURM_NTASKS_PER_NODE \
-        -maxjob $SLURM_NTASKS_PER_NODE \
+    -cpu $SLURM_NTASKS_PER_NODE \
-        -cpu $SLURM_NTASKS_PER_NODE \
+    -set stage[1].set_family.md.jlaunch_opt=[-gpu]
-        -set stage[1].set_family.md.jlaunch_opt=[-gpu]
-test $STAGE -gt 1 && \
-    multisim \
-        -WAIT \
-        -JOBNAME "$SLURM_JOB_NAME" \
-        -RESTART "${SLURM_JOB_NAME}-multisim_checkpoint:${STAGE}" \
-        -d "${SLURM_JOB_NAME}_$((STAGE-1))-out.tgz" \
-        -o "${SLURM_JOB_NAME}-out.cms" \
-        -maxjob $SLURM_NTASKS_PER_NODE \
-        -cpu $SLURM_NTASKS_PER_NODE \
-        -set stage[1].set_family.md.jlaunch_opt=[-gpu]
 </code>
-For the first stage of the Desmond multisim workflows you can use:
+Submit:
 <code>
 sbatch desmond-md-gpu.sh
-</code>
-To pass the value of the variable STAGE into the job script named ''desmond-md-gpu.sh'' you can use:
-<code>
-sbatch --export=STAGE=2 desmond-md-gpu.sh
 </code>