Annotation of /MITgcm_contrib/test_scripts/nasa_ames/test_submit_pleiades

#! /usr/bin/env bash

# $Header: /u/gcmpack/MITgcm_contrib/test_scripts/nasa_ames/test_submit_pleiades,v 1.1 2018/01/29 19:58:45 jmc Exp $
# $Name:  $

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

if test $# = 0
then
  TEST_LIST='ieee fast'
else
  TEST_LIST=$*
fi

headNode=`hostname -s`
QSUB="/PBS/bin/qsub"
QSTAT="/PBS/bin/qstat -u $USER"
#dNam=$headNode
#QSUB="/usr/bin/sbatch"
#QLIST="/usr/bin/squeue -u $USER"
dNam='pleiades'
HERE="$HOME/test_${dNam}"
TST_DISK="/nobackupp2/$USER"
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
srcCode="MITgcm_today"

logPfix='test_submit'
SUB_DIR="$HERE/nasa_ames"
OUT_DIR="$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
#- 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'
#- and which GitHub repository to use:
  git_repo='MITgcm';  git_code='MITgcm'
 #git_repo='altMITgcm'; #git_code='MITgcm66h'

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 $LOG_FIL
    git clone https://github.com/$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 $BATCH_SCRIPT slurm script
      JOB="tst_${i}"
      job_exist=`$QSTAT | grep $JOB | wc -l`
      #sJob=`printf "%8.8s" $JOB` #- squeue truncate name to only 1rst 8c
      #job_exist=`$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	1.2	# $Header: /u/gcmpack/MITgcm_contrib/test_scripts/nasa_ames/test_submit_pleiades,v 1.1 2018/01/29 19:58:45 jmc Exp $
4	jmc	1.1	# $Name: $
5
6			today=`date +%Y%m%d`
7			dInWeek=`date +%a`
8
9			if test $# = 0
10			then
11			TEST_LIST='ieee fast'
12			else
13			TEST_LIST=$*
14			fi
15
16			headNode=`hostname -s`
17			QSUB="/PBS/bin/qsub"
18			QSTAT="/PBS/bin/qstat -u $USER"
19			#dNam=$headNode
20			#QSUB="/usr/bin/sbatch"
21			#QLIST="/usr/bin/squeue -u $USER"
22			dNam='pleiades'
23			HERE="$HOME/test_${dNam}"
24			TST_DISK="/nobackupp2/$USER"
25			TST_DIR="$TST_DISK/test_${dNam}"
26	jmc	1.2	tmpFil="/tmp/"`basename $0`".$$"
27			#- where local copy of code is (need to be consistent with run-job scripts):
28			srcDIR=$TST_DIR
29			srcCode="MITgcm_today"
30
31	jmc	1.1	logPfix='test_submit'
32			SUB_DIR="$HERE/nasa_ames"
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			if test -f /etc/profile.d/modules.sh ; then . /etc/profile.d/modules.sh ; fi
62			#- load standard modules:
63			#module add fedora slurm maui svante
64			#module add slurm
65			module list >> $LOG_FIL 2>&1
66
67			#- method to acces CVS:
68			cmdCVS='cvs -d :pserver:cvsanon@mitgcm.org:/u/gcmpack -q'
69	jmc	1.2	#- and which GitHub repository to use:
70			git_repo='MITgcm'; git_code='MITgcm'
71			#git_repo='altMITgcm'; #git_code='MITgcm66h'
72	jmc	1.1
73			checkOut=1
74	jmc	1.2	addExp=''
75	jmc	1.1	updFile='updated_code'
76
77	jmc	1.2	#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-\|--+----\|
78			if [ $checkOut -ge 1 ] ; then
79			#-- Download/Update reference version of MITgcm code:
80	jmc	1.1
81	jmc	1.2	if test $srcDIR = $TST_DIR ; then
82			echo "cd $TST_DISK ; pwd (x2)" \| tee -a $LOG_FIL
83			cd $TST_DISK \| tee -a $LOG_FIL 2>&1
84			pwd \| tee -a $LOG_FIL
85			fi
86			if test ! -d $srcDIR ; then
87			echo -n "Creating a working dir: $srcDIR ..." \| tee -a $LOG_FIL
88			#/bin/rm -rf $srcDIR
89			mkdir $srcDIR
90			retVal=$?
91			if test "x$retVal" != x0 ; then
92			echo "Error: unable to make dir: $srcDIR (err=$retVal ) --> Exit" \| tee -a $LOG_FIL
93			exit 1
94			fi
95			fi
96			cd $srcDIR
97			pwd \| tee -a $LOG_FIL
98	jmc	1.1
99	jmc	1.2	#- remove date/lock-file and old copy:
100			if test -f $updFile ; then rm -f $updFile ; sleep 2 ; fi
101			test -e $srcCode && rm -rf $srcCode
102
103			if [ $checkOut -eq 1 ] ; then
104			if test -e $git_code/.git/config ; then
105			( cd $git_code ; git checkout master ) \| tee -a $LOG_FIL
106			echo -n "Updating current clone ( $git_code ) ..." \| tee -a $LOG_FIL
107			echo '' >> $LOG_FIL
108			( cd $git_code ; git pull ) >> $LOG_FIL 2>&1
109			retVal=$?
110			if test "x$retVal" != x0 ; then echo ''
111			echo "'git pull' on '"`hostname`"' fail (return val=$retVal) => exit" \| tee -a $LOG_FIL
112			exit
113			else echo " done" \| tee -a $LOG_FIL
114			fi
115			else
116			echo "missing file: $git_code/.git/config => try a new clone" \| tee -a $LOG_FIL
117			checkOut=2
118	jmc	1.1	fi
119			fi
120	jmc	1.2	if [ $checkOut -eq 2 ] ; then
121			if test -e $git_code ; then
122			echo -n " removing dir: $git_code ..." \| tee -a $LOG_FIL
123			rm -rf $git_code
124			echo " done" \| tee -a $LOG_FIL
125	jmc	1.1	fi
126	jmc	1.2	echo -n "Make a clone of $git_code from repo: $git_repo ..." \| tee -a $LOG_FIL
127			git clone https://github.com/$git_repo/${git_code}.git 2> $tmpFil
128			retVal=$?
129			if test $retVal = 0 ; then
130			echo ' --> done!' \| tee -a $LOG_FIL
131			rm -f $tmpFil
132			else echo '' \| tee -a $LOG_FIL
133			echo " Error: 'git clone' returned: $retVal" \| tee -a $LOG_FIL
134			cat $tmpFil ; rm -f $tmpFil
135			exit 2
136	jmc	1.1	fi
137	jmc	1.2	fi
138			#---- making a new working copy: MITgcm_today
139			rsync -a $git_code/ $srcCode --exclude '.git'
140			ls -ld $srcCode \| tee -a $LOG_FIL
141			if test -d $srcCode/verification ; then
142			for exp2add in $addExp ; do
143			echo " add dir: $exp2add (from Contrib:verification_other)" \| tee -a $LOG_FIL
144			( cd $srcCode/verification ; $cmdCVS co -P -d $exp2add \
145			MITgcm_contrib/verification_other/$exp2add > /dev/null )
146			done
147			fi
148			/usr/bin/find $srcCode -type d \| xargs chmod g+rxs
149			/usr/bin/find $srcCode -type f \| xargs chmod g+r
150			#- update date/lock-file:
151			if test -d $srcCode/verification ; then
152			echo $today > $updFile ; sleep 2
153			ls -l $updFile \| tee -a $LOG_FIL
154			echo '' \| tee -a $LOG_FIL
155			fi
156	jmc	1.1
157	jmc	1.2	#-- Done with Download/Update of MITgcm code
158	jmc	1.1	fi
159	jmc	1.2	#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-\|--+----\|
160	jmc	1.1
161	jmc	1.2	#-- leave srcDIR and go back to output dir
162	jmc	1.1	cd $OUT_DIR
163			#-- now really do something:
164
165			JOB_LIST=$TEST_LIST
166			NB_SUB_JOBS=0
167			for i in $JOB_LIST
168			do
169			case $i in
170			'pgiAdm') sfx='pgi_adm' ;;
171			'pgiMth') sfx='pgi_mth' ;;
172			*) sfx=`echo ${i} \| sed 's/MPI$/_mpi/'` ;;
173			esac
174			BATCH_SCRIPT="test_${dNam}_$sfx"
175			if test -f $SUB_DIR/$BATCH_SCRIPT ; then
176			#- job name ( $JOB ) & output-file name ( $JOB.std??? ) must match
177			# definition within $BATCH_SCRIPT slurm script
178			JOB="tst_${i}"
179			job_exist=`$QSTAT \| grep $JOB \| wc -l`
180			#sJob=`printf "%8.8s" $JOB` #- squeue truncate name to only 1rst 8c
181			#job_exist=`$QLIST \| grep $sJob \| wc -l`
182			if test "x_$job_exist" = x_0 ; then
183			#-- move previous output file
184			outList=`ls $JOB.std??? 2> /dev/null`
185			if test "x$outList" != x ; then
186			echo -n " moving job $JOB old output files:" \| tee -a $LOG_FIL
187			if test -d $OUT_DIR/prev ; then
188			for xx in $outList ; do
189			pp=$OUT_DIR/prev/$xx ; echo -n " $xx" \| tee -a $LOG_FIL
190			test -f $pp.sav && mv -f $pp.sav $pp.old
191			test -f $pp && mv -f $pp $pp.sav
192			chmod a+r $xx ; mv -f $xx $OUT_DIR/prev
193			done
194			echo " to dir ./prev" \| tee -a $LOG_FIL
195			else
196			echo " <-- missing dir $OUT_DIR/prev" \| tee -a $LOG_FIL
197			fi
198			else echo " no old output files from job '$JOB'" \| tee -a $LOG_FIL
199			fi
200			#-- submit job
201			echo -n "--> $JOB : " \| tee -a $LOG_FIL
202			$QSUB $SUB_DIR/$BATCH_SCRIPT \| tee -a $LOG_FIL
203			NB_SUB_JOBS=`expr $NB_SUB_JOBS + 1`
204			else
205			echo "--> $JOB :" \| tee -a $LOG_FIL
206			$QSTAT \| grep $JOB \| tee -a $LOG_FIL
207			#$QLIST \| grep $sJob \| tee -a $LOG_FIL
208			echo ' job already exist => skip this test' \| tee -a $LOG_FIL
209			fi
210			else
211			echo 'no file:' $BATCH_SCRIPT 'to submit' \| tee -a $LOG_FIL
212			fi
213			done
214			echo "info-sub-list: NB_SUB_JOBS='$NB_SUB_JOBS'" >> $LOG_FIL
215			echo -n '-- Finished at: ' \| tee -a $LOG_FIL
216			date \| tee -a $LOG_FIL
217
218			#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-\|--+----\|
219			exit 0