Commit 9bf662e2 authored by Christian Meesters's avatar Christian Meesters

tmp output on local disk, writing back, when instance ready

parent 0559a7e9
......@@ -610,10 +610,16 @@ echo 'module load bio/BLAST+' >> $cmd
printf "$BLASTEXE -num_threads $SLURM_CPUS_PER_TASK -db $RAMDISK/$(basename $DATABASE) $BLASTPARAMS " >> $cmd
#printf "$BLASTEXE -num_threads 2 -db $RAMDISK/$(basename $DATABASE) " >> $cmd
#TODO: write output to local host, copy back, when ready
echo '-query ./$1 -out ./output/$(basename ${1%fasta}out)' >> $cmd
echo 'outfname=$(basename ${1%fasta}out)' >> $cmd
# temporary output goes here:
printf "tmp_out=$JOBDIR/" >> $cmd
echo '$outfname' >> $cmd
echo 'trap "rm -f $tmp_output" EXIT' >> $cmd
echo '-query ./$1 -out $tmp_out' >> $cmd
# copy back, when ready
echo 'cp $tmp_out ./output/$outfname' >> $cmd
chmod +x $cmd
HOSTLIST=$(scontrol show hostname $SLURM_JOB_NODELIST | paste -d, -s )
#parallel --controlmaster --workdir --sshdelay 0.2 $PWD -S $HOSTLIST -j $(($SLURM_JOB_NUM_NODES*$SLURM_CPUS_ON_NODE/$SLURM_CPUS_PER_TASK)) --env run_blast run_blast ::: $(find -type f -name 'group*.fasta')
parallel --workdir $PWD --sshdelay 0.2 -S $HOSTLIST -j 64 $cmd ::: $(find -type f -name 'group*.fasta')
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