| 1 |
jmc |
1.1 |
#! /usr/bin/env bash |
| 2 |
|
|
|
| 3 |
jmc |
1.5 |
# $Header: /u/gcmpack/MITgcm_contrib/test_scripts/nasa_ames/test_submit_pleiades,v 1.4 2022/05/10 18:41:31 jmc Exp $ |
| 4 |
jmc |
1.1 |
# $Name: $ |
| 5 |
|
|
|
| 6 |
|
|
today=`date +%Y%m%d` |
| 7 |
|
|
dInWeek=`date +%a` |
| 8 |
|
|
|
| 9 |
|
|
if test $# = 0 |
| 10 |
|
|
then |
| 11 |
jmc |
1.5 |
#TEST_LIST='ieee fast' |
| 12 |
|
|
TEST_LIST='ieee fast1 fast2' |
| 13 |
jmc |
1.1 |
else |
| 14 |
|
|
TEST_LIST=$* |
| 15 |
|
|
fi |
| 16 |
|
|
|
| 17 |
|
|
headNode=`hostname -s` |
| 18 |
|
|
QSUB="/PBS/bin/qsub" |
| 19 |
|
|
QSTAT="/PBS/bin/qstat -u $USER" |
| 20 |
|
|
#dNam=$headNode |
| 21 |
|
|
#QSUB="/usr/bin/sbatch" |
| 22 |
|
|
#QLIST="/usr/bin/squeue -u $USER" |
| 23 |
|
|
dNam='pleiades' |
| 24 |
|
|
HERE="$HOME/test_${dNam}" |
| 25 |
jmc |
1.4 |
TST_DISK="/nobackupp17/$USER" |
| 26 |
jmc |
1.1 |
TST_DIR="$TST_DISK/test_${dNam}" |
| 27 |
jmc |
1.2 |
tmpFil="/tmp/"`basename $0`".$$" |
| 28 |
|
|
#- where local copy of code is (need to be consistent with run-job scripts): |
| 29 |
|
|
srcDIR=$TST_DIR |
| 30 |
|
|
srcCode="MITgcm_today" |
| 31 |
|
|
|
| 32 |
jmc |
1.1 |
logPfix='test_submit' |
| 33 |
|
|
SUB_DIR="$HERE/nasa_ames" |
| 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 |
|
|
if test -f /etc/profile.d/modules.sh ; then . /etc/profile.d/modules.sh ; fi |
| 63 |
|
|
#- load standard modules: |
| 64 |
|
|
#module add fedora slurm maui svante |
| 65 |
|
|
#module add slurm |
| 66 |
|
|
module list >> $LOG_FIL 2>&1 |
| 67 |
|
|
|
| 68 |
|
|
#- method to acces CVS: |
| 69 |
|
|
cmdCVS='cvs -d :pserver:cvsanon@mitgcm.org:/u/gcmpack -q' |
| 70 |
jmc |
1.2 |
#- and which GitHub repository to use: |
| 71 |
|
|
git_repo='MITgcm'; git_code='MITgcm' |
| 72 |
|
|
#git_repo='altMITgcm'; #git_code='MITgcm66h' |
| 73 |
jmc |
1.1 |
|
| 74 |
|
|
checkOut=1 |
| 75 |
jmc |
1.2 |
addExp='' |
| 76 |
jmc |
1.1 |
updFile='updated_code' |
| 77 |
|
|
|
| 78 |
jmc |
1.2 |
#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-|--+----| |
| 79 |
|
|
if [ $checkOut -ge 1 ] ; then |
| 80 |
|
|
#-- Download/Update reference version of MITgcm code: |
| 81 |
jmc |
1.1 |
|
| 82 |
jmc |
1.2 |
if test $srcDIR = $TST_DIR ; then |
| 83 |
|
|
echo "cd $TST_DISK ; pwd (x2)" | tee -a $LOG_FIL |
| 84 |
|
|
cd $TST_DISK | tee -a $LOG_FIL 2>&1 |
| 85 |
|
|
pwd | tee -a $LOG_FIL |
| 86 |
|
|
fi |
| 87 |
|
|
if test ! -d $srcDIR ; then |
| 88 |
|
|
echo -n "Creating a working dir: $srcDIR ..." | tee -a $LOG_FIL |
| 89 |
|
|
#/bin/rm -rf $srcDIR |
| 90 |
|
|
mkdir $srcDIR |
| 91 |
|
|
retVal=$? |
| 92 |
|
|
if test "x$retVal" != x0 ; then |
| 93 |
|
|
echo "Error: unable to make dir: $srcDIR (err=$retVal ) --> Exit" | tee -a $LOG_FIL |
| 94 |
|
|
exit 1 |
| 95 |
|
|
fi |
| 96 |
|
|
fi |
| 97 |
|
|
cd $srcDIR |
| 98 |
|
|
pwd | tee -a $LOG_FIL |
| 99 |
jmc |
1.1 |
|
| 100 |
jmc |
1.2 |
#- remove date/lock-file and old copy: |
| 101 |
|
|
if test -f $updFile ; then rm -f $updFile ; sleep 2 ; fi |
| 102 |
|
|
test -e $srcCode && rm -rf $srcCode |
| 103 |
|
|
|
| 104 |
|
|
if [ $checkOut -eq 1 ] ; then |
| 105 |
|
|
if test -e $git_code/.git/config ; then |
| 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 |
jmc |
1.3 |
echo " and checkout master:" | tee -a $LOG_FIL |
| 116 |
|
|
( cd $git_code ; git checkout master -- . ) | tee -a $LOG_FIL |
| 117 |
jmc |
1.2 |
else |
| 118 |
|
|
echo "missing file: $git_code/.git/config => try a new clone" | tee -a $LOG_FIL |
| 119 |
|
|
checkOut=2 |
| 120 |
jmc |
1.1 |
fi |
| 121 |
|
|
fi |
| 122 |
jmc |
1.2 |
if [ $checkOut -eq 2 ] ; then |
| 123 |
|
|
if test -e $git_code ; then |
| 124 |
|
|
echo -n " removing dir: $git_code ..." | tee -a $LOG_FIL |
| 125 |
|
|
rm -rf $git_code |
| 126 |
|
|
echo " done" | tee -a $LOG_FIL |
| 127 |
jmc |
1.1 |
fi |
| 128 |
jmc |
1.2 |
echo -n "Make a clone of $git_code from repo: $git_repo ..." | tee -a $LOG_FIL |
| 129 |
|
|
git clone https://github.com/$git_repo/${git_code}.git 2> $tmpFil |
| 130 |
|
|
retVal=$? |
| 131 |
|
|
if test $retVal = 0 ; then |
| 132 |
|
|
echo ' --> done!' | tee -a $LOG_FIL |
| 133 |
|
|
rm -f $tmpFil |
| 134 |
|
|
else echo '' | tee -a $LOG_FIL |
| 135 |
|
|
echo " Error: 'git clone' returned: $retVal" | tee -a $LOG_FIL |
| 136 |
|
|
cat $tmpFil ; rm -f $tmpFil |
| 137 |
|
|
exit 2 |
| 138 |
jmc |
1.1 |
fi |
| 139 |
jmc |
1.2 |
fi |
| 140 |
|
|
#---- making a new working copy: MITgcm_today |
| 141 |
|
|
rsync -a $git_code/ $srcCode --exclude '.git' |
| 142 |
|
|
ls -ld $srcCode | tee -a $LOG_FIL |
| 143 |
|
|
if test -d $srcCode/verification ; then |
| 144 |
|
|
for exp2add in $addExp ; do |
| 145 |
|
|
echo " add dir: $exp2add (from Contrib:verification_other)" | tee -a $LOG_FIL |
| 146 |
|
|
( cd $srcCode/verification ; $cmdCVS co -P -d $exp2add \ |
| 147 |
|
|
MITgcm_contrib/verification_other/$exp2add > /dev/null ) |
| 148 |
|
|
done |
| 149 |
|
|
fi |
| 150 |
|
|
/usr/bin/find $srcCode -type d | xargs chmod g+rxs |
| 151 |
|
|
/usr/bin/find $srcCode -type f | xargs chmod g+r |
| 152 |
|
|
#- update date/lock-file: |
| 153 |
|
|
if test -d $srcCode/verification ; then |
| 154 |
|
|
echo $today > $updFile ; sleep 2 |
| 155 |
|
|
ls -l $updFile | tee -a $LOG_FIL |
| 156 |
|
|
echo '' | tee -a $LOG_FIL |
| 157 |
|
|
fi |
| 158 |
jmc |
1.1 |
|
| 159 |
jmc |
1.2 |
#-- Done with Download/Update of MITgcm code |
| 160 |
jmc |
1.1 |
fi |
| 161 |
jmc |
1.2 |
#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-|--+----| |
| 162 |
jmc |
1.1 |
|
| 163 |
jmc |
1.2 |
#-- leave srcDIR and go back to output dir |
| 164 |
jmc |
1.1 |
cd $OUT_DIR |
| 165 |
|
|
#-- now really do something: |
| 166 |
|
|
|
| 167 |
|
|
JOB_LIST=$TEST_LIST |
| 168 |
|
|
NB_SUB_JOBS=0 |
| 169 |
|
|
for i in $JOB_LIST |
| 170 |
|
|
do |
| 171 |
|
|
case $i in |
| 172 |
|
|
'pgiAdm') sfx='pgi_adm' ;; |
| 173 |
|
|
'pgiMth') sfx='pgi_mth' ;; |
| 174 |
|
|
*) sfx=`echo ${i} | sed 's/MPI$/_mpi/'` ;; |
| 175 |
|
|
esac |
| 176 |
|
|
BATCH_SCRIPT="test_${dNam}_$sfx" |
| 177 |
|
|
if test -f $SUB_DIR/$BATCH_SCRIPT ; then |
| 178 |
|
|
#- job name ( $JOB ) & output-file name ( $JOB.std??? ) must match |
| 179 |
|
|
# definition within $BATCH_SCRIPT slurm script |
| 180 |
|
|
JOB="tst_${i}" |
| 181 |
|
|
job_exist=`$QSTAT | grep $JOB | wc -l` |
| 182 |
|
|
#sJob=`printf "%8.8s" $JOB` #- squeue truncate name to only 1rst 8c |
| 183 |
|
|
#job_exist=`$QLIST | grep $sJob | wc -l` |
| 184 |
|
|
if test "x_$job_exist" = x_0 ; then |
| 185 |
|
|
#-- move previous output file |
| 186 |
|
|
outList=`ls $JOB.std??? 2> /dev/null` |
| 187 |
|
|
if test "x$outList" != x ; then |
| 188 |
|
|
echo -n " moving job $JOB old output files:" | tee -a $LOG_FIL |
| 189 |
|
|
if test -d $OUT_DIR/prev ; then |
| 190 |
|
|
for xx in $outList ; do |
| 191 |
|
|
pp=$OUT_DIR/prev/$xx ; echo -n " $xx" | tee -a $LOG_FIL |
| 192 |
|
|
test -f $pp.sav && mv -f $pp.sav $pp.old |
| 193 |
|
|
test -f $pp && mv -f $pp $pp.sav |
| 194 |
|
|
chmod a+r $xx ; mv -f $xx $OUT_DIR/prev |
| 195 |
|
|
done |
| 196 |
|
|
echo " to dir ./prev" | tee -a $LOG_FIL |
| 197 |
|
|
else |
| 198 |
|
|
echo " <-- missing dir $OUT_DIR/prev" | tee -a $LOG_FIL |
| 199 |
|
|
fi |
| 200 |
|
|
else echo " no old output files from job '$JOB'" | tee -a $LOG_FIL |
| 201 |
|
|
fi |
| 202 |
|
|
#-- submit job |
| 203 |
jmc |
1.5 |
if test $sfx != 'fast2' ; then |
| 204 |
jmc |
1.1 |
echo -n "--> $JOB : " | tee -a $LOG_FIL |
| 205 |
|
|
$QSUB $SUB_DIR/$BATCH_SCRIPT | tee -a $LOG_FIL |
| 206 |
|
|
NB_SUB_JOBS=`expr $NB_SUB_JOBS + 1` |
| 207 |
jmc |
1.5 |
fi |
| 208 |
jmc |
1.1 |
else |
| 209 |
|
|
echo "--> $JOB :" | tee -a $LOG_FIL |
| 210 |
|
|
$QSTAT | grep $JOB | tee -a $LOG_FIL |
| 211 |
|
|
#$QLIST | grep $sJob | tee -a $LOG_FIL |
| 212 |
|
|
echo ' job already exist => skip this test' | tee -a $LOG_FIL |
| 213 |
|
|
fi |
| 214 |
|
|
else |
| 215 |
|
|
echo 'no file:' $BATCH_SCRIPT 'to submit' | tee -a $LOG_FIL |
| 216 |
|
|
fi |
| 217 |
|
|
done |
| 218 |
|
|
echo "info-sub-list: NB_SUB_JOBS='$NB_SUB_JOBS'" >> $LOG_FIL |
| 219 |
|
|
echo -n '-- Finished at: ' | tee -a $LOG_FIL |
| 220 |
|
|
date | tee -a $LOG_FIL |
| 221 |
|
|
|
| 222 |
|
|
#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-|--+----| |
| 223 |
|
|
exit 0 |
Parent Directory
| 
Revision Log
| 
Revision Graph