hot fix - untested

blast/parallel_BLAST/parallel_BLAST

@@ -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