| 1 |
#! /usr/bin/env bash |
| 2 |
|
| 3 |
# $Header: /u/gcmpack/MITgcm/tools/example_scripts/ACESgrid/test_submit_aces,v 1.17 2014/05/07 16:16:04 jmc Exp $ |
| 4 |
# $Name: $ |
| 5 |
|
| 6 |
# submit list of jobs or get list of submitted jobs |
| 7 |
sub_list_jobs() |
| 8 |
{ |
| 9 |
# sub_list_jobs |
| 10 |
# input : JOB_LIST |
| 11 |
# output: NB_SUB_JOBS (+ status of jobs: M_{sfx}=submitted or skipped ) |
| 12 |
|
| 13 |
NB_SUB_JOBS=0 |
| 14 |
for i in $JOB_LIST |
| 15 |
do |
| 16 |
case $i in |
| 17 |
'mth') sfx='path_'${i} ;; |
| 18 |
'tuv') sfx='op64_'${i} ;; |
| 19 |
'mp2') sfx='gnu_'${i} ;; |
| 20 |
'oad') sfx='pgi_'${i} ;; |
| 21 |
'iad') sfx='ifc_adm' ;; |
| 22 |
*) sfx=${i}'_mpi' ;; |
| 23 |
esac |
| 24 |
if test -f $SUB_DIR/test_aces_$sfx ; then |
| 25 |
JOB="tst_"$i |
| 26 |
job_exist=`$QSTAT -a | grep $USER | grep $JOB | wc -l` |
| 27 |
if [ $action -eq 2 ] ; then |
| 28 |
#-- to get outp back: |
| 29 |
if test "x_$job_exist" = x_0 ; then |
| 30 |
echo "did not find any job: $JOB" | tee -a $LOG_FIL |
| 31 |
eval M_$i='skipped' |
| 32 |
else |
| 33 |
echo -n "found a job: $JOB" | tee -a $LOG_FIL |
| 34 |
$QSTAT -a | grep $USER | grep $JOB | tee -a $LOG_FIL |
| 35 |
eval M_$i='submitted' |
| 36 |
NB_SUB_JOBS=`expr $NB_SUB_JOBS + 1` |
| 37 |
fi |
| 38 |
else |
| 39 |
#-- to submit job |
| 40 |
if test "x_$job_exist" = x_0 ; then |
| 41 |
#-- update code if not done within submitted script |
| 42 |
doUp=`grep -c '^ *checkOut=0' $SUB_DIR/test_aces_$sfx` |
| 43 |
if test ! -e $TST_DIR/MITgcm_$i ; then doUp=0; fi |
| 44 |
if [ $doUp -ge 1 ] ; then |
| 45 |
echo "" >> $LOG_FIL |
| 46 |
echo " update $TST_DIR/MITgcm_$i :" | tee -a $LOG_FIL |
| 47 |
( cd $TST_DIR/MITgcm_$i |
| 48 |
cvs -q -d :pserver:cvsanon@mitgcm.org:/u/gcmpack update -P -d |
| 49 |
) >> $LOG_FIL 2>&1 |
| 50 |
fi |
| 51 |
echo -n " $JOB : " | tee -a $LOG_FIL |
| 52 |
$QSUB $SUB_DIR/test_aces_$sfx | tee -a $LOG_FIL |
| 53 |
eval M_$i='submitted' |
| 54 |
NB_SUB_JOBS=`expr $NB_SUB_JOBS + 1` |
| 55 |
else |
| 56 |
echo $JOB | tee -a $LOG_FIL |
| 57 |
$QSTAT -a | grep $USER | grep $JOB | tee -a $LOG_FIL |
| 58 |
echo 'job already exist => skip this test' | tee -a $LOG_FIL |
| 59 |
eval M_$i='skipped' |
| 60 |
fi |
| 61 |
fi |
| 62 |
else |
| 63 |
echo 'no file:' test_aces_$sfx 'to submit' | tee -a $LOG_FIL |
| 64 |
eval M_$i='skipped' |
| 65 |
fi |
| 66 |
done |
| 67 |
echo " info-sub-list: NB_SUB_JOBS='$NB_SUB_JOBS'" >> $LOG_FIL |
| 68 |
} |
| 69 |
|
| 70 |
# retrieve output when job is finished |
| 71 |
get_outp_back() |
| 72 |
{ |
| 73 |
# get_outp_back number_of_jobs |
| 74 |
# input : JOB_LIST (+ status of jobs: M_{sfx}=submitted ) |
| 75 |
# output: REJECTED (= list of fast-to-fail jobs) |
| 76 |
# (+ change status of jobs to: M_{sfx}=done ) |
| 77 |
|
| 78 |
nbJobs=$1 |
| 79 |
REJECTED= |
| 80 |
minutes=0 ; freq=10 ; waitLimit=1800 ; #-- all in minutes |
| 81 |
# "long" queue is 24.h = 24*60 = 1440mn ; 36.h = 2160mn ; 30.h = 1800mn |
| 82 |
|
| 83 |
echo "Check every $freq mn for $nbJobs test(s) to finish" | tee -a $LOG_FIL |
| 84 |
echo "- start at :" `date` | tee -a $LOG_FIL |
| 85 |
fsec=`expr $freq \* 60` |
| 86 |
while test $nbJobs != 0 ; do |
| 87 |
|
| 88 |
sleep $fsec |
| 89 |
minutes=$(( $minutes + $freq )) |
| 90 |
|
| 91 |
for i in $JOB_LIST ; do |
| 92 |
|
| 93 |
eval comm=\$M_$i |
| 94 |
if test $comm = 'submitted' ; then |
| 95 |
JOB="tst_"$i |
| 96 |
$QSTAT -a > $TMP_FIL |
| 97 |
RETVAL=$? |
| 98 |
ready_to_send=`grep $USER $TMP_FIL | grep $JOB | wc -l` |
| 99 |
rm -f $TMP_FIL |
| 100 |
if test "x$RETVAL" != x0 ; then |
| 101 |
echo " $QSTAT returned with error code: $RETVAL" | tee -a $LOG_FIL |
| 102 |
continue |
| 103 |
fi |
| 104 |
|
| 105 |
if test "x_$ready_to_send" = x_0 ; then |
| 106 |
run_dir=${TST_DIR}"/MITgcm_"$i"/verification" |
| 107 |
#- results output: |
| 108 |
tdir=`ls -1 -t $run_dir | grep -v tr_out | grep "^tr_$outPfix" | head -1` |
| 109 |
if test "x$tdir" != x ; then |
| 110 |
#- check this is the right output |
| 111 |
chk=`echo $tdir | grep -c $today` |
| 112 |
if test $chk = '0' ; then |
| 113 |
curday=`date +%Y%m%d` |
| 114 |
chk=`echo $tdir | grep -c $curday` |
| 115 |
fi |
| 116 |
if test $chk = '0' ; then |
| 117 |
echo "tdir='$tdir'" | tee -a $LOG_FIL |
| 118 |
echo "Output do not match, no email sent for $i" | tee -a $LOG_FIL |
| 119 |
if [ $minutes -eq $freq ] ; then |
| 120 |
#- add to rejected list if it fails in less than "freq" minutes |
| 121 |
REJECTED="$REJECTED $i" |
| 122 |
fi |
| 123 |
else |
| 124 |
rm -f "/tmp/tr_$outPfix-"$i".tar.gz" |
| 125 |
( cd $run_dir ; tar -czf "/tmp/tr_$outPfix-"$i".tar.gz" ./$tdir ) |
| 126 |
if test "x$HAVE_MPACK" = xt ; then |
| 127 |
$MPACK -s MITgcm-test -m 3555000 "/tmp/tr_$outPfix-"$i".tar.gz" jmc@mitgcm.org |
| 128 |
echo "Email sent for $i at: " `date` | tee -a $LOG_FIL |
| 129 |
else |
| 130 |
echo " no email sent for $i (no mpack)" | tee -a $LOG_FIL |
| 131 |
fi |
| 132 |
fi |
| 133 |
else |
| 134 |
echo " no output found for $i" | tee -a $LOG_FIL |
| 135 |
if [ $minutes -eq $freq ] ; then |
| 136 |
#- add to rejected list if it fails in less than "freq" minutes |
| 137 |
REJECTED="$REJECTED $i" |
| 138 |
fi |
| 139 |
fi |
| 140 |
#- restart output: |
| 141 |
tdir=`ls -1 -t $run_dir | grep -v tr_out | grep "^rs_$outPfix" | head -1` |
| 142 |
if test "x$tdir" != x ; then |
| 143 |
#- check this is the right output |
| 144 |
chk=`echo $tdir | grep -c $today` |
| 145 |
if test $chk = '0' ; then |
| 146 |
curday=`date +%Y%m%d` |
| 147 |
chk=`echo $tdir | grep -c $curday` |
| 148 |
fi |
| 149 |
if test $chk = '0' ; then |
| 150 |
echo "tdir='$tdir'" | tee -a $LOG_FIL |
| 151 |
echo "Restart output do not match, no email sent for $i" | tee -a $LOG_FIL |
| 152 |
else |
| 153 |
rm -f "/tmp/rs_$outPfix-"$i".tar.gz" |
| 154 |
( cd $run_dir ; tar -czf "/tmp/rs_$outPfix-"$i".tar.gz" ./$tdir ) |
| 155 |
if test "x$HAVE_MPACK" = xt ; then |
| 156 |
$MPACK -s MITgcm-test -m 3555000 "/tmp/rs_$outPfix-"$i".tar.gz" jmc@mitgcm.org |
| 157 |
echo "Email sent for $i restart:" `date` | tee -a $LOG_FIL |
| 158 |
else |
| 159 |
echo " no email sent for $i restart (no mpack)" | tee -a $LOG_FIL |
| 160 |
fi |
| 161 |
fi |
| 162 |
else |
| 163 |
echo " no restart output for $i" | tee -a $LOG_FIL |
| 164 |
fi |
| 165 |
#- record successful sending |
| 166 |
eval M_$i=done |
| 167 |
nbJobs=`expr $nbJobs - 1` |
| 168 |
chmod 644 output/tst_$i.std* |
| 169 |
fi |
| 170 |
fi |
| 171 |
done |
| 172 |
|
| 173 |
if test $minutes -gt $waitLimit ; then |
| 174 |
hrs=$(( $minutes / 60 )); |
| 175 |
echo "Time expired after $minutes minutes ($hrs hours)" | tee -a $LOG_FIL |
| 176 |
echo ' ' $nbJobs '/' $NB_SUB_JOBS 'tests not yet finished' | tee -a $LOG_FIL |
| 177 |
exit 1 |
| 178 |
fi |
| 179 |
|
| 180 |
done |
| 181 |
|
| 182 |
echo "Retrieving $NB_SUB_JOBS tests finish :" `date` | tee -a $LOG_FIL |
| 183 |
echo " info-get-outp: REJECTED='$REJECTED'" >> $LOG_FIL |
| 184 |
|
| 185 |
} |
| 186 |
|
| 187 |
#---+----1----+----2----+----3----+----4----+----5----+----6----+----7-|--+----| |
| 188 |
#-- Sequential part of the script starts here: |
| 189 |
#--------------------------------------------- |
| 190 |
|
| 191 |
# action =1 : submit test jobs ; =2 : get jobs output ; =3 : do both |
| 192 |
case $1 in |
| 193 |
'-subOnly') action=1 ; shift ;; |
| 194 |
'-getOnly') action=2 ; shift ;; |
| 195 |
'-sub+get') action=3 ; shift ;; |
| 196 |
'-double' ) action=4 ; shift ;; |
| 197 |
*) action=1 ;; |
| 198 |
esac |
| 199 |
#echo "action= $action , Arg= $# " |
| 200 |
|
| 201 |
today=`date +%Y%m%d` |
| 202 |
dInWeek=`date +%a` |
| 203 |
|
| 204 |
if test $# = 0 |
| 205 |
then |
| 206 |
TEST_LIST='gnu mp2 adm pgi path mth op64 tuv' |
| 207 |
if test "x$dInWeek" = xSat ; then TEST_LIST="$TEST_LIST iad ifc oad" ; fi |
| 208 |
if test "x$dInWeek" = xSun ; then TEST_LIST="$TEST_LIST iad ifc oad" ; fi |
| 209 |
else |
| 210 |
TEST_LIST=$* |
| 211 |
fi |
| 212 |
|
| 213 |
QSUB="/usr/bin/qsub" |
| 214 |
QSTAT="/usr/bin/qstat" |
| 215 |
logPfix='tst_submit' |
| 216 |
outPfix='acesgrid' |
| 217 |
HERE="$HOME/test_$outPfix" |
| 218 |
#TST_DIR="/data/jm_c/test_$outPfix" |
| 219 |
TST_DIR="/scratch/jm_c/test_$outPfix" |
| 220 |
# QSUB=qsub |
| 221 |
# QSTAT=qstat |
| 222 |
# logPfix='tst_all' |
| 223 |
# outPfix='aces' |
| 224 |
# HERE="$HOME/test_$outPfix" |
| 225 |
# TST_DIR=$HERE |
| 226 |
|
| 227 |
MPACK="MITgcm_tools/mpack-1.6/mpack" |
| 228 |
SUB_DIR="MITgcm_tools/example_scripts/ACESgrid" |
| 229 |
TMP_FIL="$HERE/output/TTT.$$" |
| 230 |
LOG_FIL="$HERE/output/$logPfix."`date +%m%d`".log" |
| 231 |
|
| 232 |
#-- clean up old log files and start a new one: |
| 233 |
cd $HERE/output |
| 234 |
|
| 235 |
rm -f $logPfix.*.log_bak |
| 236 |
if test -f $LOG_FIL ; then mv -f $LOG_FIL ${LOG_FIL}_bak ; fi |
| 237 |
echo -n '-- Starting: ' | tee -a $LOG_FIL |
| 238 |
date | tee -a $LOG_FIL |
| 239 |
|
| 240 |
n=$(( `ls $logPfix.*.log | wc -l` - 10 )) |
| 241 |
if test $n -gt 0 ; then |
| 242 |
echo ' remove old log files:' | tee -a $LOG_FIL |
| 243 |
ls -lt $logPfix.*.log | tail -"$n" | tee -a $LOG_FIL |
| 244 |
ls -t $logPfix.*.log | tail -"$n" | xargs rm -f |
| 245 |
fi |
| 246 |
|
| 247 |
. /etc/profile.d/modules.sh |
| 248 |
module list >> $LOG_FIL 2>&1 |
| 249 |
|
| 250 |
#-- now really do something: |
| 251 |
cd $HERE |
| 252 |
|
| 253 |
JOB_LIST=$TEST_LIST |
| 254 |
sub_list_jobs |
| 255 |
#echo " info-main: NB_SUB_JOBS='$NB_SUB_JOBS'" >> $LOG_FIL |
| 256 |
|
| 257 |
if test $action = 1 ; then |
| 258 |
NB_JOBS2GET=0 |
| 259 |
else |
| 260 |
#date_str=`date +%Y%m%d`"_0" |
| 261 |
|
| 262 |
echo "" | tee -a $LOG_FIL |
| 263 |
#- build the mpack utility (from build_mpack in testreport): |
| 264 |
MPACKDIR=`dirname $MPACK` |
| 265 |
( cd $MPACKDIR && ./configure && make ) > TTT.build_mpack.$$ 2>&1 |
| 266 |
RETVAL=$? |
| 267 |
if test "x$RETVAL" != x0 ; then |
| 268 |
echo "Error building the mpack tools at: $MPACK_DIR" | tee -a $LOG_FIL |
| 269 |
if test -x $MPACK ; then |
| 270 |
HAVE_MPACK=t |
| 271 |
echo " use (old ?) executable:" | tee -a $LOG_FIL |
| 272 |
ls -l $MPACK | tee -a $LOG_FIL |
| 273 |
else |
| 274 |
HAVE_MPACK=f |
| 275 |
fi |
| 276 |
else |
| 277 |
if test -x $MPACK ; then |
| 278 |
rm -f TTT.build_mpack.$$ |
| 279 |
HAVE_MPACK=t |
| 280 |
echo "Building mpack: OK" | tee -a $LOG_FIL |
| 281 |
else |
| 282 |
echo " $MPACK not executable" | tee -a $LOG_FIL |
| 283 |
HAVE_MPACK=f |
| 284 |
fi |
| 285 |
fi |
| 286 |
echo "" >> $LOG_FIL |
| 287 |
|
| 288 |
NB_JOBS2GET=$NB_SUB_JOBS |
| 289 |
fi |
| 290 |
|
| 291 |
#- when it's done, retrieve output and send e-mail |
| 292 |
get_outp_back $NB_JOBS2GET |
| 293 |
#echo " info-main: REJECTED='$REJECTED'" >> $LOG_FIL |
| 294 |
|
| 295 |
if test $action = 4 -a "x$REJECTED" != x ; then |
| 296 |
|
| 297 |
echo "" >> $LOG_FIL |
| 298 |
echo "Try 2nd round for fast-failed jobs: '$REJECTED'" | tee -a $LOG_FIL |
| 299 |
JOB_LIST=$REJECTED |
| 300 |
sub_list_jobs |
| 301 |
#echo " info-main: NB_SUB_JOBS='$NB_SUB_JOBS'" >> $LOG_FIL |
| 302 |
|
| 303 |
echo "" >> $LOG_FIL |
| 304 |
get_outp_back $NB_SUB_JOBS |
| 305 |
#echo " info-main: REJECTED='$REJECTED'" >> $LOG_FIL |
| 306 |
|
| 307 |
fi |
| 308 |
|
| 309 |
#------------------------ |
| 310 |
exit 0 |
Parent Directory
| 
Revision Log
| 
Revision Graph