so far so ungood

blast/parallel_BLAST/LA_Wrapper

@@ -43,7 +43,13 @@ module purge
 # load the most current version of GNU parallel
 module load tools/parallel
 
-module load lang/Python/3.6.4-foss-2018a
+#module load lang/Python/3.6.4-foss-2018a
+module load lang/Python/3.7.4-GCCcore-8.3.0
+#TODO: find a solution for the bug in BLAST+ AND to select the version by hand
+module load bio/BLAST+/2.9.0-gompi-2019a
+#module load bio/BLAST+/2.7.1-foss-2018a
+
+
 
 ### setup variable for THIS script; giving absolute path if necessary
 SCRIPT="$0"
@@ -433,6 +439,16 @@ done
 FASTA=$_arg_fasta
 DATABASE=$_arg_database
 
+### checking db for integrity
+if [ -e ${DATABASE}*.fa ]; then
+    DBSUFFIX=".fa"
+elif [ -e ${DATABASE}*.fasta ]; then
+    DBSUFFIX=".fasta"
+else
+    error "no file '.fa' or '.fasta' found in ${DATABASE} - unable to proceed reliably"
+    exit 1
+fi
+
 ### check if query & database exist
 if [[ $_arg_test == "off" ]] && [ ! -e "$FASTA" ]; then
     error "FASTA input was: '$FASTA' - no such file!"
@@ -545,7 +561,7 @@ if [ -z "$SLURM_JOB_ID" ] && [[ $_arg_test == "off" ]]; then
             echo "removing directory $JOBTAG"
             rm -r $JOBTAG
         else
-            echo "So you want to continue regardless? (e.g. scratch files already existing) ([y]/n)"
+            echo "So, you want to continue regardless (using the existing scratch files)? ([y]/n)"
             echo -n '>'
             read ENTER
             if [[ ${ENTER,,} = 'n' || ${ENTER,,} == 'no' ]] ; then
@@ -572,11 +588,13 @@ FASTA="$FASTAPATH/$FASTAID"
 
 ### setup blast and splitup executable; check if exist
 allowed_executables="blastx blastp blastn"
-if [[ ! $allowed_executables =~ (^|[[:space:]])"$_arg_executable"($|[[:space:]]) ]]; then
-#    BLASTEXE=$(which $_arg_executable)
-#else
+if [[ ! $allowed_executables =~ (^| [[:space:]])"$_arg_executable"($| )  ]]; then
+    BLASTEXE=$(which $_arg_executable)
+else
     error "$_arg_executable ought to be one of [$allowed_executables]"
+    exit 1
 fi
+export _arg_executable
 
 ### which is the reference directory size?
 _arg_ramdisk=$(du -shL --block-size=1M "$_arg_database" | cut -f1 )M
@@ -665,40 +683,30 @@ RAMDISK=$JOBDIR/ramdisk
 HOSTLIST=$(scontrol show hostname $SLURM_JOB_NODELIST | paste -d, -s | tr ',', ' ')
 QUEUE=''
 
+#myhost=$(hostname -f)
+stagefile=/localscratch/$SLURM_JOB_ID/dummy_stagein.sh
+rstagefile=/localscratch/$SLURM_JOB_ID/stagein.sh
+source "${SCRIPT_PATH}"/stage_in.sh
+stage_in_writer
+chmod +x $stagefile
+
+# distribute the stagewriter
+sbcast $stagefile $rstagefile
+
+rm $stagefile
+stagefile=$rstagefile
 
+# we would not need this loop with regard to slurm, but as we have
+# asynchronous tasks already, we keep track with the queue
 for HOST in $HOSTLIST; do
-    if [ -L  ${DATABASEPATH} ]; then
-        warning "If the reference directory is a link, fast stage-in is not possible."
-        for fname in ${DATABASEPATH}/*; do
-            eval "ssh $HOST cp -L $fname ${RAMDISK}/$(basename $fname)" &
-            PID=$!
-            queue $PID
-        done
-    else
-        for fname in ${DATABASEPATH}/*; do
-            if [ -L "$fname" ]; then
-                eval "ssh $HOST cp -L $fname ${RAMDISK}/$(basename $fname)" &
-                PID=$!
-                queue $PID
-            else
-                eval "ssh $HOST dd bs=4096 if=$fname of=${RAMDISK}/$(basename $fname)" &
-                PID=$!
-                queue $PID
-            fi
-        done
-    fi
-   # TODO: check for dereferencing links, before enabling
-   # TODO: check for performance, before re-enabling
-   #sbcast $FILE $RAMDISK/$(basename $FILE)
+   srun -w $HOST -N1 -n1 -c1 --mem-per-cpu=5000M $stagefile &
+   queue $!
 done
 
-#DATABASE=$RAMDISK/$DATABASE
-DATABASE=$RAMDISK #/$(basename $DATABASEPATH)
-
 WORKDIR=$PWD/$BLASTDIR/$SLURM_JOB_NAME
 # this script may never output to a user's $HOME
 if [[ *"$WORKDIR"* = 'home' ]]; then
-    eror "Cowardly refusing to operate in a home directory."
+    error "Cowardly refusing to operate in a home directory."
 fi
 # set path names to ease maintance
 SPLITFILEDIR=scratch
@@ -709,9 +717,8 @@ if [ ! -d "$WORKDIR/$SPLITFILEDIR" ]; then
     mkdir -p "$WORKDIR/output" || exit 1;
     cd "$WORKDIR"
     echo "executing scratch generator on $FASTA ($_arg_splitup_per_queryfile entries per file)"
-    eval "${SCRIPT_PATH}/splitter.py $FASTA $_arg_splitup_per_queryfile" &     # splitup queryfile
-    PID=$!
-    queue $PID
+    "${SCRIPT_PATH}/splitter.py $FASTA $_arg_splitup_per_queryfile" &     # splitup queryfile
+    queue $!
 fi
 
 # wait until the copy and a possible scratch generation are finished
@@ -720,6 +727,16 @@ while  [[ ! -z "$(echo $QUEUE| tr -d ' ')" ]]; do
    sleep 5
 done
 
+set -x
+ls $RAMDISK/*
+DATABASE=$(find $RAMDISK -name "*${DBSUFFIX}" -print -quit)
+set +x
+#DATABASE=$RAMDISK/db${DBSUFFIX} #/$(basename $DATABASEPATH)
+if [[ -z $DATABASE ]]; then
+    error "Unable to recognize database, please get in touch with hpc@uni-mainz.de"
+    exit 1
+fi
+
 cd "$WORKDIR"
 
 # calculating the degree of parallelism is necessary in order not to oversaturate with srun processes.
@@ -728,15 +745,6 @@ if [[ -z "$SLURM_CPUS_PER_TASK" ]]; then
    declare -i SLURM_CPUS_PER_TASK=1
 fi
 
-if [[ -z $DATABASE ]]; then
-    error "Unable to recognize database, please get in touch with hpc@uni-mainz.de"
-fi
-
-# see whether we find a  file in the db
-tmp=$(find $DATABASE -type f -print -quit)
-# remove the 2nd suffix
-DATABASE=${tmp%.*}
-
 ### a temporary script to conduct the alignment
 cmdfile=/localscratch/$SLURM_JOB_ID/dummy.sh
 cmdfilewriter
@@ -749,6 +757,12 @@ sbcast $cmdfile $newcmd
 rm $cmdfile
 cmdfile=$newcmd
 
+echo "command file:"
+cat $newcmd
+echo
+ls /localscratch/$SLURM_JOBID/ramdisk
+
+
 ### append a finishing token to the samples
 samples+=('done')