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 1.20 2018/02/09 22:43:36 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}"
tmpFil="/tmp/"`basename $0`".$$"
#- 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 access CVS:
  cmdCVS='cvs -d :pserver:cvsanon@mitgcm.org:/u/gcmpack -q'
#- which GitHub repository to use and how to access it:
  git_repo='MITgcm';  git_code='MITgcm'
 #git_repo='altMITgcm'; #git_code='MITgcm66h'
#--
  git_repo="https://github.com/$git_repo"
 #git_repo="git://github.com/$git_repo"
 #git_repo="git@github.com:$git_repo"

checkOut=1
addExp=''
updFile='updated_code'

#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-|--+----|
if [ $checkOut -ge 1 ] ; then
#-- Download/Update reference version of MITgcm 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 and old copy:
  if test -f $updFile ; then rm -f $updFile ; sleep 2 ; fi
  test -e $srcCode && rm -rf $srcCode

  if [ $checkOut -eq 1 ] ; then
    if test -e $git_code/.git/config ; then
      ( cd $git_code ; git checkout master )			| tee -a $LOG_FIL
      echo -n "Updating current clone ( $git_code ) ..."	| tee -a $LOG_FIL
      echo '' >> $LOG_FIL
      ( cd $git_code ; git pull )				>> $LOG_FIL 2>&1
      retVal=$?
      if test "x$retVal" != x0 ; then echo ''
         echo "'git pull' on '"`hostname`"' fail (return val=$retVal) => exit" | tee -a $LOG_FIL
         exit
      else echo "  done"					| tee -a $LOG_FIL
      fi
    else
      echo "missing file: $git_code/.git/config => try a new clone"	| tee -a $LOG_FIL
      checkOut=2
    fi
  fi
  if [ $checkOut -eq 2 ] ; then
    if test -e $git_code ; then
       echo -n " removing dir: $git_code ..."           | tee -a $LOG_FIL
       rm -rf $git_code
       echo "  done"                                    | tee -a $LOG_FIL
    fi
    echo -n "Make a clone of $git_code from repo: $git_repo ..."	| tee -a $LOG_FIL
    git clone $git_repo/${git_code}.git 2> $tmpFil
    retVal=$?
    if test $retVal = 0 ; then
       echo ' --> done!'				| tee -a $LOG_FIL
       rm -f $tmpFil
    else echo ''					| tee -a $LOG_FIL
       echo " Error: 'git clone' returned: $retVal"	| tee -a $LOG_FIL
       cat $tmpFil ; rm -f $tmpFil
       exit 2
    fi
  fi
  #---- making a new working copy: MITgcm_today
  rsync -a $git_code/ $srcCode --exclude '.git'
  ls -ld $srcCode					| tee -a $LOG_FIL
  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
  #- update date/lock-file:
  if test -d $srcCode/verification ; then
    echo $today > $updFile ; sleep 2
    ls -l $updFile					| tee -a $LOG_FIL
    echo ''						| tee -a $LOG_FIL
  fi

#-- Done with Download/Update of MITgcm code
fi
#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-|--+----|

#-- leave srcDIR and go back to output dir
cd $OUT_DIR
#-- 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`
          sleep 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	1.21	# $Header: /u/gcmpack/MITgcm_contrib/test_scripts/svante/test_submit_svante,v 1.20 2018/02/09 22:43:36 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	1.18	tmpFil="/tmp/"`basename $0`".$$"
27	jmc	1.16	#- where local copy of code is (need to be consistent with run-job scripts):
28	jmc	1.17	#srcDIR=$TST_DIR
29			srcDIR=$HERE
30	jmc	1.16	srcCode="MITgcm_today"
31
32	jmc	1.1	logPfix='test_submit'
33			SUB_DIR="$HERE/$dNam"
34			OUT_DIR="$HERE/output"
35			LOG_FIL="$OUT_DIR/$logPfix."`date +%m%d`".log"
36			#SUB_DIR="$HERE/temp"
37
38			#-- clean up old log files and start a new one:
39			cd $OUT_DIR
40
41			rm -f $logPfix.*.log_bak
42			if test -f $LOG_FIL ; then mv -f $LOG_FIL ${LOG_FIL}_bak ; fi
43			echo -n '-- Starting: ' \| tee -a $LOG_FIL
44			date \| tee -a $LOG_FIL
45
46			n=$(( `ls $logPfix.*.log \| wc -l` - 10 ))
47			if test $n -gt 0 ; then
48			echo ' remove old log files:' \| tee -a $LOG_FIL
49			ls -lt $logPfix.*.log \| tail -"$n" \| tee -a $LOG_FIL
50			ls -t $logPfix.*.log \| tail -"$n" \| xargs rm -f
51			fi
52
53			#-------------------------------------------------------------
54			# defaults
55			#export PATH="$PATH:/usr/local/bin"
56			if [ -d ~/bin ]; then export PATH=$PATH:~/bin ; fi
57			#- to get case insensitive "ls" (and order of tested experiments)
58			export LC_ALL="en_US.UTF-8"
59			# Turn off stack limit for FIZHI & AD-tests
60			ulimit -s unlimited
61
62	jmc	1.5	if test -f /etc/profile.d/modules.sh ; then . /etc/profile.d/modules.sh ; fi
63			if test -f /etc/profile.d/zz_modules.sh ; then . /etc/profile.d/zz_modules.sh ; fi
64	jmc	1.1	#- load standard modules:
65	jmc	1.5	#module add fedora slurm maui svante
66			module add slurm
67	jmc	1.1	module list >> $LOG_FIL 2>&1
68
69	jmc	1.21	#- method to access CVS:
70	jmc	1.18	cmdCVS='cvs -d :pserver:cvsanon@mitgcm.org:/u/gcmpack -q'
71	jmc	1.21	#- which GitHub repository to use and how to access it:
72	jmc	1.18	git_repo='MITgcm'; git_code='MITgcm'
73			#git_repo='altMITgcm'; #git_code='MITgcm66h'
74	jmc	1.21	#--
75			git_repo="https://github.com/$git_repo"
76			#git_repo="git://github.com/$git_repo"
77			#git_repo="git@github.com:$git_repo"
78	jmc	1.18
79			checkOut=1
80			addExp=''
81			updFile='updated_code'
82	jmc	1.1
83			#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-\|--+----\|
84	jmc	1.20	if [ $checkOut -ge 1 ] ; then
85	jmc	1.1	#-- Download/Update reference version of MITgcm code:
86
87	jmc	1.18	if test $srcDIR = $TST_DIR ; then
88			echo "cd $TST_DISK ; pwd (x2)" \| tee -a $LOG_FIL
89			cd $TST_DISK \| tee -a $LOG_FIL 2>&1
90			pwd \| tee -a $LOG_FIL
91			fi
92			if test ! -d $srcDIR ; then
93			echo -n "Creating a working dir: $srcDIR ..." \| tee -a $LOG_FIL
94			#/bin/rm -rf $srcDIR
95			mkdir $srcDIR
96			retVal=$?
97			if test "x$retVal" != x0 ; then
98			echo "Error: unable to make dir: $srcDIR (err=$retVal ) --> Exit" \| tee -a $LOG_FIL
99			exit 1
100			fi
101			fi
102			cd $srcDIR
103	jmc	1.16	pwd \| tee -a $LOG_FIL
104	jmc	1.1
105	jmc	1.18	#- remove date/lock-file and old copy:
106			if test -f $updFile ; then rm -f $updFile ; sleep 2 ; fi
107			test -e $srcCode && rm -rf $srcCode
108
109			if [ $checkOut -eq 1 ] ; then
110			if test -e $git_code/.git/config ; then
111	jmc	1.19	( cd $git_code ; git checkout master ) \| tee -a $LOG_FIL
112	jmc	1.18	echo -n "Updating current clone ( $git_code ) ..." \| tee -a $LOG_FIL
113			echo '' >> $LOG_FIL
114			( cd $git_code ; git pull ) >> $LOG_FIL 2>&1
115			retVal=$?
116			if test "x$retVal" != x0 ; then echo ''
117			echo "'git pull' on '"`hostname`"' fail (return val=$retVal) => exit" \| tee -a $LOG_FIL
118			exit
119			else echo " done" \| tee -a $LOG_FIL
120			fi
121			else
122			echo "missing file: $git_code/.git/config => try a new clone" \| tee -a $LOG_FIL
123			checkOut=2
124	jmc	1.1	fi
125			fi
126	jmc	1.18	if [ $checkOut -eq 2 ] ; then
127	jmc	1.20	if test -e $git_code ; then
128			echo -n " removing dir: $git_code ..." \| tee -a $LOG_FIL
129			rm -rf $git_code
130			echo " done" \| tee -a $LOG_FIL
131			fi
132	jmc	1.18	echo -n "Make a clone of $git_code from repo: $git_repo ..." \| tee -a $LOG_FIL
133	jmc	1.21	git clone $git_repo/${git_code}.git 2> $tmpFil
134	jmc	1.18	retVal=$?
135			if test $retVal = 0 ; then
136			echo ' --> done!' \| tee -a $LOG_FIL
137			rm -f $tmpFil
138			else echo '' \| tee -a $LOG_FIL
139			echo " Error: 'git clone' returned: $retVal" \| tee -a $LOG_FIL
140			cat $tmpFil ; rm -f $tmpFil
141			exit 2
142	jmc	1.1	fi
143	jmc	1.18	fi
144			#---- making a new working copy: MITgcm_today
145			rsync -a $git_code/ $srcCode --exclude '.git'
146	jmc	1.19	ls -ld $srcCode \| tee -a $LOG_FIL
147	jmc	1.18	if test -d $srcCode/verification ; then
148			for exp2add in $addExp ; do
149			echo " add dir: $exp2add (from Contrib:verification_other)" \| tee -a $LOG_FIL
150			( cd $srcCode/verification ; $cmdCVS co -P -d $exp2add \
151			MITgcm_contrib/verification_other/$exp2add > /dev/null )
152			done
153			fi
154			/usr/bin/find $srcCode -type d \| xargs chmod g+rxs
155			/usr/bin/find $srcCode -type f \| xargs chmod g+r
156			#- update date/lock-file:
157			if test -d $srcCode/verification ; then
158			echo $today > $updFile ; sleep 2
159			ls -l $updFile \| tee -a $LOG_FIL
160	jmc	1.19	echo '' \| tee -a $LOG_FIL
161	jmc	1.18	fi
162	jmc	1.1
163	jmc	1.18	#-- Done with Download/Update of MITgcm code
164	jmc	1.1	fi
165	jmc	1.20	#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-\|--+----\|
166	jmc	1.1
167	jmc	1.18	#-- leave srcDIR and go back to output dir
168	jmc	1.1	cd $OUT_DIR
169			#-- now really do something:
170
171			JOB_LIST=$TEST_LIST
172			NB_SUB_JOBS=0
173			for i in $JOB_LIST
174			do
175			case $i in
176			'pgiAdm') sfx='pgi_adm' ;;
177	jmc	1.13	'pgiMth') sfx='pgi_mth' ;;
178			*) sfx=`echo ${i} \| sed 's/MPI$/_mpi/'` ;;
179	jmc	1.1	esac
180	jmc	1.14	BATCH_SCRIPT="test_${dNam}_$sfx"
181	jmc	1.1	if test -f $SUB_DIR/$BATCH_SCRIPT ; then
182	jmc	1.9	#- job name ( $JOB ) & output-file name ( $JOB.std??? ) must match
183			# definition within $BATCH_SCRIPT slurm script
184	jmc	1.13	JOB="${i}_tst"
185	jmc	1.9	sJob=`printf "%8.8s" $JOB` #- squeue truncate name to only 1rst 8c
186			#job_exist=`$QSTAT \| grep $JOB \| wc -l`
187			job_exist=`$QLIST \| grep $sJob \| wc -l`
188	jmc	1.1	if test "x_$job_exist" = x_0 ; then
189			#-- move previous output file
190			outList=`ls $JOB.std??? 2> /dev/null`
191			if test "x$outList" != x ; then
192			echo -n " moving job $JOB old output files:" \| tee -a $LOG_FIL
193			if test -d $OUT_DIR/prev ; then
194			for xx in $outList ; do
195			pp=$OUT_DIR/prev/$xx ; echo -n " $xx" \| tee -a $LOG_FIL
196			test -f $pp.sav && mv -f $pp.sav $pp.old
197			test -f $pp && mv -f $pp $pp.sav
198			chmod a+r $xx ; mv -f $xx $OUT_DIR/prev
199			done
200			echo " to dir ./prev" \| tee -a $LOG_FIL
201			else
202			echo " <-- missing dir $OUT_DIR/prev" \| tee -a $LOG_FIL
203			fi
204			else echo " no old output files from job '$JOB'" \| tee -a $LOG_FIL
205			fi
206			#-- submit job
207			echo -n "--> $JOB : " \| tee -a $LOG_FIL
208			$QSUB $SUB_DIR/$BATCH_SCRIPT \| tee -a $LOG_FIL
209			NB_SUB_JOBS=`expr $NB_SUB_JOBS + 1`
210	jmc	1.18	sleep 1
211	jmc	1.1	else
212			echo "--> $JOB :" \| tee -a $LOG_FIL
213	jmc	1.9	#$QSTAT \| grep $JOB \| tee -a $LOG_FIL
214			$QLIST \| grep $sJob \| tee -a $LOG_FIL
215	jmc	1.1	echo ' job already exist => skip this test' \| tee -a $LOG_FIL
216			fi
217			else
218			echo 'no file:' $BATCH_SCRIPT 'to submit' \| tee -a $LOG_FIL
219			fi
220			done
221			echo "info-sub-list: NB_SUB_JOBS='$NB_SUB_JOBS'" >> $LOG_FIL
222			echo -n '-- Finished at: ' \| tee -a $LOG_FIL
223			date \| tee -a $LOG_FIL
224
225			#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-\|--+----\|
226			exit 0