Commit 879e5f51 authored by Christian Meesters's avatar Christian Meesters

hot fix - untested

parent 47938455
......@@ -690,13 +690,21 @@ chmod +x $cmd
trap "rm -f $cmd" EXIT
# define our srun-dropin for the subsequent call to be distributed amoung the reserved nodes
srun="srun -n 1 -N1 --exclusive -c $SLURM_CPUS_PER_TASK --jobid $SLURM_JOBID --mem-per-cpu=$((SLURM_MEM_PER_NODE / SLURM_NTASKS))"
#srun="srun -n 1 -N1 --exclusive -c $SLURM_CPUS_PER_TASK --jobid $SLURM_JOBID --mem-per-cpu=$((SLURM_MEM_PER_NODE / SLURM_NTASKS))"
# likewise the correct number of semaphores
parallel="parallel --no-notice -j $(($SLURM_CPUS_ON_NODE / $SLURM_CPUS_PER_TASK * $SLURM_JOB_NUM_NODES)) "
#parallel="parallel --no-notice -j $(($SLURM_CPUS_ON_NODE / $SLURM_CPUS_PER_TASK * $SLURM_JOB_NUM_NODES)) "
HOSTLIST=$(scontrol show hostname $SLURM_JOB_NODELIST | paste -d, -s )
#HOSTLIST=$(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 0.1 -S $HOSTLIST -j $(($SLURM_CPUS_ON_NODE / $SLURM_CPUS_PER_TASK)) $cmd ::: $(find $(pwd) -type f -name 'group*.fasta')
task_cpus=$((SLURM_NTASKS_PER_NODE * SLURM_CPUS_PER_TASK))
mem_per_process=$((SLURM_MEM_PER_NODE / task_cpus))
srun="srun --cpu-bind=q --mem-bind=q -n 1 -N1 --exclusive -c $SLURM_CPUS_PER_TASK --jobid $SLURM_JOBID --mem-per-cpu=$((SLURM_MEM_PER_NODE / task_cpus))"
parallel="parallel --no-notice -j $SLURM_NTASKS -P $SLURM_NTASKS "
$parallel $cmd ::: $(find $(pwd) -type f -name 'group*.fasta')
wait
......
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