diff --git a/sge/grepper.sge b/sge/grepper.sge index cb8c047..14eae5d 100755 --- a/sge/grepper.sge +++ b/sge/grepper.sge @@ -5,4 +5,4 @@ source activate mypython35 set -o nounset -"$BASEDIR/ExtensionCrawler/grepper" -a "/shared/brucker_research1/Shared/BrowserExtensions" -n $SGE_TASK_ID -N $SGE_TASK_LAST "$PATTERN" | bzip2 > "$BASEDIR/$SGE_TASK_ID.bz2" +"$BASEDIR/ExtensionCrawler/grepper" -a "/shared/brucker_research1/Shared/BrowserExtensions" -n $SGE_TASK_ID -N $SGE_TASK_LAST "$PATTERN" | bzip2 > "$BASEDIR/out/$SGE_TASK_ID.bz2" diff --git a/sge/grepper.sh b/sge/grepper.sh index 073ad90..0a9e5f2 100755 --- a/sge/grepper.sh +++ b/sge/grepper.sh @@ -8,8 +8,10 @@ TARGETDIR='/data/$USER/grepper-'$(date +%Y%m%d-%H%M%S) SGEFILE="$BASEDIR/sge/grepper.sge" -echo "Creating $HOST:$TARGETDIR/ExtensionCrawler ..." +echo "Creating dirs ..." ssh "$HOST" mkdir -p $TARGETDIR/ExtensionCrawler +ssh "$HOST" mkdir -p $TARGETDIR/logs +ssh "$HOST" mkdir -p $TARGETDIR/out echo "Pushing $BASEDIR to $HOST:$TARGETDIR/ExtensionCrawler ..." rsync -zr "$BASEDIR" $HOST:"$TARGETDIR/ExtensionCrawler" @@ -22,5 +24,5 @@ ssh "$HOST" qsub \ -v BASEDIR="$TARGETDIR",PATTERN="$PATTERN" \ -t 1-256 \ -j yes \ - -o "$TARGETDIR" \ + -o "$TARGETDIR/logs" \ "$TARGETDIR/grepper.sge"