started migration of cluster tools to github

bash/lsf_utils.sh

+
+alias bj='bjobs -w'
+alias isub='bsub -q interactive -Is bash'
+alias isub8='bsub -n 4 -R span[hosts=1] -q interactive -Is bash'
+
+
+joblist(){
+    ## use default joblist-filename or user-provided name
+    if [ $# -ne 1 ]; then
+        joblistFile=".jobs"
+    else
+        joblistFile=$1
+    fi
+
+    # add the job-id to the list
+    cat - | tee /dev/stderr |  cut -f2 -d" " | sed 's/[<>]//g' >> $joblistFile
+}
+export -f joblist
+
+
+jlistKill(){
+    if [ $# -ne 1 ]; then
+        joblistFile=".jobs"
+    else
+        joblistFile=$1
+    fi
+
+#    cat $joblistFile | xargs -L1 bkill
+    cat $joblistFile | while read id ; do bkill "$id" ; done
+}
+export -f jlistKill
+
+
+killByName(){
+    echo killing jobs which include: $1 ...
+    bjobs -w | grep $1 | awk '{ print $1 }'   | while read id ; do bkill $id ; done
+}
+export -f killByName
+
+
+jlistBtop(){
+    if [ $# -ne 1 ]; then
+        joblistFile=".jobs"
+    else
+        joblistFile=$1
+    fi
+
+    cat $joblistFile | xargs -L1 btop
+}
+export -f jlistBtop
+
+
+jlistStatus(){
+    if [ $# -ne 1 ]; then
+        joblistFile=".jobs"
+    else
+        joblistFile=$1
+    fi
+
+    bjobs -w | grep -Ff $joblistFile
+}
+export -f jlistStatus
+
+
+jlistReport(){
+    if [ $# -ne 1 ]; then
+        joblistFile=$(ls -a | grep "cluster_snapshots.txt" | sed "s/.cluster_snapshots.txt//g")
+    else
+        joblistFile=$1
+    fi
+
+    echo "reportName='$joblistFile'; source('http://dl.dropboxusercontent.com/u/113630701/rlibs/BjobsReport.R',local=T)" | R --no-save --no-restore 2>&1 > /dev/null
+}
+export -f jlistReport
+
+
+wait4jobs(){
+    ## use default joblist-filename or user-provided name
+    if [ $# -ne 1 ]; then
+        joblistFile=".jobs"
+    else
+        joblistFile=$1
+    fi
+
+    # wait until all jobs from the list are done
+    sleep 2
+    while [ -n "$(bjobs 2>&1 | grep -f $joblistFile)" ]; do
+        sleep 15; ## or use bparams output
+    done
+
+    # remove the joblist-file
+    rm $joblistFile
+}
+export -f wait4jobs
+
+
+blockScript(){
+    if [ $# -ne 1 ]; then
+        joblistFile=".jobs"
+    else
+        joblistFile=$1
+    fi
+
+    joblist $joblistFile
+    echo "waiting now for joblist:
+     $(cat $joblistFile)"
+
+    ## add jobs to top of queue
+    jlistBtop $joblistFile
+
+    wait4jobs $joblistFile
+}
+export -f blockScript
+
+
+
+wait4jobsReport(){
+    ## use default joblist-filename or user-provided name
+    if [ $# -ne 1 ]; then
+        joblistFile=".jobs"
+    else
+        joblistFile=$1
+    fi
+
+#    rm $joblistFile.cluster_usage.txt $joblistFile.cluster_snapshots.txt
+
+    # wait until all jobs from the list are done
+    sleep 2
+    while [ -n "$(bjobs 2>&1 | grep -f $joblistFile)" ]; do
+        sleep 15; ## or use bparams output
+        export curTime=$(date +"%d-%m-%Y_%H:%M:%S")
+#        bjobs -W $(cat $joblistFile ) 2>/dev/null | sed 's/ \+/\t/g' | tail -n +2  | awk -v OFS='\t' '{print $0, ENVIRON["curTime"]}'  >> $joblistFile.cluster_snapshots.txt
+        bjobs -W $(cat $joblistFile ) 2>/dev/null | sed 's/ \+/\t/g' | tail -n +2  | awk -v OFS='\t' '{print $0, ENVIRON["curTime"]}'  >> $joblistFile.cluster_snapshots.txt
+    done
+
+#    bjobs -W $(cat $joblistFile )  >> $joblistFile.cluster_usage.txt
+    echo "reportName='$joblistFile'; source('http://dl.dropbox.com/u/113630701/rlibs/BjobsReport.R',local=T)" | R --vanilla 2>&1 > /dev/null
+#    echo "source('http://dl.dropbox.com/u/113630701/rlibs/BjobsReport.R',local=T)" | R --vanilla 2>&1 > /dev/null
+
+    # remove the joblist-file
+    rm $joblistFile
+}
+export -f wait4jobsReport
+
+
+blockScriptReport(){
+    if [ $# -ne 1 ]; then
+        joblistFile=".jobs"
+    else
+        joblistFile=$1
+    fi
+
+    joblist $joblistFile
+    echo "waiting now for joblist:
+     $(cat $joblistFile)"
+
+    ## add jobs to top of queue
+    jlistBtop $joblistFile
+
+    wait4jobsReport $joblistFile
+}
+export -f blockScriptReport
+
+
+mailme(){
+    echo "Subject:"$1 "$2" | sendmail -v $(whoami)@mpi-cbg.de > /dev/null ;
+}
+export -f mailme
+
+
+lsloop(){
+    while :
+    do
+        lsload | sort -k1
+        sleep 1
+    done
+}
+
+
+bjloop(){
+    while :
+    do
+        echo "----------------------------------------------------------------------------------------------------"
+        ## http://theunixshell.blogspot.de/2012/12/print-first-80-characters-in-line.html
+        bjobs -w | head -n 50 | cut -c1-100
+        bjobs | awk '{print $3}' | sort | uniq -c | head -n2
+        sleep 2
+    done
+}
+
+
+bstatus(){ bjobs -u all | awk '{print $2 " " $4}' | sort | uniq -c ; }
+
+
+bjsloop(){
+    while :
+    do
+        bjobs | grep short |  head -n 50
+        sleep 1
+    done
+}
+
+retouch(){
+    find $1 | xargs -n1 touch
+}
+export -f retouch
+
+
+# old output redirection scheme
+#mysub(){
+#    if [ $# -lt 2 ]; then echo "Usage: mysub <jobname> <script> [<additional bsub arguments>]"; return; fi
+#
+#    jobName=$1; shift
+#    jobCmd=$1; shift
+#
+#    bsub -e $jobName.err.log -o $jobName.out.log -J $jobName $@ "$jobCmd"
+#}
+mysub(){
+    if [ $# -lt 2 ]; then echo "Usage: mysub <jobname> <script> [<additional bsub arguments>]"; return; fi
+
+    jobName=$(echo $1| tr ' ' '_'); shift
+    jobCmd=$1; shift
+
+    bsub  -J $jobName $@ "( $jobCmd ) 2>$jobName.err.log 1>$jobName.out.log"
+}
+export -f mysub
+#mysub testjob "echo test; echo  blabla 1>&2;" -q medium
+
+rmEmptyLogFiles(){ find . -maxdepth 1 -name ".log" -type f -empty -print0 | xargs -0 echo rm -f ; }
+export -f rmEmptyLogFiles
+
+
+zipRmLogFiles(){
+    if [ $# -lt 2 ]; then echo "Usage: zipRmLogFiles <tarbasename> [<logfile>]+"; return; fi
+
+    tarName=$(date +'%y%m%d')_"$1"_logs.tar.gz; shift
+    tar czf $tarName $@; rm $@;
+}
+export -f zipRmLogFiles
+
+
+## lock a node
+lockNode(){
+
+    bsub -J "node_locker" -R span[hosts=1] -n 6 -q long 'echo "locked $HOSTNAME" >> ~/locked_worker.txt; sleep 10h' | joblist /tmp/tmp.gHDskZ7c77
+
+    mailme "locked node: $(tail -n1 ~/locked_worker.txt | cut -d' ' -f2)"
+#    ssx $(tail -n1 ~/locked_hosts.txt | cut -d' ' -f2)
+#    jlistKill $tmpJoblistFile
+}
+
+#isubNode(){
+#    tmpJoblistFile=$(mktemp)
+#    bsub -J "node_locker" -R span[hosts=1] -n 8 -q long 'echo "locked $HOSTNAME" >> ~/locked_hosts.txt; sleep 10h'  | wait4jobs $tmpJoblistFile
+#    ssx $(tail -n1 ~/locked_hosts.txt | cut -d' ' -f2)
+#    jlistKill $tmpJoblistFile
+#}
+
+