| 1 |
#! /bin/csh -f |
| 2 |
# Script to generate or fill in HMI cosmic ray tables |
| 3 |
# |
| 4 |
# this is run in the task instance directory where there is a 'ticket' file that specifies |
| 5 |
# the request. |
| 6 |
|
| 7 |
# XXXXXXXXXX test |
| 8 |
set echo |
| 9 |
# XXXXXXXXXX test |
| 10 |
|
| 11 |
set HERE = $cwd |
| 12 |
set LOG = $HERE/runlog |
| 13 |
set BABBLE = $HERE/babble |
| 14 |
|
| 15 |
# post processing flag. Set to 1 for cosmic_rays to be made in su_production.cosmic_rays |
| 16 |
# with cosmic_ray_post program used to merge and move to hmi.cosmic_rays |
| 17 |
# set to 1 to enable, otherwise only hmi.cosmic_rays will be used. |
| 18 |
set DO_POST = 0 |
| 19 |
|
| 20 |
date > $LOG |
| 21 |
|
| 22 |
if ($?WORKFLOW_ROOT) then |
| 23 |
set WFDIR = $WORKFLOW_DATA |
| 24 |
set WFCODE = $WORKFLOW_ROOT |
| 25 |
else |
| 26 |
echo Need WORKFLOW_ROOT variable to be set. >>$LOG |
| 27 |
env >>$LOG |
| 28 |
exit 1 |
| 29 |
endif |
| 30 |
|
| 31 |
set wantlow = `cat wantlow` |
| 32 |
set wanthigh = `cat wanthigh` |
| 33 |
hostname >> $LOG |
| 34 |
date >> $LOG |
| 35 |
echo "wanthigh = " $wanthigh >> $LOG |
| 36 |
echo "wantlow = " $wantlow >> $LOG |
| 37 |
set ACTION = `grep ACTION ticket` |
| 38 |
set $ACTION |
| 39 |
|
| 40 |
set CAMERA = 0 |
| 41 |
|
| 42 |
# process SPECIAL ticket args |
| 43 |
set FIXMISSING = 0 |
| 44 |
set SPECIAL = (`grep SPECIAL ticket`) |
| 45 |
set $SPECIAL |
| 46 |
set special = (`echo $SPECIAL | sed -e 's/,/ /g'`) |
| 47 |
# now special contains a=b c=d |
| 48 |
set NSPECARGS = $#special |
| 49 |
set SPECARG = 1 |
| 50 |
while ($SPECARG <= $NSPECARGS) |
| 51 |
echo Extracting SPECIAL component $SPECARG which is $special[$SPECARG] |
| 52 |
if ($special[$SPECARG] == NONE) then |
| 53 |
else |
| 54 |
set $special[$SPECARG] |
| 55 |
endif |
| 56 |
@ SPECARG = $SPECARG + 1 |
| 57 |
end |
| 58 |
|
| 59 |
if ($CAMERA > 0) then |
| 60 |
set CAMARG = '[? CAMERA='$CAMERA' ?]' |
| 61 |
else |
| 62 |
set CAMARG |
| 63 |
endif |
| 64 |
|
| 65 |
# set QUALMASK = 0x2F000 |
| 66 |
set QUALMASK = 192512 |
| 67 |
|
| 68 |
set FFSN = `show_info hmi.lev1'['$wantlow'-'$wanthigh'][? (QUALITY & '$QUALMASK') = 0 ?]' n=1 -q key=FSN` |
| 69 |
set LFSN = `show_info hmi.lev1'['$wantlow'-'$wanthigh'][? (QUALITY & '$QUALMASK') = 0 ?]' n=-1 -q key=FSN` |
| 70 |
|
| 71 |
if ($LFSN <= $FFSN) then |
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echo No good records to process between $wantlow and $wanthigh >>$LOG |
| 73 |
echo Allow OK status to let higher level code generate missing records. >>$LOG |
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set retstatus = 0 |
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goto FAILUREEXIT |
| 76 |
endif |
| 77 |
|
| 78 |
# get expected list of cosmic_ray records |
| 79 |
show_info hmi.lev1'[]['$FFSN'-'$LFSN'][? FID >= 10050 AND FID < 11000 ?][? (QUALITY & '$QUALMASK') = 0 ?][? T_OBS > 0 ?]'"$CAMARG" -q key=FSN > FSN_lev1 |
| 80 |
|
| 81 |
set N_NOCR = 100000000 |
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# unless a SPECIAL arg of FIXMISSING=1 is present, just wait here until all records are present. I.e. convert to a proper action=3 |
| 83 |
if ($ACTION == 4 && $FIXMISSING == 0) then |
| 84 |
set loopcount = 0 |
| 85 |
while ($N_NOCR > 0) |
| 86 |
show_info hmi.cosmic_rays'[]['$FFSN'-'$LFSN'][? FID >= 10050 AND FID < 11000 ?][? T_OBS > 0 ?]'"$CAMARG" -q key=FSN > FSN_cosmic |
| 87 |
comm -23 FSN_lev1 FSN_cosmic > NOCR |
| 88 |
set N_NOCR = `wc -l <NOCR` |
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echo "Lev1 records without cosmic ray records count = " $N_NOCR >>$LOG |
| 90 |
if ($N_NOCR < 1) exit 0 |
| 91 |
if ($loopcount > 576) then |
| 92 |
echo "FAIL - give up waiting after 4 days." >>$LOG |
| 93 |
echo "FAIL - give up waiting after 4 days." >>FAIL_reason |
| 94 |
cat N_NOCR >>FAIL_reason |
| 95 |
echo " " >>FAIL_reason |
| 96 |
set retstat = 9 |
| 97 |
goto FAILUREEXIT |
| 98 |
endif |
| 99 |
sleep 600 |
| 100 |
@ loopcount = $loopcount + 1 |
| 101 |
end |
| 102 |
endif |
| 103 |
|
| 104 |
if ($ACTION == 4) then |
| 105 |
show_info hmi.cosmic_rays'[]['$FFSN'-'$LFSN'][? FID >= 10050 AND FID < 11000 ?][? T_OBS > 0 ?]'"$CAMARG" -q key=FSN > FSN_cosmic |
| 106 |
comm -23 FSN_lev1 FSN_cosmic > NOCR |
| 107 |
set N_NOCR = `wc -l <NOCR` |
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echo "Lev1 records without cosmic ray records count = " $N_NOCR >>$LOG |
| 109 |
|
| 110 |
if ($N_NOCR < 1) exit 0 |
| 111 |
|
| 112 |
set FIRST_FSN = `head -1 NOCR` |
| 113 |
set LAST_FSN = `tail -1 NOCR` |
| 114 |
else # ACTION == 5 |
| 115 |
set FIRST_FSN = $FFSN |
| 116 |
set LAST_FSN = $LFSN |
| 117 |
endif |
| 118 |
|
| 119 |
# increase range to allow preceeding and following filtergrams |
| 120 |
@ FIRST_FSN = $FIRST_FSN - 96 |
| 121 |
# set CHK_FSN1 = `show_info hmi.lev1'[? FSN = '$FIRST_FSN' ?]' n=-1 -q key=T_OBS` |
| 122 |
set CHK_FSN1 = `show_info hmi.lev1'[][$FIRST_FSN]' n=1 -q key=T_OBS_index` |
| 123 |
while ( $CHK_FSN1 < 0 ) |
| 124 |
# @ FIRST_FSN = $FIRST_FSN - 1 |
| 125 |
# set CHK_FSN1 = `show_info hmi.lev1'[? FSN = '$FIRST_FSN' ?]' n=-1 -q key=T_OBS` |
| 126 |
@ FIRST_FSN = $FIRST_FSN + 1 |
| 127 |
set CHK_FSN1 = `show_info hmi.lev1'[][$FIRST_FSN]' n=1 -q key=T_OBS_index` |
| 128 |
end |
| 129 |
|
| 130 |
@ LAST_FSN = $LAST_FSN + 96 |
| 131 |
# set CHK_FSN2 = `show_info hmi.lev1'[? FSN = '$LAST_FSN' ?]' n=-1 -q key=T_OBS` |
| 132 |
set CHK_FSN2 = `show_info hmi.lev1'[][$LAST_FSN]' n=1 -q key=T_OBS_index` |
| 133 |
while ( $CHK_FSN2 < 0 ) |
| 134 |
# @ LAST_FSN = $LAST_FSN + 1 |
| 135 |
# set CHK_FSN2 = `show_info hmi.lev1'[? FSN = '$LAST_FSN' ?]' n=-1 -q key=T_OBS` |
| 136 |
@ LAST_FSN = $LAST_FSN - 1 |
| 137 |
set CHK_FSN2 = `show_info hmi.lev1'[][$LAST_FSN]' n=1 -q key=T_OBS_index` |
| 138 |
end |
| 139 |
|
| 140 |
|
| 141 |
# get day of first FSN |
| 142 |
|
| 143 |
# note that there may be a missing T_OBS along with a good T_OBS for a given FSN |
| 144 |
set LFSNDAY = `show_info key=T_OBS -q hmi.lev1'[]['$LAST_FSN'][? T_OBS > 0 ?]'` |
| 145 |
set yyyymmdd = `printf "%.10s" $LFSNDAY` |
| 146 |
set mmdd = `echo $yyyymmdd | sed -e "s/.....//" -e "s/://" ` |
| 147 |
|
| 148 |
# For now assume that the list of missing CR records is contiguous, later use show_coverage key=FSN for |
| 149 |
# special conditions on FIDs and do only the UNKs. |
| 150 |
|
| 151 |
# Run Richard's flat field program in cosmic_rays only mode |
| 152 |
# modified from module_flatfield_daily_qsub_48_CRonly2_PZT_FSN.pl |
| 153 |
|
| 154 |
mkdir CRlogs |
| 155 |
set CRLOG = $HERE/CRlogs |
| 156 |
# set module_flatfield = /home/jsoc/cvs/Development/JSOC/bin/linux_x86_64/module_flatfield |
| 157 |
set module_flatfield = /home/jsoc/cvs/Development/JSOC/bin/linux_x86_64/module_flatfield |
| 158 |
set cosmic_ray_post = /home/jsoc/cvs/Development/JSOC/bin/linux_x86_64/cosmic_ray_post |
| 159 |
|
| 160 |
set QSUBCMD = CRY_$mmdd |
| 161 |
set QSTAT = $HERE/CRY_status |
| 162 |
touch $QSTAT |
| 163 |
cat > $QSUBCMD <<ENDCAT |
| 164 |
# |
| 165 |
#\$ -cwd |
| 166 |
set echo |
| 167 |
echo $HOST |
| 168 |
setenv OMP_NUM_THREADS 8 |
| 169 |
ENDCAT |
| 170 |
|
| 171 |
# Do these serially in a single node |
| 172 |
# 135, camera=1 |
| 173 |
set FIDLIST_1 = (10054 10055 10056 10057 10058 10059 10074 10075 10076 10077 10078 10079 \ |
| 174 |
10094 10095 10096 10097 10098 10099 10114 10115 10116 10117 10118 10119 \ |
| 175 |
10134 10135 10136 10137 10138 10139 10154 10155 10156 10157 10158 10159) |
| 176 |
# 45s, camera=2 |
| 177 |
set FIDLIST_2 = (10058 10059 10078 10079 10098 10099 10118 10119 10138 10139 10158 10159) |
| 178 |
|
| 179 |
# set ID = \$SGE_TASK_ID |
| 180 |
set ID = 1 |
| 181 |
while ($ID <= 48) |
| 182 |
if ($ID <= 36) then |
| 183 |
set ID1 = $ID |
| 184 |
set cadence = "135s" |
| 185 |
set camera = 1 |
| 186 |
set fid = $FIDLIST_1[$ID1] |
| 187 |
else |
| 188 |
@ ID2 = $ID - 36 |
| 189 |
set cadence = "45s" |
| 190 |
set camera = 2 |
| 191 |
set fid = $FIDLIST_2[$ID2] |
| 192 |
endif |
| 193 |
|
| 194 |
if ($DO_POST) then |
| 195 |
cat >>$QSUBCMD <<ENDCAT |
| 196 |
$module_flatfield -L input_series=hmi.lev1 cadence=$cadence cosmic_rays=1 flatfield=0 fid=$fid camera=$camera fsn_first=$FIRST_FSN fsn_last=$LAST_FSN datum=$yyyymmdd >>& $CRLOG/$ID.log |
| 197 |
if (\$status) echo "$ID error" >> $QSTAT |
| 198 |
ENDCAT |
| 199 |
else |
| 200 |
cat >>$QSUBCMD <<ENDCAT |
| 201 |
$module_flatfield -L input_series=hmi.lev1 cosmic_ray_series=hmi.cosmic_rays cadence=$cadence cosmic_rays=1 flatfield=0 fid=$fid camera=$camera fsn_first=$FIRST_FSN fsn_last=$LAST_FSN datum=$yyyymmdd >>& $CRLOG/$ID.log |
| 202 |
if (\$status) echo "$ID error" >> $QSTAT |
| 203 |
ENDCAT |
| 204 |
endif |
| 205 |
|
| 206 |
@ ID = $ID + 1 |
| 207 |
end |
| 208 |
|
| 209 |
# qsub -q j.q -o $LOG -e $LOG -t 1-48 -sync yes $QSUBCMD |
| 210 |
qsub -q j8.q -o $LOG -e $LOG -sync yes $QSUBCMD |
| 211 |
# qsub -q p8.q -o $LOG -e $LOG -sync yes $QSUBCMD |
| 212 |
set QSUBSTATUS = $status |
| 213 |
if ($QSUBSTATUS) then |
| 214 |
echo qsub failed with exit status $QSUBSTATUS >>$LOG |
| 215 |
set retstatus = 11 |
| 216 |
echo qsub failure >>$FAIL_REASON |
| 217 |
goto FAILUREEXIT |
| 218 |
endif |
| 219 |
|
| 220 |
set QSTAT_errcnt = `wc -l < $QSTAT` |
| 221 |
if ($QSTAT_errcnt) then |
| 222 |
echo $QSTAT_errcnt " status errors in module_flatfield" >>$LOG |
| 223 |
echo $QSTAT_errcnt " status errors in module_flatfield" >>$FAIL_reason |
| 224 |
set retstatus = 7 |
| 225 |
goto FAILUREEXIT |
| 226 |
endif |
| 227 |
|
| 228 |
if ($DO_POST) then |
| 229 |
# Now do the post processing |
| 230 |
set QSUBCMD = POS_$mmdd |
| 231 |
set QSTAT = $HERE/POS_status |
| 232 |
touch $QSTAT |
| 233 |
cat > $QSUBCMD <<ENDCAT |
| 234 |
# |
| 235 |
set echo |
| 236 |
setenv OMP_NUM_THREADS 1 |
| 237 |
$cosmic_ray_post -L input_series=su_production.cosmic_rays fsn_first=$FIRST_FSN fsn_last=$LAST_FSN camera=1 >>& $CRLOG/post.log |
| 238 |
if (\$status) echo "Cam1 error" >> $QSTAT |
| 239 |
$cosmic_ray_post -L input_series=su_production.cosmic_rays fsn_first=$FIRST_FSN fsn_last=$LAST_FSN camera=2 >>& $CRLOG/post.log |
| 240 |
if (\$status) echo "Cam2 error" >> $QSTAT |
| 241 |
ENDCAT |
| 242 |
|
| 243 |
qsub -q j.q -o $LOG -e $LOG -sync yes $QSUBCMD |
| 244 |
|
| 245 |
set QSTAT_errcnt = `wc -l < $QSTAT` |
| 246 |
if ($QSTAT_errcnt) then |
| 247 |
echo $QSTAT_errcnt " status errors in cosmic_ray_post" >>$LOG |
| 248 |
echo $QSTAT_errcnt " status errors in cosmic_ray_post" >>$FAIL_reason |
| 249 |
set retstatus = 7 |
| 250 |
goto FAILUREEXIT |
| 251 |
endif |
| 252 |
|
| 253 |
endif # DO_POST |
| 254 |
|
| 255 |
# verify make of cosmic ray records |
| 256 |
|
| 257 |
show_info hmi.cosmic_rays'[]['$FFSN'-'$LFSN'][? FID >= 10050 AND FID < 11000 ?][? T_OBS > 0 ?]'"$CAMARG" -q key=FSN > FSN_cosmic |
| 258 |
comm -23 FSN_lev1 FSN_cosmic > NOCR |
| 259 |
set N_NOCR = `wc -l <NOCR` |
| 260 |
echo "Lev1 records now without cosmic ray records count = " $N_NOCR >>$LOG |
| 261 |
|
| 262 |
if ($N_NOCR > 10) then |
| 263 |
echo "$N_NOCR lev1 records are still missing matching cosmic_ray records. " >>FAIL_reason |
| 264 |
echo "The missing cosmic_ray records are FSNs: ">>FAIL_reason |
| 265 |
cat NOCR >>FAIL_reason |
| 266 |
echo " " >>FAIL_reason |
| 267 |
set retstatus = 3 |
| 268 |
goto FAILUREEXIT |
| 269 |
endif |
| 270 |
|
| 271 |
exit 0 |
| 272 |
|
| 273 |
FAILUREEXIT: |
| 274 |
|
| 275 |
echo "No CR records available" >>$LOG |
| 276 |
exit $retstatus |
