Cleanup.

sge/grepper.sge

@@ -1,11 +0,0 @@
-#!/bin/bash
-set -o nounset
-
-SING_EXEC="singularity exec --pwd /opt/ExtensionCrawler -B $TMPDIR:/tmp $SING_IMG"
-
-printenv
-echo "The following parameter were passed: $*"
-echo "Printing the content of $ARCHIVE to force mounting:"
-ls "$ARCHIVE"
-
-/usr/bin/time $SING_EXEC ./grepper -t 1 -a "$ARCHIVE" -n $SGE_TASK_ID -N $MAX_SGE_TASK_ID $* | bzip2 > "$BASEDIR/out/$SGE_TASK_ID.bz2"

sge/grepper.sh

@@ -1,56 +0,0 @@
-#!/usr/bin/bash
-set -o nounset
-set -o errexit
-
-BASEDIR=$( cd $(dirname "$0"); cd ..; pwd -P )
-
-NRJOBS=${NRJOBS:-256}
-echo "Using $NRJOBS jobs"
-
-JOBRANGE=${JOBRANGE:-1-$NRJOBS}
-echo "Executing jobs $JOBRANGE"
-
-ARCHIVE=${ARCHIVE:-$(ssh sharc.shef.ac.uk find /shared/brucker_research1/Shared/BrowserExtensions/archive/.snapshot -maxdepth 1 -name \"D*\" | sort -r | head -n1)}
-echo "Using archive: $ARCHIVE"
-
-TARGETDIR="${TARGETDIR:-/data/\$USER}/grepper-$(date +%Y%m%d-%H%M%S)"
-echo "Using target dir: $TARGETDIR"
-
-SING_IMG_SRC="${SING_IMG_SRC:-/shared/brucker_research1/Shared/BrowserExtensions/excrawl.img}"
-SING_IMG="$TARGETDIR/excrawl.img"
-if ! ssh sharc.shef.ac.uk [ -f "$SING_IMG_SRC" ]; then
-  echo -n "$SING_IMG_SRC does not exist! Generate new image and push? (yes/abort): "
-  read confirm
-  if [ "$confirm" != yes ]; then
-    exit 0
-  fi
-  echo "Creating new image ..."
-  (cd "$BASEDIR/singularity"; ./build.sh)
-  echo "Pushing new image ..."
-  scp "$BASEDIR/singularity/ExtensionCrawler.img" sharc.shef.ac.uk:"$SING_IMG_SRC"
-  rm "$BASEDIR/singularity/ExtensionCrawler.img"
-fi
-echo "Creating dirs ..."
-ssh sharc.shef.ac.uk mkdir -p $TARGETDIR/{logs,out}
-
-echo "Copying $SING_IMG_SRC to $SING_IMG"
-ssh sharc.shef.ac.uk cp "$SING_IMG_SRC" "$SING_IMG"
-
-echo "Pushing sge script ..."
-scp "$BASEDIR/sge/grepper.sge" sharc.shef.ac.uk:"$TARGETDIR/grepper.sge"
-
-echo "Starting job ..."
-ssh sharc.shef.ac.uk \
-  SING_IMG=\"$SING_IMG\" \
-  ARCHIVE=\"$ARCHIVE\" \
-  BASEDIR=\"$TARGETDIR\" \
-  MAX_SGE_TASK_ID=\"$NRJOBS\" \
-  qsub \
-  -V \
-  -m a \
-  -M "msherzberg1@sheffield.ac.uk" \
-  -t $JOBRANGE \
-  -j yes \
-  -o "$TARGETDIR/logs" \
-  "$TARGETDIR/grepper.sge" \
-  $*