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Thu, Jul 24, 23:39

tst_2+2
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#! /usr/bin/env bash
# $Header: /u/gcmpack/MITgcm/tools/tst_2+2,v 1.13 2016/01/11 20:46:05 jmc Exp $
# $Name: $
rnp_loc()
{
# rnp_loc arg_1 arg_2
# rename files with prefix = 'arg_1' to files with prefix = 'arg_2'
if [ $prt -ge 1 ] ; then echo ' rnp_loc:' $1 $2 ; fi
# rnp -s $1 $2
listY=`ls -1 $1*`
for yy in $listY
do
zz=`echo $yy | sed "s/^$1/$2/"`
if [ $prt -ge 2 ] ; then echo ' '$cmdMV $yy $zz ; fi
if test $action = 1 ; then $cmdMV $yy $zz ; fi
done
}
#-----------
move_outp()
{
# move_outp arg_1
# move mitgcm output files to directory 'arg_1'
if [ $prt -ge 1 ] ; then echo ' move_outp:' $1 ; fi
mv *.data *.meta $1
listF=`ls -1 *.txt STD???.00?? 2> /dev/null`
if test "x$listF" != x ; then mv $listF $1 ; fi
#- move back sym link:
listL=`find $1 -type l`
ttd=`echo $listL | wc -w`
#echo "ttd=$ttd"
if test $ttd != 0 ; then
#echo "listL='$listL'"
if [ $prt -ge 2 ] ; then echo " mv back:" $listL | sed "s/$1\///g" ; fi
mv $listL .
fi
}
#---------------------------
#- exit status:
# 0 -> test is successful
# 1 -> fail in 1rst run
# 2 -> fail in 2nd run
# 3 -> fail in 3rd run
# 4 -> pickup*.data (written at the end of 2+2 & 4 it run) are different
# 5 -> pickup*.meta (written at the end of 2+2 & 4 it run) are different
# 6 -> missing 'data.tst' file (removed or not yet generated ?)
# 7 -> missing executable or standard output from previous run
# 8 -> missing information (in standard output of previous run) about pickup
# 9 -> error in argument list
#- default:
Nit=2
prt=1 # 1 = print some informations ; 2 = print more informations
action=1
cmdMV='mv -f'
tmpDir='temp_tst'
wait2run=0 # if needs sometime for file system syncro on all nodes
#- default executable, command-line , using MPI:
gcmEXE=./mitgcmuv
cmdEXE=
mpi=0
nArg=$#
prev=
for xx ; do
#echo "xx='$xx'"
# If the previous option needs an argument, assign it.
if test -n "$prev"; then
eval "$prev=\$xx"
prev=
nArg=`expr $nArg - 2`
continue
fi
case $xx in
-mpi ) mpi=1 ; nArg=`expr $nArg - 1` ;;
-exe ) prev=gcmEXE ;;
-command ) prev=cmdEXE ;;
*) flag=$xx ;;
esac
done
#echo "cmdEXE='$cmdEXE'"
#echo "nArg=$nArg ; mpi=$mpi ; flag='$flag'"
case $nArg in
1) ;;
*) echo "Usage: `basename $0` flag [-mpi] [-exe EXECUTABLE] [-command COMMAND]"
echo " Check restart: compare 1 run of 2 x $Nit it long"
echo " with 2 consecutive runs of $Nit it long each"
echo " where: flag = 0 -> prepare (from a previous run) pickup & data files"
echo " flag = 1 -> do the 3 runs (using COMMAND"
echo " or simply using EXECUTABLE, default=$gcmEXE)"
echo " flag = 2 -> compare std_outp"
echo " flag = 3 -> compare pickup files"
echo " flag = 4 -> clean-up output files"
echo " flag = NC -> do 0,1,2,3 sequentially (no cleaning)"
echo " flag = All -> do 0,1,2,3,4 sequentially"
exit 9 ;;
esac
if test $flag = 'NC' -o $flag = 'All' ; then Multi=1 ; else Multi=0 ; fi
#-- set the run-command :
if test "x$cmdEXE" = x
then
if [ $mpi -ge 1 ] ; then
cmdEXE="mpirun -machinefile ../../mf -v -np 2 $gcmEXE"
else
cmdEXE=$gcmEXE
fi
fi
echo "cmdEXE='$cmdEXE'"
#=========================
if test $flag = '0' -o $Multi = '1' ; then
#----------------------------------------------------------------------
# check for executable:
if test ! -x $gcmEXE ; then
echo "file '$gcmEXE' does not exist or is not executable"
exit 7
fi
# last pickup written (from previous run):
if [ $mpi -ge 1 ]
then outpRun='STDOUT.0000'
else outpRun='output.txt'
fi
if test -r $outpRun
then
# grep ' %CHECKPOINT ' $outpRun | tail -1
lastPick=`grep ' %CHECKPOINT ' $outpRun | sed 's/^.*%CHECKPOINT //' | tail -1`
if test "x$lastPick" = x
then
echo "no pickup information written in '$outpRun' from previous run"
exit 8
else
iter=`echo $lastPick | awk '{print $1}'`
sufx=`echo $lastPick | awk '{print $2}'`
echo "from previous run $outpRun, lastPick='$lastPick' ; iter='$iter' ; sufx='$sufx'"
fi
else
echo "no standard output file '$outpRun' from previous run"
exit 7
fi
#-------------------------
echo "prepare parameter file 'data.tst' :"
cp -p -f data data.tst
listOut='startTime endTime nIter0 nTimeSteps nEndIter chkPtFreq pChkPtFreq'
listOut=$listOut' pickupSuff usePickupBeforeC54 mdsioLocalDir pickupStrictlyMatch'
#- comment out (in data.tst) all parameters from list: 'listOut'
for yy in $listOut
do
if [ $prt -ge 2 ] ; then echo -n ' commenting out:' $yy ; fi
nn=`grep -i -c "^ *$yy *=" data.tst`
if [ $nn -ge 1 ]
then
listN=`grep -i -n "^ *$yy *=" data.tst | sed 's/:.*$//'`
if [ $prt -ge 2 ] ; then echo " : found on line: $listN" ; fi
for ll in $listN
do
sed "$ll s/^./#&/" data.tst > data.tmp_$$
# diff data.tmp_$$ data.tst
mv -f data.tmp_$$ data.tst
done
else if [ $prt -ge 2 ] ; then echo ' : not found' ; fi
fi
done
if [ $prt -ge 2 ] ; then echo ' ' ; fi
# add nIter0 & nTimeSteps in namelist "PARM03":
Dbl=`expr $Nit \* 2`
sed "/^ *\&PARM03/a \ nTimeSteps=$Dbl," data.tst > data.tmp_$$
mv -f data.tmp_$$ data.tst
sed "/^ *\&PARM03/a \ nIter0=$iter," data.tst > data.tmp_$$
mv -f data.tmp_$$ data.tst
echo "prepare file 'data.tst' : done"
if [ $prt -ge 1 ] ; then
echo ' diff data.tst data' ; diff data.tst data ; echo ' ' ;
fi
#---- clean up current dir: move output to temp_tst dir:
if test $action = 1 ; then
rm -rf $tmpDir
mkdir $tmpDir
mv -f *.data $tmpDir
mv -f *.meta $tmpDir
mv -f *.txt $tmpDir 2> /dev/null
mv -f STD???.0[0-9][0-9][0-9] $tmpDir
#- move main parameter file "data":
mv -f data $tmpDir
#- do not deal with MNC pickup at all:
cp -p -f data.pkg data.tmp_$$
mv -f data.pkg $tmpDir
mv -f data.tmp_$$ data.pkg
yy='useMNC'
if [ $prt -ge 2 ] ; then echo -n " commenting out: $yy in data.pkg" ; fi
nn=`grep -i -c "^ *$yy *=" data.pkg`
if [ $nn -ge 1 ]
then
listN=`grep -i -n "^ *$yy *=" data.pkg | sed 's/:.*$//'`
if [ $prt -ge 2 ] ; then echo " : found on line: $listN" ; fi
for ll in $listN
do
sed "$ll s/^./#&/" data.pkg > data.tmp_$$
if [ $prt -ge 1 ] ; then echo ' changes in data.pkg'
diff data.tmp_$$ data.pkg ; echo ' ' ; fi
mv -f data.tmp_$$ data.pkg
done
else if [ $prt -ge 2 ] ; then echo ' : not found' ; echo ' ' ; fi
fi
fi
#-------------------------
#-- link back pickup files
listS=`ls $tmpDir/pickup*.${sufx}* 2> /dev/null | head -1`
if test "x$listS" != x ; then
if [ $prt -ge 1 ] ; then echo ' link back:' $tmpDir'/pickup*.'${sufx}'*' ; fi
if test $action = 1 ; then ln -s $tmpDir/pickup*.${sufx}* . ; fi
fi
#- rename pickup (if needed)
nIt0c=`printf "%10.10i\n" $iter`
if test $sufx = $nIt0c
then
echo "no need to change pickup sufix"
else
listP=`ls pickup*.${sufx}* 2> /dev/null | sed 's/\..*//g' | uniq`
if test "x$listP" = x
then echo ' rename' $sufx '->' $nIt0c ': no file to rename'
else
if [ $prt -ge 1 ] ; then echo ' rename' $sufx '->' $nIt0c 'for all:' $listP ; fi
for yy in $listP
do
rnp_loc $yy.${sufx} $yy.$nIt0c
done
fi
fi
#----------------------------------------------------------------------
fi
#=========================
if test -r data.tst ; then
#- extract length of runs & starting iter number from file "data.tst"
num0=`sed -n 's/^ nIter0=//p' data.tst | sed 's/,//g' | sed 's/ //g'`
Dbl=`sed -n 's/^ nTimeSteps=//p' data.tst | sed 's/,//g'`
Nit=`expr $Dbl / 2`
# Nit = Nb of iter of 2nd & 3rd run (1rst one is 2 x Nit iter long)
else
echo '=> Need a readable "data.tst" file for the 2 x Nit iterations run'
exit 6
fi
#- dir where to put the results :
dir1=res_2it
dir2=res_1iA
dir3=res_1iB
#---------------------------
num1=`expr $num0 + $Nit`
num2=`expr $num0 + $Dbl`
num0c=`printf "%10.10i\n" $num0`
num1c=`printf "%10.10i\n" $num1`
num2c=`printf "%10.10i\n" $num2`
echo " start-end iter: $num0 , $num1 , $num2"
echo " sufix: '$num0c' '$num1c' '$num2c'"
echo ' cmdEXE='$cmdEXE
#exit
#---------------------------
if test $flag = '1' -o $Multi = '1' ; then
#----------------------------------------------------------------------
#- check at the end of each run for pickup with prefix:
pref='pickup'
offLine=`grep -i -c '^ *useOffLine *= *\.TRUE\.' data.pkg`
if [ $offLine -ge 1 ] ; then pref='pickup_ptracers' ; fi
#---------------------------
if test -d $dir1 -o -d $dir2 -o -d $dir3
then echo -n 'remove dir: '
if test -d $dir1 ; then echo -n $dir1 ' , ' ; rm -r $dir1 ; fi
if test -d $dir2 ; then echo -n $dir2 ' , ' ; rm -r $dir2 ; fi
if test -d $dir3 ; then echo -n $dir3 ' , ' ; rm -r $dir3 ; fi
echo ' '
fi
mkdir $dir1 $dir2 $dir3
rm -f STDERR.0000
#--- 1rst run ( 2 x Nit iter )
cp -p data.tst data
echo '==> START RUN 2 x' $Nit 'it'
if [ $mpi -ge 1 ]
then
sleep $wait2run
$cmdEXE > TTT.out.2it 2>&1
mv STDOUT.0000 std_outp.2it
cat TTT.out.2it
else $cmdEXE > std_outp.2it
fi
if test ! -s std_outp.2it
then echo "empty or no output file: 'std_outp.2it' => exit" ; exit 1 ; fi
mv STDERR.0000 std__err.2it
out=`egrep -c 'STOP ABNORMAL END' std_outp.2it`
if test $out != 0
then echo "==> RUN 2 x $Nit it : ABNORMAL END => exit" ; exit 1 ; fi
listF=`ls -1 $pref.ckptA*.data 2> /dev/null`
if test "x$listF" = x
then echo "==> RUN 2 x $Nit it STOP without writing $pref => exit" ; exit 1
else echo "==> END RUN 2 x $Nit it" ; fi
listP=`ls pickup*.ckptA* | sed 's/\..*//g' | uniq`
echo ' listP=' $listP
for xx in $listP
do
rnp_loc $xx.ckptA $xx.$num2c
done
move_outp $dir1
#--- 2nd run ( Nit iter , restart from same Iter = num0 as 1rst run )
sed "s/^ nTimeSteps=$Dbl/ nTimeSteps=$Nit/g" data.tst > data.tmp
mv -f data.tmp data
echo '==> START RUN 1iA'
if [ $mpi -ge 1 ]
then
sleep $wait2run
$cmdEXE > TTT.out.1iA 2>&1
mv STDOUT.0000 std_outp.1iA
cat TTT.out.1iA
else $cmdEXE > std_outp.1iA
fi
if test ! -s std_outp.1iA
then echo "empty or no output file: 'std_outp.1iA' => exit" ; exit 2 ; fi
mv STDERR.0000 std__err.1iA
out=`egrep -c 'STOP ABNORMAL END' std_outp.1iA`
if test $out != 0
then echo "==> RUN 1iA : ABNORMAL END => exit" ; exit 2 ; fi
listF=`ls -1 $pref.ckptA*.data 2> /dev/null`
if test "x$listF" = x
then echo "==> RUN 1iA STOP without writing $pref => exit" ; exit 2
else echo "==> END RUN 1iA" ; fi
for xx in $listP
do
rnp_loc $xx.ckptA $xx.$num1c
done
move_outp $dir2
#--- 3rd run ( Nit iter , restart from 2nd )
ln -s $dir2/pickup*.$num1c.* .
sed "s/^ nIter0=$num0/ nIter0=$num1/g" data > data.tmp
mv -f data.tmp data
echo '==> START RUN 1iB'
if [ $mpi -ge 1 ]
then
sleep $wait2run
$cmdEXE > TTT.out.1iB 2>&1
mv STDOUT.0000 std_outp.1iB
cat TTT.out.1iB
else $cmdEXE > std_outp.1iB
fi
if test ! -s std_outp.1iB
then echo "empty or no output file: 'std_outp.1iB' => exit" ; exit 3 ; fi
mv STDERR.0000 std__err.1iB
out=`egrep -c 'STOP ABNORMAL END' std_outp.1iB`
if test $out != 0
then echo "==> RUN 1iB : ABNORMAL END => exit" ; exit 3 ; fi
listF=`ls -1 $pref.ckptA*.data 2> /dev/null`
if test "x$listF" = x
then echo "==> RUN 1iB STOP without writing $pref => exit" ; exit 3
else echo "==> END RUN 1iB" ; fi
for xx in $listP
do
rnp_loc $xx.ckptA $xx.$num2c
done
# remove pickup*.$mun1c* sym-link:
find . ! -name . -prune -type l -name 'pickup*.'${num1c}'*' -exec rm {} \;
move_outp $dir3
rm data
#----------------------------------------------------------------------
fi
if test $flag = '2' -o $Multi = '1' ; then
#----------------------------------------------------------------------
listCGini="2"
#-- check if using 3-D solver
nn=`grep -i -c "^ *nonHydrostatic *= *\.TRUE\." data.tst`
if [ $nn -eq 0 ] ; then
nn=`grep -i -c "^ *implicitIntGravWave *= *\.TRUE\." data.tst`
fi
if [ $nn -ge 1 ] ; then listCGini="$listCGini 3"; fi
for nn in $listCGini
do
echo ' ' ; echo "== compare cg${nn}d_init_res :"
echo ' run 1iA:'
grep "cg${nn}d_init_res" std_outp.1iA \
| sed "s/.* cg${nn}d_init_res =//"
echo ' run 1iB:'
grep "cg${nn}d_init_res" std_outp.1iB \
| sed "s/.* cg${nn}d_init_res =//"
echo ' run 2it:'
grep "cg${nn}d_init_res" std_outp.2it \
| sed "s/.* cg${nn}d_init_res =//"
done
#----------------------------------------------------------------------
fi
if test $flag = '3' -o $Multi = '1' ; then
#----------------------------------------------------------------------
echo ' '
echo "== diff pickup files : end of 1rst run (2x$Nit it) & end of 3rd run (2nd $Nit it)"
listP=`( cd $dir1 ; ls pickup*.$num2c* | sed 's/\..*//g' | uniq )`
chkmeta='Y'
for yy in $listP
do
listY=`(cd $dir1 ; ls $yy.$num2c*.data | sed "s/$yy\.$num2c//" | sed "s/data$//")`
zz=$yy.$num2c
echo '--> file='$zz', listY='$listY
for xx in $listY
do
echo ' diff' $dir1/$zz${xx}data $dir3
diff $dir1/$zz${xx}data $dir3
out=$?
if test $out != 0 ; then
#-- refined check: exclude diff between +0 and -0
nbDif=`cmp -l $dir1/$zz${xx}data $dir3/$zz${xx}data \
| sed -e '/ 0 200$/d' -e '/ 200 0$/d' | wc -l`
if test $nbDif != 0 ; then
echo "Diff outp= $out (nb-Diff= $nbDif ) ==> stop"
exit 4
fi
fi
if test $chkmeta = 'Y' -a -f $dir1/$zz${xx}meta ; then
echo ' diff' $dir1/$zz${xx}meta $dir3
diff $dir1/$zz${xx}meta $dir3
out=$?
if test $out != 0 ; then
echo 'Diff outp=' $out ' ==> stop'
exit 5
fi
fi
done
done
#----------------------------------------------------------------------
fi
if test $flag = '4' -o $flag = 'All' ; then
#-------------
echo ' '
echo "== clean-up and reset :"
echo '--> remove pickup*.'$num0c'* sym-links:'
#find . ! -name . -prune -type l -name 'pickup*.'${num0c}'*' -exec rm {} \;
listS=`find . ! -name . -prune -type l -name 'pickup*.'${num0c}'*'`
if [ $prt -ge 2 ] ; then echo ' rm' $listS ; fi
rm -f $listS
echo '--> remove output dir and output files:'
echo ' rm -rf' $dir1 $dir2 $dir3
rm -rf $dir1 $dir2 $dir3
echo ' rm -f' std_????.?i?
rm -f std_????.?i?
rm -f TTT.out.?i? 2> /dev/null
echo ' rm -f' data.pkg data.tst
rm -f data.pkg data.tst
#- move back files from temp_tst dir:
if test -d $tmpDir ; then
echo "--> move back files from 'temp_tst' dir."
cd $tmpDir ; mv -f * .. ; cd ..
rmdir $tmpDir
fi
#-------------
fi
exit 0

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