fisbatch -- removed --export option and check of screen test

sjeff, sueff, slogs -- extra cmd line args passed along to slurm command
snodes -- handle longer node names
docs/stubl_thumb.gif -- new logo

Author: lsmatott

bin/fisbatch

@@ -119,7 +119,8 @@ fi
 # Submit the job and get the job id
 MyExport=SLURM_CPUS_PER_TASK,SLURM_JOB_NAME,SLURM_NTASKS_PER_NODE,SLURM_PRIO_PROCESS,SLURM_SUBMIT_DIR,SLURM_SUBMIT_HOST
 #JOB=`sbatch --export=$MyExport --job-name=FISBATCH --output=/dev/null --error=/dev/null $@ $BS 2>&1 | egrep -o -e "\b[0-9]+$"`
-JOB=`sbatch --export=$MyExport --job-name=FISBATCH --output=/dev/null --error=/dev/null $@ $BS 2>&1 | egrep -o -e "\b[0-9]+"`
+#JOB=`sbatch --export=$MyExport --job-name=FISBATCH --output=/dev/null --error=/dev/null $@ $BS 2>&1 | egrep -o -e "\b[0-9]+"`
+JOB=`sbatch --job-name=FISBATCH --output=/dev/null --error=/dev/null $@ $BS 2>&1 | egrep -o -e "\b[0-9]+"`
 JOB=`echo $JOB | awk '{ printf("%d", $1 + 0); }'`
 
 # Make sure the job is always canceled
@@ -155,7 +156,8 @@ usr=`whoami`
 NODE=`squeue -h --clusters=${cluster} --partition=${partition} --jobs=${JOB} -o %N | grep -v "^CLUSTER"`
 NODE=`nodeset -e $NODE`
 for i in $NODE; do
-   if [ `ssh $i "ps -ef | grep $usr | grep [S]CREEN | wc -l"` != "0" ]; then
+   screenTest=`ssh $i "ps -ef | grep $usr | grep [S]CREEN | wc -l"`
+   if [ "$screenTest" != "0" ]; then
       HNODE=$i
       break
    fi

bin/sjeff

@@ -16,6 +16,10 @@ if [ "$1" == "" -o "$1" == "--help" ]; then
   echo "    list of jobids or --all for all     "
   echo "    running jobs.                       "
   echo " "
+  echo "    All other command line arguments are"
+  echo "    passed along to SLURM. For example: "
+  echo "    --partition and/or --clusters       "
+  echo " "
   echo "  Environment Variables:                "
   echo "    STUBL_SJEFF_PCPU=(ps|top)           "
   echo " "
@@ -32,16 +36,19 @@ if [ "$1" == "" -o "$1" == "--help" ]; then
 fi
 
 if [ "$1" == "--all" ]; then
-  jobList=`squeue -h --state='R' -o %A`
+  jobList=`squeue -h $@ --state='R' -o %A | grep -v CLUSTER`
 else
   jobList=`echo $1 | tr ',' ' '`
 fi
 
+# pop first arg off list, all others passed on to SLURM commands
+shift
+
 #display header
 echo "Job_ID    Username  Efficiency  Number_of_CPUs_In_Use"
 
 for job in $jobList; do
-  jobInfo=`squeue -h --job=$job --state='R' 2>/dev/null`
+  jobInfo=`squeue -h $@ --job=$job --state='R' 2>/dev/null | grep -v CLUSTER`
 
   if [ "$jobInfo" == "" -a "$1" != "--all" ]; then
     echo "Invalid job ID ($job)"
@@ -51,7 +58,7 @@ for job in $jobList; do
     nodelist=`nodeset -e $nodelist | tr ' ' ','`
 
     # how many cpus were requested for the job
-    ncpus=`squeue -h --job=$job -o %C`
+    ncpus=`squeue -h $@ --job=$job -o %C | grep -v CLUSTER`
 
     # accumulate efficiency of each requested cpu
     bStackedJobs=no
@@ -65,7 +72,7 @@ for job in $jobList; do
     if [ "$effsum" == "" ]; then
       effsum=0
     fi
-    njobs=`squeue -h --nodes=$nodelist --user=$user -o %A | sort -u | wc -l`
+    njobs=`squeue -h $@ --nodes=$nodelist --user=$user -o %A | grep -v CLUSTER |sort -u | wc -l`
     if [ "$njobs" -gt "1" ]; then
       bStackedJobs=yes
     fi

bin/slogs

@@ -38,13 +38,15 @@ if [ "$1" == "--help" ]; then
   echo "  For each job run after the given start date, the     "
   echo "  following information is gathered from the SLURM     "
   echo "  accounting logs:  " 
-  echo "     number of CPUS, start time, elapsed time, Amount  "
-  echo "     of RAM Requested, Avg RAM Used, and Max RAM Used  "
+  echo "     number of CPUS, wait time, start time, elapsed    "
+  echo "     time, Amount of RAM Requested, Avg RAM Used, and  "
+  echo "     Max RAM Used "
   echo ""
-  echo "  Usage:  slogs [start_date] [users]"
+  echo "  Usage:  slogs [start_date] [users] [sacct_args]      "
   echo ""
   echo "  Notes: start_date should be in MMDDYY format.        "
   echo "         Use a comma-separated list for multiple users."
+  echo "         All sacct_args passed along to sacct command. "
   echo ""
   echo " Defaults:                                             "
   echo "    start_date : 010113 if no start date is given.     "
@@ -56,7 +58,7 @@ if [ "$1" == "--help" ]; then
   exit
 fi
 
-# try to figure out is users are in first or second arg
+# try to figure out if users are in first or second arg
 if [ "$1" != "" -a "`echo $1 | tr ',' '\n' | head -n1 | xargs id 2>/dev/null | wc -l`" != 0 ]; then
   dol1=$2
   dol2=$1
@@ -65,35 +67,38 @@ else
   dol2=$2
 fi
 
-if [ "$dol1" == "" ]; then
+dol1Test=`echo $dol1 | grep '\--' | wc -l`
+if [ "$dol1" == "" -o "$dol1Test" == "1" ]; then
   StartDate=010113
 else
   StartDate=$dol1
+  shift
 fi
 
 if [ "$dol2" == "" ]; then
   TheGroup=`whoami`
 else
   TheGroup=$dol2
+  shift
 fi
 TheList=`echo "$TheGroup" | tr ',' ' '`
 
 EndDate=`date +%m%d%y`
 
-export SACCT_FORMAT="jobid,User,ncpus,start,elapsed,ReqMem,AveRSS,MaxRSS"
+export SACCT_FORMAT="jobid%20,User,ncpus,start,elapsed,ReqMem,AveRSS,MaxRSS"
 
 TMPFILE=${TheGroup}_usage_logs_${StartDate}_to_${EndDate}.tmp
 OUTFILE=${TheGroup}_usage_logs_${StartDate}_to_${EndDate}.txt
 
-echo "JobID        User      NCPUS   Start Date Time          Elapsed     ReqMem    AveRSS     MaxRSS" > $TMPFILE
+echo "JobID                User      NCPUS   Start Date Time         Elapsed     ReqMem    AveRSS     MaxRSS" > $TMPFILE
 for i in $TheList; do
   echo "Retrieving accouning data for user $i ..."
-  sacct --start=${StartDate} --user=$i | \
-   grep 'K' | \
-   sed "s/\.bat+/ $i/g" | \
-   sed "s/\.[0-9]*/& $i/g" | \
-   sed "s/T/ /g" | \
-   awk '{ printf("%-12s %-8s  %5s   %10s %8s   %10s   %8s  %8s   %8s\n", $1, $2, $3, $4, $5, $6, $7, $8, $9); }' \
+  sacct --start=${StartDate} --user=$i $@ | \
+  sed "s/$i//g" |
+  sed "s/T/ /g" | \
+  awk -vuser=$i '{ 
+         printf("%-20s %-8s  %5s   %10s %8s   %10s   %8s  %9s   %9s\n", $1, user, $2, $3, $4, $5, $6, $7, $8, $9);
+       }' \
    >> $TMPFILE
 done
 

bin/snodes

@@ -78,17 +78,17 @@ fi
 # so use grep filter instead....
 if [ "$cluster" != "all" ]; then
   if [ "$3" == "mix" -o "$3" == "mixed" ]; then
-    sinfo $OPTIONS -o "%10n %8t %4c %8z %15C %8O %8m %8G %18P %f" | grep -v "^CLUSTER" | head -n1
-    sinfo $OPTIONS -o "%10n %8t %4c %8z %15C %8O %8m %8G %18P %f" | grep -v "^CLUSTER" | grep 'mix'
+    sinfo $OPTIONS -o "%13n %8t %4c %8z %15C %8O %8m %8G %18P %f" | grep -v "^CLUSTER" | head -n1
+    sinfo $OPTIONS -o "%13n %8t %4c %8z %15C %8O %8m %8G %18P %f" | grep -v "^CLUSTER" | grep 'mix'
   else
-    sinfo $OPTIONS -o "%10n %8t %4c %8z %15C %8O %8m %8G %18P %f" | grep -v "^CLUSTER"
+    sinfo $OPTIONS -o "%13n %8t %4c %8z %15C %8O %8m %8G %18P %f" | grep -v "^CLUSTER"
   fi
 else
   if [ "$3" == "mix" -o "$3" == "mixed" ]; then
-    sinfo $OPTIONS -o "%10n %8t %4c %8z %15C %8O %8m %8G %18P %f"  | head -n1
-    sinfo $OPTIONS -o "%10n %8t %4c %8z %15C %8O %8m %8G %18P %f"  | grep 'mix'
+    sinfo $OPTIONS -o "%13n %8t %4c %8z %15C %8O %8m %8G %18P %f"  | head -n1
+    sinfo $OPTIONS -o "%13n %8t %4c %8z %15C %8O %8m %8G %18P %f"  | grep 'mix'
   else
-    sinfo $OPTIONS -o "%10n %8t %4c %8z %15C %8O %8m %8G %18P %f" 
+    sinfo $OPTIONS -o "%13n %8t %4c %8z %15C %8O %8m %8G %18P %f" 
   fi
 fi
 

bin/sueff

@@ -11,6 +11,10 @@ if [ "$1" == "" -o "$1" == "--help" ]; then
   echo "    arg1 = userid (or comma-separated   "
   echo "    list of userids or --all for all    "
   echo "    users with currently active jobs.   "
+  echo " "
+  echo "    All other command line args will be "
+  echo "    passed along to SLURM.              "
+  echo "    (e.g. --clusters, --partition, etc.)"
   echo "========================================"
   exit
 fi
@@ -21,19 +25,21 @@ else
   userList=`echo $1 | tr ',' ' '`
 fi
 
+shift
+
 #display header
 echo "Username  Efficiency  Number_of_CPUs_In_Use"
 
 for user in $userList; do
-  nodelist=`squeue -h --state='R' --user=$user -o %N | sort -u | tr '\n' ' '`
+  nodelist=`squeue -h --state='R' --user=$user -o %N $@ | grep -v "CLUSTER" | sort -u | tr '\n' ' '`
 
   if [ "$nodelist" == ""  -a "$1" != "--all" ]; then
     echo "$user has no running jobs!"
   else
     nodelist=`nodeset -e $nodelist | tr ' ' ','`
 
     # how many cpus were requested for the users jobs
-    ncpus=`squeue -h --state='R' --user=$user -o %C | awk '{ SUM += $1;} END {print SUM }'`
+    ncpus=`squeue -h --state='R' --user=$user -o %C $@ | grep -v "CLUSTER" | awk '{ SUM += $1;} END {print SUM }'`
 
     # accumulate efficiency 
     effsum=`clush -w $nodelist -N "ps -u $user -o pcpu= " 2>/dev/null | awk 'BEGIN {sum=0} {sum+=$1} END {print sum}'`