Annotation of /MITgcm_contrib/test_scripts/svante/test_submit_svante

#! /usr/bin/env bash

# $Header: /u/gcmpack/MITgcm_contrib/test_scripts/svante/test_submit_svante,v 1.16 2018/02/04 21:03:20 jmc Exp $
# $Name:  $

today=`date +%Y%m%d`
dInWeek=`date +%a`

if test $# = 0
then
  TEST_LIST='ifcMPI pgiMPI pgiAdm pgiMth'
else
  TEST_LIST=$*
fi

headNode=`hostname -s`
#QSUB="qsub"
#QSTAT="qstat -u $USER"
#dNam=$headNode
QSUB="/usr/bin/sbatch"
QLIST="/usr/bin/squeue -u $USER"
dNam='svante'
HERE="$HOME/test_${dNam}"
TST_DISK="/net/fs09/d1/jm_c"
TST_DIR="$TST_DISK/test_${dNam}"
#- where local copy of code is (need to be consistent with run-job scripts):
#srcDIR=$TST_DIR
srcDIR=$HERE
srcCode="MITgcm_today"

logPfix='test_submit'
SUB_DIR="$HERE/$dNam"
OUT_DIR="$HERE/output"
LOG_FIL="$OUT_DIR/$logPfix."`date +%m%d`".log"
#SUB_DIR="$HERE/temp"

#-- clean up old log files and start a new one:
cd $OUT_DIR

rm -f $logPfix.*.log_bak
if test -f $LOG_FIL ; then mv -f $LOG_FIL ${LOG_FIL}_bak ; fi
echo -n '-- Starting: '					| tee -a $LOG_FIL
date							| tee -a $LOG_FIL

n=$(( `ls $logPfix.*.log | wc -l` - 10 ))
if test $n -gt 0 ; then
  echo ' remove old log files:'				| tee -a $LOG_FIL
    ls -lt $logPfix.*.log | tail -"$n"			| tee -a $LOG_FIL
    ls -t  $logPfix.*.log | tail -"$n" | xargs rm -f
fi

#-------------------------------------------------------------
# defaults
#export PATH="$PATH:/usr/local/bin"
if [ -d ~/bin ]; then export PATH=$PATH:~/bin ; fi
#- to get case insensitive "ls" (and order of tested experiments)
export LC_ALL="en_US.UTF-8"
#  Turn off stack limit for FIZHI & AD-tests
ulimit -s unlimited

if test -f /etc/profile.d/modules.sh    ; then . /etc/profile.d/modules.sh    ; fi
if test -f /etc/profile.d/zz_modules.sh ; then . /etc/profile.d/zz_modules.sh ; fi
#- load standard modules:
#module add fedora slurm maui svante
module add slurm
module list 						>> $LOG_FIL 2>&1

#- method to acces CVS:
cmdCVS='cvs -d :pserver:cvsanon@mitgcm.org:/u/gcmpack -q'

#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-|--+----|
#-- Download/Update reference version of MITgcm code:
checkOut=1
exp2add=''
updFile='updated_code'

if test $srcDIR = $TST_DIR ; then
  echo "cd $TST_DISK ; pwd (x2)" | tee -a $LOG_FIL
  cd $TST_DISK	| tee -a $LOG_FIL 2>&1
  pwd		| tee -a $LOG_FIL
fi
if test ! -d $srcDIR ; then
   echo -n "Creating a working dir: $srcDIR ..."	| tee -a $LOG_FIL
  #/bin/rm -rf $srcDIR
   mkdir $srcDIR
   retVal=$?
   if test "x$retVal" != x0 ; then
      echo "Error: unable to make dir: $srcDIR (err=$retVal ) --> Exit" | tee -a $LOG_FIL
      exit 1
   fi
fi
cd $srcDIR
pwd		| tee -a $LOG_FIL

#- remove date/lock-file:
if test -f $updFile ; then rm -f $updFile ; sleep 2 ; fi

if [ $checkOut -eq 1 ] ; then
  if test -d $srcCode/CVS ; then
    echo -n "Update dir $srcCode using '$cmdCVS update -P -d' ..." | tee -a $LOG_FIL
    echo '' >> $LOG_FIL
    ( cd $srcCode ; $cmdCVS update -P -d )		>> $LOG_FIL 2>&1
    RETVAL=$?
    if test "x$RETVAL" != x0 ; then echo ''
       echo "cvs update on '"`hostname`"' fail (return val=$RETVAL) => exit" | tee -a $LOG_FIL
       exit
    else echo "  done"					| tee -a $LOG_FIL
    fi
 else
    echo "no dir: $srcCode/CVS => try a fresh check-out"	| tee -a $LOG_FIL
    checkOut=2
  fi
fi
if [ $checkOut -eq 2 ] ; then
    test -e $srcCode && rm -rf $srcCode
    echo -n "Downloading using '$cmdCVS co -P -d $srcCode MITgcm' ..."	| tee -a $LOG_FIL
    $cmdCVS co -P -d $srcCode MITgcm > /dev/null
    RETVAL=$?
    if test "x$RETVAL" != x0 ; then echo ''		| tee -a $LOG_FIL
      echo "cvs co on '"`hostname`"' fail (return val=$RETVAL) => exit"	| tee -a $LOG_FIL
      exit
    else echo "  done"					| tee -a $LOG_FIL
    fi
    if test -d $srcCode/verification ; then
      for exp2add in $addExp ; do
        echo " add dir: $exp2add (from Contrib:verification_other)" | tee -a $LOG_FIL
        ( cd $srcCode/verification ; $cmdCVS co -P -d $exp2add \
                       MITgcm_contrib/verification_other/$exp2add > /dev/null )
      done
    fi
    /usr/bin/find $srcCode -type d | xargs chmod g+rxs
    /usr/bin/find $srcCode -type f | xargs chmod g+r
fi

#- update date/lock-file:
if test -d $srcCode/verification ; then
  echo $today > $updFile ; sleep 2
  ls -l $updFile					| tee -a $LOG_FIL
fi

#-- leave TST Dir and go back to output dir
cd $OUT_DIR
#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-|--+----|
#-- now really do something:

  JOB_LIST=$TEST_LIST
  NB_SUB_JOBS=0
  for i in $JOB_LIST
  do
    case $i in
      'pgiAdm') sfx='pgi_adm' ;;
      'pgiMth') sfx='pgi_mth' ;;
             *) sfx=`echo ${i} | sed 's/MPI$/_mpi/'`  ;;
    esac
    BATCH_SCRIPT="test_${dNam}_$sfx"
    if test -f $SUB_DIR/$BATCH_SCRIPT ; then
      #- job name ( $JOB ) & output-file name ( $JOB.std??? ) must match
      #  definition within $BATCH_SCRIPT slurm script
      JOB="${i}_tst"
      sJob=`printf "%8.8s" $JOB` #- squeue truncate name to only 1rst 8c
      #job_exist=`$QSTAT | grep $JOB | wc -l`
      job_exist=`$QLIST | grep $sJob | wc -l`
      if test "x_$job_exist" = x_0 ; then
        #-- move previous output file
        outList=`ls $JOB.std??? 2> /dev/null`
        if test "x$outList" != x ; then
          echo -n " moving job $JOB old output files:"	| tee -a $LOG_FIL
          if test -d $OUT_DIR/prev ; then
            for xx in $outList ; do
              pp=$OUT_DIR/prev/$xx ; echo -n " $xx"	| tee -a $LOG_FIL
              test -f $pp.sav && mv -f $pp.sav $pp.old
              test -f $pp     && mv -f $pp     $pp.sav
              chmod a+r $xx ; mv -f $xx $OUT_DIR/prev
            done
            echo " to dir ./prev"			| tee -a $LOG_FIL
          else
            echo " <-- missing dir $OUT_DIR/prev"	| tee -a $LOG_FIL
          fi
        else echo " no old output files from job '$JOB'" | tee -a $LOG_FIL
        fi
        #-- submit job
          echo -n "--> $JOB : "				| tee -a $LOG_FIL
          $QSUB $SUB_DIR/$BATCH_SCRIPT			| tee -a $LOG_FIL
          NB_SUB_JOBS=`expr $NB_SUB_JOBS + 1`
      else
          echo "--> $JOB :"				| tee -a $LOG_FIL
          #$QSTAT | grep $JOB				| tee -a $LOG_FIL
          $QLIST | grep $sJob				| tee -a $LOG_FIL
          echo ' job already exist => skip this test'	| tee -a $LOG_FIL
      fi
    else
       echo 'no file:' $BATCH_SCRIPT 'to submit'	| tee -a $LOG_FIL
    fi
  done
  echo "info-sub-list: NB_SUB_JOBS='$NB_SUB_JOBS'"	>> $LOG_FIL
  echo -n '-- Finished at: '				| tee -a $LOG_FIL
  date							| tee -a $LOG_FIL

#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-|--+----|
exit 0
1	jmc	1.1	#! /usr/bin/env bash
2
3	jmc	1.17	# $Header: /u/gcmpack/MITgcm_contrib/test_scripts/svante/test_submit_svante,v 1.16 2018/02/04 21:03:20 jmc Exp $
4	jmc	1.1	# $Name: $
5
6			today=`date +%Y%m%d`
7			dInWeek=`date +%a`
8
9			if test $# = 0
10			then
11	jmc	1.13	TEST_LIST='ifcMPI pgiMPI pgiAdm pgiMth'
12	jmc	1.1	else
13			TEST_LIST=$*
14			fi
15
16	jmc	1.7	headNode=`hostname -s`
17	jmc	1.5	#QSUB="qsub"
18	jmc	1.8	#QSTAT="qstat -u $USER"
19	jmc	1.7	#dNam=$headNode
20	jmc	1.5	QSUB="/usr/bin/sbatch"
21	jmc	1.10	QLIST="/usr/bin/squeue -u $USER"
22	jmc	1.5	dNam='svante'
23	jmc	1.2	HERE="$HOME/test_${dNam}"
24	jmc	1.15	TST_DISK="/net/fs09/d1/jm_c"
25	jmc	1.6	TST_DIR="$TST_DISK/test_${dNam}"
26	jmc	1.16	#- where local copy of code is (need to be consistent with run-job scripts):
27	jmc	1.17	#srcDIR=$TST_DIR
28			srcDIR=$HERE
29	jmc	1.16	srcCode="MITgcm_today"
30
31	jmc	1.1	logPfix='test_submit'
32			SUB_DIR="$HERE/$dNam"
33			OUT_DIR="$HERE/output"
34			LOG_FIL="$OUT_DIR/$logPfix."`date +%m%d`".log"
35			#SUB_DIR="$HERE/temp"
36
37			#-- clean up old log files and start a new one:
38			cd $OUT_DIR
39
40			rm -f $logPfix.*.log_bak
41			if test -f $LOG_FIL ; then mv -f $LOG_FIL ${LOG_FIL}_bak ; fi
42			echo -n '-- Starting: ' \| tee -a $LOG_FIL
43			date \| tee -a $LOG_FIL
44
45			n=$(( `ls $logPfix.*.log \| wc -l` - 10 ))
46			if test $n -gt 0 ; then
47			echo ' remove old log files:' \| tee -a $LOG_FIL
48			ls -lt $logPfix.*.log \| tail -"$n" \| tee -a $LOG_FIL
49			ls -t $logPfix.*.log \| tail -"$n" \| xargs rm -f
50			fi
51
52			#-------------------------------------------------------------
53			# defaults
54			#export PATH="$PATH:/usr/local/bin"
55			if [ -d ~/bin ]; then export PATH=$PATH:~/bin ; fi
56			#- to get case insensitive "ls" (and order of tested experiments)
57			export LC_ALL="en_US.UTF-8"
58			# Turn off stack limit for FIZHI & AD-tests
59			ulimit -s unlimited
60
61	jmc	1.5	if test -f /etc/profile.d/modules.sh ; then . /etc/profile.d/modules.sh ; fi
62			if test -f /etc/profile.d/zz_modules.sh ; then . /etc/profile.d/zz_modules.sh ; fi
63	jmc	1.1	#- load standard modules:
64	jmc	1.5	#module add fedora slurm maui svante
65			module add slurm
66	jmc	1.1	module list >> $LOG_FIL 2>&1
67
68			#- method to acces CVS:
69			cmdCVS='cvs -d :pserver:cvsanon@mitgcm.org:/u/gcmpack -q'
70
71			#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-\|--+----\|
72			#-- Download/Update reference version of MITgcm code:
73			checkOut=1
74			exp2add=''
75			updFile='updated_code'
76
77	jmc	1.16	if test $srcDIR = $TST_DIR ; then
78			echo "cd $TST_DISK ; pwd (x2)" \| tee -a $LOG_FIL
79			cd $TST_DISK \| tee -a $LOG_FIL 2>&1
80			pwd \| tee -a $LOG_FIL
81			fi
82			if test ! -d $srcDIR ; then
83			echo -n "Creating a working dir: $srcDIR ..." \| tee -a $LOG_FIL
84			#/bin/rm -rf $srcDIR
85			mkdir $srcDIR
86	jmc	1.1	retVal=$?
87			if test "x$retVal" != x0 ; then
88	jmc	1.16	echo "Error: unable to make dir: $srcDIR (err=$retVal ) --> Exit" \| tee -a $LOG_FIL
89	jmc	1.1	exit 1
90			fi
91			fi
92	jmc	1.16	cd $srcDIR
93	jmc	1.6	pwd \| tee -a $LOG_FIL
94	jmc	1.1
95			#- remove date/lock-file:
96			if test -f $updFile ; then rm -f $updFile ; sleep 2 ; fi
97
98			if [ $checkOut -eq 1 ] ; then
99	jmc	1.16	if test -d $srcCode/CVS ; then
100			echo -n "Update dir $srcCode using '$cmdCVS update -P -d' ..." \| tee -a $LOG_FIL
101	jmc	1.1	echo '' >> $LOG_FIL
102	jmc	1.16	( cd $srcCode ; $cmdCVS update -P -d ) >> $LOG_FIL 2>&1
103	jmc	1.1	RETVAL=$?
104			if test "x$RETVAL" != x0 ; then echo ''
105			echo "cvs update on '"`hostname`"' fail (return val=$RETVAL) => exit" \| tee -a $LOG_FIL
106			exit
107			else echo " done" \| tee -a $LOG_FIL
108			fi
109			else
110	jmc	1.16	echo "no dir: $srcCode/CVS => try a fresh check-out" \| tee -a $LOG_FIL
111	jmc	1.1	checkOut=2
112			fi
113			fi
114			if [ $checkOut -eq 2 ] ; then
115	jmc	1.16	test -e $srcCode && rm -rf $srcCode
116			echo -n "Downloading using '$cmdCVS co -P -d $srcCode MITgcm' ..." \| tee -a $LOG_FIL
117			$cmdCVS co -P -d $srcCode MITgcm > /dev/null
118	jmc	1.1	RETVAL=$?
119			if test "x$RETVAL" != x0 ; then echo '' \| tee -a $LOG_FIL
120			echo "cvs co on '"`hostname`"' fail (return val=$RETVAL) => exit" \| tee -a $LOG_FIL
121			exit
122			else echo " done" \| tee -a $LOG_FIL
123			fi
124	jmc	1.16	if test -d $srcCode/verification ; then
125	jmc	1.1	for exp2add in $addExp ; do
126			echo " add dir: $exp2add (from Contrib:verification_other)" \| tee -a $LOG_FIL
127	jmc	1.16	( cd $srcCode/verification ; $cmdCVS co -P -d $exp2add \
128	jmc	1.1	MITgcm_contrib/verification_other/$exp2add > /dev/null )
129			done
130			fi
131	jmc	1.16	/usr/bin/find $srcCode -type d \| xargs chmod g+rxs
132			/usr/bin/find $srcCode -type f \| xargs chmod g+r
133	jmc	1.1	fi
134
135			#- update date/lock-file:
136	jmc	1.16	if test -d $srcCode/verification ; then
137	jmc	1.1	echo $today > $updFile ; sleep 2
138			ls -l $updFile \| tee -a $LOG_FIL
139			fi
140
141			#-- leave TST Dir and go back to output dir
142			cd $OUT_DIR
143			#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-\|--+----\|
144			#-- now really do something:
145
146			JOB_LIST=$TEST_LIST
147			NB_SUB_JOBS=0
148			for i in $JOB_LIST
149			do
150			case $i in
151			'pgiAdm') sfx='pgi_adm' ;;
152	jmc	1.13	'pgiMth') sfx='pgi_mth' ;;
153			*) sfx=`echo ${i} \| sed 's/MPI$/_mpi/'` ;;
154	jmc	1.1	esac
155	jmc	1.14	BATCH_SCRIPT="test_${dNam}_$sfx"
156	jmc	1.1	if test -f $SUB_DIR/$BATCH_SCRIPT ; then
157	jmc	1.9	#- job name ( $JOB ) & output-file name ( $JOB.std??? ) must match
158			# definition within $BATCH_SCRIPT slurm script
159	jmc	1.13	JOB="${i}_tst"
160	jmc	1.9	sJob=`printf "%8.8s" $JOB` #- squeue truncate name to only 1rst 8c
161			#job_exist=`$QSTAT \| grep $JOB \| wc -l`
162			job_exist=`$QLIST \| grep $sJob \| wc -l`
163	jmc	1.1	if test "x_$job_exist" = x_0 ; then
164			#-- move previous output file
165			outList=`ls $JOB.std??? 2> /dev/null`
166			if test "x$outList" != x ; then
167			echo -n " moving job $JOB old output files:" \| tee -a $LOG_FIL
168			if test -d $OUT_DIR/prev ; then
169			for xx in $outList ; do
170			pp=$OUT_DIR/prev/$xx ; echo -n " $xx" \| tee -a $LOG_FIL
171			test -f $pp.sav && mv -f $pp.sav $pp.old
172			test -f $pp && mv -f $pp $pp.sav
173			chmod a+r $xx ; mv -f $xx $OUT_DIR/prev
174			done
175			echo " to dir ./prev" \| tee -a $LOG_FIL
176			else
177			echo " <-- missing dir $OUT_DIR/prev" \| tee -a $LOG_FIL
178			fi
179			else echo " no old output files from job '$JOB'" \| tee -a $LOG_FIL
180			fi
181			#-- submit job
182			echo -n "--> $JOB : " \| tee -a $LOG_FIL
183			$QSUB $SUB_DIR/$BATCH_SCRIPT \| tee -a $LOG_FIL
184			NB_SUB_JOBS=`expr $NB_SUB_JOBS + 1`
185			else
186			echo "--> $JOB :" \| tee -a $LOG_FIL
187	jmc	1.9	#$QSTAT \| grep $JOB \| tee -a $LOG_FIL
188			$QLIST \| grep $sJob \| tee -a $LOG_FIL
189	jmc	1.1	echo ' job already exist => skip this test' \| tee -a $LOG_FIL
190			fi
191			else
192			echo 'no file:' $BATCH_SCRIPT 'to submit' \| tee -a $LOG_FIL
193			fi
194			done
195			echo "info-sub-list: NB_SUB_JOBS='$NB_SUB_JOBS'" >> $LOG_FIL
196			echo -n '-- Finished at: ' \| tee -a $LOG_FIL
197			date \| tee -a $LOG_FIL
198
199			#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-\|--+----\|
200			exit 0