added ramdisk size inference to hot fix

blast/parallel_BLAST/parallel_BLAST

@@ -293,23 +293,6 @@ do
                         fi
                         _arg_blastparams="$_val"
                         ;;
-                -r*|--ramdisk|--ramdisk=*)
-                        _val_from_long="${_key##--ramdisk=}"
-                        _val_from_short="${_key##-r}"
-                        if test "$_val_from_long" != "$_key"
-                        then
-                                _val="$_val_from_long"
-                        elif test "$_val_from_short" != "$_key" -a -n "$_val_from_short"
-                        then
-                                _val="$_val_from_short"
-                        else
-                                test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
-                                _val="$2"
-                                shift
-                        fi
-                        _arg_ramdisk="$_val"
-                        [[ $_arg_ramdisk != *"G"* ]] && _arg_ramdisk=$_arg_ramdisk"G"
-                        ;;
                 -t*|--threads|--threads=*)
                         _val_from_long="${_key##--threads=}"
                         _val_from_short="${_key##-t}"
@@ -503,6 +486,9 @@ if [ -z $BLASTEXE ] && [[ $_arg_test == "off" ]]; then
     exit
 fi
 
+### which is the reference directory size?
+_arg_ramdisk=$(du -shL --block-size=1M &quot;$_arg_reference&quot; | cut -f1 )M</pre>
+
 ### setup variable for THIS script; giving absolute path if necessary
 SCRIPT="$0"
 
@@ -555,7 +541,7 @@ EOF
 
 ### check if this script is on node by checking env-variable $SLURM_JOB_ID, else send it to SLURM with given parameters and exit
 if [ -z "$SLURM_JOB_ID" ]; then
-    submit_call="sbatch --no-requeue -o ${JOBTAG}_%j.out -J $JOBTAG -p $_arg_queue -A $_arg_assoc -t $_arg_runlimit -N $_arg_nodes -n $((64 * $_arg_nodes / $_arg_blast_threads)) --mem=$_arg_mem --gres=ramdisk:$_arg_ramdisk -c $_arg_blast_threads --reservation=$_arg_reservation $SCRIPT --partition $_arg_queue --account $_arg_assoc --nodes $_arg_nodes --time $_arg_runlimit --reservation=$_arg_reservation --ramdisk $_arg_ramdisk --threads $_arg_blast_threads --splitup $_arg_splitup_per_queryfile --blastparams=\"$BLASTPARAMS\" --executable=$_arg_executable $FASTA $DATABASE"
+    submit_call="sbatch --no-requeue -o ${JOBTAG}_%j.out -J $JOBTAG -p $_arg_queue -A $_arg_assoc -t $_arg_runlimit -N $_arg_nodes -n $((64 * $_arg_nodes / $_arg_blast_threads)) --mem=$_arg_mem --ramdisk=${_arg_ramdisk} -c $_arg_blast_threads --reservation=$_arg_reservation $SCRIPT --partition $_arg_queue --account $_arg_assoc --nodes $_arg_nodes --time $_arg_runlimit --reservation=$_arg_reservation --ramdisk $_arg_ramdisk --threads $_arg_blast_threads --splitup $_arg_splitup_per_queryfile --blastparams=\"$BLASTPARAMS\" --executable=$_arg_executable $FASTA $DATABASE"
     if [[ $_arg_test == "on" ]]; then
         echo "Just testing - this command would be submitted:"
         echo $submit_call