/[MITgcm]/MITgcm_contrib/jmc_script/tst_2+2_cpl

Diff of /MITgcm_contrib/jmc_script/tst_2+2_cpl

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-revision 1.9 by jmc,
Mon Dec  6 02:57:56 2010 UTC
+revision 1.10 by jmc,
Wed Dec  8 18:23:25 2010 UTC
 Line 7 
 rnp_loc()
  {
  #   rnp_loc arg_1 arg_2
  #   rename files with prefix = 'arg_1' to files with prefix = 'arg_2'
-     echo 'rnp_loc:' $1 $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/"`
-       mv $yy $zz
+       if [ $prt -ge 2 ] ; then echo '   mv' $yy $zz ; fi
+       if test $action = 1 ; then    mv $yy $zz ; fi
      done
  }
-Line 62 
 move_outp()
+Line 63 
 move_outp()
      fi
  }
- #===============================================================================
+ #----------------------------------------------------------------------
- if test -f input_ocn/data.tst ; then
+ prepare_first()
-  noc0=`sed -n 's/nIter0=//p' input_ocn/data.tst | sed 's/,//g' | sed 's/ //g'`
+ {
-  Dbl=`sed -n 's/nTimeSteps=//p' input_ocn/data.tst | sed 's/,//g'`
+ #   prepare_first arg_1 arg_2 arg_3
-  NiOc=`expr $Dbl / 2`
+ #-----------------------------------------------------------
-  Nit=$NiOc
+ #   from a previous run in "arg_2" dir: collect info for
- else echo " file: 'input_ocn/data.tst' not found"
+ #     test: arg_1 (iters) + arg_1 (iter) = 2x arg_1 (iter) ;
-  NiOc=0 ; Nit=2
+ #     move output files from "arg_2" dir to 'arg_3" dir ;
- fi
+ #     create "data.tst" in arg_2 dir ;
- if test -f input_atm/data.tst ; then
+ #     and prepare pickup and params file for 1rst run.
-  nat0=`sed -n 's/nIter0=//p' input_atm/data.tst | sed 's/,//g' | sed 's/ //g'`
+ #-----------------------------------------------------------
-  Dbl=`sed -n 's/nTimeSteps=//p' input_atm/data.tst | sed 's/,//g'`
-  NiAt=`expr $Dbl / 2`
+   nIt=$1 ; dFr=$2 ; dTo=$3
- else echo " file: 'input_atm/data.tst' not found"
+   if [ $prt -ge 1 ] ; then
-  NiAt=0
+       echo " run 'prepare_first' : nIt=$nIt, from '$dFr' to '$dTo'" ; fi
- fi
+   outpRun="$dFr/STDOUT.0000"
- if test -f pr_group ; then
+ #- last pickup written (from previous run):
-  Npr=`cat pr_group | wc -l`
+   if test -r $outpRun
-  NpOc=`grep -c '\/build_ocn\/mitgcmuv' pr_group`
+   then
- else echo " file: 'pr_group' not found"
+ #   grep ' %CHECKPOINT ' $outpRun | tail -1
-  Npr=0
+     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 $2}'`
+      echo " from '$outpRun' : lastPick='$lastPick' > iter='$iter', sufx='$sufx'"
+     fi
+   else
+     echo "no standard output file '$outpRun' from previous run"
+     exit 7
+   fi
+ #- create parameter file "data.tst":
+   echo " preparing parameter file 'data.tst' :"
+   pFile="$dFr/data.tst"
+   if test -h $pFile ; then rm -f $pFile ; fi
+   cp -p -f $dFr/data $pFile
+   listOut='startTime endTime nIter0 nTimeSteps nEndIter chkPtFreq pChkPtFreq'
+   listOut=$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 *=" $pFile`
+     if [ $nn -ge 1 ]
+     then
+       listN=`grep -i -n "^ *$yy *=" $pFile | sed 's/:.*$//'`
+       if [ $prt -ge 2 ] ; then echo " : found on line: $listN" ; fi
+       for ll in $listN
+       do
+         sed "$ll s/^./#&/" $pFile > data.tmp_$$
+        #diff data.tmp_$$ $pFile
+         mv -f data.tmp_$$ $pFile
+       done
+     else if [ $prt -ge 2 ] ; then echo ' : not found' ; fi
+     fi
+   done
+   if [ $prt -ge 2 ] ; then echo ' ' ; fi
+ # add nIter0 & nTimeSteps in namelist "PARM03":
+   Dbl=`expr $nIt \* 2`
+   sed "/^ *\&PARM03/a \ nTimeSteps=$Dbl," $pFile > data.tmp_$$
+   mv -f data.tmp_$$ $pFile
+   sed "/^ *\&PARM03/a \ nIter0=$iter," $pFile > data.tmp_$$
+   mv -f data.tmp_$$ $pFile
+   echo "preparing file '$pFile' : done"
+   if  [ $prt -ge 1 ] ; then
+     echo " diff $pFile $dFr/data" ; diff $pFile $dFr/data ; echo ' ' ;
+   fi
+ #---- clean up current dir: move output to temp_tst dir:
+ if test $action = 1 ; then
+   ( cd $dFr ; move_outp ../$dTo )
+   listF=`ls -1 $dFr/STD???.0[0-9][0-9][0-9] 2> /dev/null`
+   if test "x$listF" != x ; then mv $listF $dTo ; fi
+ #- move main parameter file "data":
+   mv $dFr/data $dTo
+ #- do not deal with MNC pickup at all:
+   cp -p -f $dFr/data.pkg data.tmp_$$
+   mv -f $dFr/data.pkg $dTo
+   mv -f data.tmp_$$ $dFr/data.pkg
+   yy='useMNC'
+   if [ $prt -ge 2 ] ; then echo -n "  commenting out: $yy in data.pkg" ; fi
+   nn=`grep -i -c "^ *$yy *=" $dFr/data.pkg`
+   if [ $nn -ge 1 ] ; then
+     listN=`grep -i -n "^ *$yy *=" $dFr/data.pkg | sed 's/:.*$//'`
+     if [ $prt -ge 2 ] ; then echo " : found on line: $listN" ; fi
+     for ll in $listN
+     do
+       sed "$ll s/^./#&/" $dFr/data.pkg > data.tmp_$$
+       if  [ $prt -ge 1 ] ; then echo ' changes in data.pkg'
+         diff data.tmp_$$ $dFr/data.pkg ; echo ' ' ; fi
+       mv -f data.tmp_$$ $dFr/data.pkg
+     done
+   else if [ $prt -ge 2 ] ; then echo ' : not found' ; echo ' ' ; fi
+   fi
+ #-- link back pickup files
+   listS=`ls $dTo/pickup*.${sufx}.* 2> /dev/null | head -1`
+   if test "x$listS" != x ; then
+     if [ $prt -ge 1 ] ; then echo ' link back:' ../$dTo'/pickup*.'${sufx}'*' ; fi
+     ( cd $dFr ; ln -s ../$dTo/pickup*.${sufx}* . )
+   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=`(cd $dFr ; ls pickup*.${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
+      ( cd $dFr ; for yy in $listP
+        do rnp_loc $yy.${sufx} $yy.$nIt0c
+        done )
+     fi
+   fi
  fi
+ #----------------------------------------------------------------------
+ }
+ #===============================================================================
+ #-- sequential part start here
+ #===============================================================================
  #- default:
+ Nit=2
  prt=1    # 1 = print some informations ; 2 = print more informations
  action=1
  tmpDir='temp_tst'
+ pickRef='pickup'
+ # offLine=`grep -i -c '^ *useOffLine *= *\.TRUE\.' data.pkg`
+ # if [ $offLine -ge 1 ] ; then pickRef='pickup_ptracers' ; fi
+ #- dir where to put the results :
+ dir1=res_2it
+ dir2=res_1iA
+ dir3=res_1iB
+ #- get number of procs from file "pr_group":
+ if test -f pr_group ; then
+  Npr=`cat pr_group | wc -l`
+  NpOc=`grep -c '\/build_ocn\/mitgcmuv' pr_group`
+ else echo " file: 'pr_group' not found"
+  Npr=0
+ fi
  #- parse options:
  CMD='run_cpl_test'
  MTH=
-Line 98 
 argList=$*
+Line 220 
 argList=$*
  for xx in $argList
  do
   if test $xx = '-mth' ; then MTH=$xx ; shift ; continue ; fi
-  if test -x ${CMD}_$xx ; then CMD="${CMD}_$xx" ; shift ; continue ; fi
+  if test -x ${CMD}.$xx ; then CMD="${CMD}.$xx" ; shift ; continue ; fi
  done
  if [ $# -ne 1 ] ; then
-Line 106 
 if [ $# -ne 1 ] ; then
+Line 228 
 if [ $# -ne 1 ] ; then
     echo " Check restart of coupled set-up: compare 1 run of 2 x $Nit it long"
     echo "                       with 2 consecutive runs of $Nit it long each"
     echo "opt = -mth : run script '$CMD' with option '-mth'"
-    echo "opt = sufx : run script 'run_cpl_test_{sufx}'"
+    echo "opt = sufx : run script 'run_cpl_test.{sufx}'"
     echo " where: flag = 0  -> prepare for 1rst run"
     echo "        flag = r1 -> do 1rst run and step 1"
     echo "        flag =  1 -> move res. after 1rst run & prepare for 2nd"
-Line 121 
 if [ $# -ne 1 ] ; then
+Line 243 
 if [ $# -ne 1 ] ; then
     echo "        flag = 7  -> clean-up output files"
     exit
  fi
- if test $NiAt = 0 -o $NiOc = 0 ; then
-     echo " needs 2 data files: 'input_ocn/data.tst' & 'input_atm/data.tst'"
-     echo "  (corresponding to 1rst run) to continue"
-   exit
- fi
- if test $Npr = 0 ; then
-     echo " needs file: 'pr_group' to continue" ; exit
- fi
  arg1=$1
  xx=`echo $arg1 | sed 's/\+$//'`
  if test $xx != $arg1
-Line 141 
 ksel=$arg1
+Line 255 
 ksel=$arg1
  CMD="./${CMD} $MTH 3"
  echo " doRun='$doRun' ; ksel='$ksel' ; kUp='$kUp' ; command='$CMD'"
+ #- set dir of Master-Proc for 3 components (coupler == rank_0):
+ if test $Npr = 0 ; then
+     echo " needs file: 'pr_group' to continue" ; exit
+ fi
+ rnkO=1 ; rnkA=`expr $rnkO + $NpOc`
  #make sure that local dir & ~jmc/bin is in the path:
  #export PATH=${PATH}:.
- rnkO=1 ; rnkA=`expr $rnkO + $NpOc`
+ #----------------------------------------------------------------------
- Nit=$NiOc
- Dbl=`expr $Nit + $Nit`
+ if test $ksel = 0 ; then
- noc1=`expr $noc0 + $Nit`
+ #-- from STDOUT of previous run, get Nb of iters for each component,
+   yy='(PID.TID 0000.0001) nTimeSteps = '
+   outpRun="rank_$rnkO/STDOUT.0000"
+   nTsO=`grep -A1 "$yy" $outpRun | tail -1 | sed 's/(PID.TID 0000.0001) *//'`
+   outpRun="rank_$rnkA/STDOUT.0000"
+   nTsA=`grep -A1 "$yy" $outpRun | tail -1 | sed 's/(PID.TID 0000.0001) *//'`
+ #-  then calculate the ratio and set Nb of time-step for Atmos comp.
+   RatioTs=`expr $nTsA / $nTsO`
+   if [ $prt -ge 1 ] ; then echo " nTsA= $nTsA , nTsO= $nTsO , Ratio= $RatioTs"; fi
+   NiOc=$Nit ;
+   NiAt=`expr $NiOc \* $RatioTs`
+ #---- clean up current dir: rename pickup files and move output to temp_tst dir:
+  /bin/rm -rf $tmpDir.0 $tmpDir.1 $tmpDir.2
+  mkdir $tmpDir.0 $tmpDir.1 $tmpDir.2
+  mv std_outp rank_0/*.clog rank_0/data $tmpDir.0
+  mv rank_$rnkO/*.0001.clog $tmpDir.0
+  mv rank_$rnkA/*.0001.clog $tmpDir.0
+  echo ' '
+  echo "=> prepare OCN dir:"
+  prepare_first $NiOc rank_$rnkO $tmpDir.1
+  echo "=> prepare ATM dir:"
+  prepare_first $NiAt rank_$rnkA $tmpDir.2
+ #-- prepare for running Dbl
+  echo '=> prepare for running Dbl:'
+  Dbl=`expr $NiOc + $NiOc`
+  sed "1 s/[0-9]*/$Dbl/" input_cpl/data > rank_0/data
+  cp -p rank_$rnkO/data.tst rank_$rnkO/data
+  cp -p rank_$rnkA/data.tst rank_$rnkA/data
+  echo 'rank_0/data:' `head -1 rank_0/data`
+  egrep 'nIter0|nTimeSteps' rank_$rnkO/data rank_$rnkA/data
+ fi
+ #----------------------------------------------------------------------
+ #- extract length of runs & starting iter number from file "data.tst"
+ #  Nit = Nb of iter of 2nd & 3rd run (1rst one is 2 x Nit iter long)
+ pFile="rank_$rnkO/data.tst"
+ if test -f $pFile ; then
+   noc0=`sed -n 's/^ nIter0=//p' $pFile | sed 's/,//g' | sed 's/ //g'`
+   Dbl=`sed -n 's/^ nTimeSteps=//p' $pFile | sed 's/,//g'`
+   NiOc=`expr $Dbl / 2`
+   Nit=$NiOc
+ else echo " file: '$pFile' not found"
+   NiOc=0 ; Nit=2
+ fi
+ pFile="rank_$rnkA/data.tst"
+ if test -f $pFile ; then
+   nat0=`sed -n 's/^ nIter0=//p' $pFile | sed 's/,//g' | sed 's/ //g'`
+   Dbl=`sed -n 's/^ nTimeSteps=//p' $pFile | sed 's/,//g'`
+   NiAt=`expr $Dbl / 2`
+ else echo " file: '$pFile' not found"
+   NiAt=0
+ fi
+ if test $NiAt = 0 -o $NiOc = 0 ; then
+     echo " needs 2 data files: 'rank_$rnkO/data.tst' & 'rank_$rnkA/data.tst'"
+     echo "  (corresponding to 1rst run) to continue"
+   exit
+ fi
+ nit=$NiOc
+ Dbl=`expr $nit + $nit`
+ noc1=`expr $noc0 + $nit`
  noc2=`expr $noc0 + $Dbl`
  noc0c=`printf "%10.10i\n" $noc0`
  noc1c=`printf "%10.10i\n" $noc1`
-Line 155 
 noc2c=`printf "%10.10i\n" $noc2`
+Line 336 
 noc2c=`printf "%10.10i\n" $noc2`
  echo " Oce (rank_$rnkO):" $noc0  $noc1  $noc2
  echo "     " $noc0c $noc1c $noc2c
- Nit=$NiAt
+ nit=$NiAt
- Dbl=`expr $Nit + $Nit`
+ Dbl=`expr $nit + $nit`
- nat1=`expr $nat0 + $Nit`
+ nat1=`expr $nat0 + $nit`
  nat2=`expr $nat0 + $Dbl`
  nat0c=`printf "%10.10i\n" $nat0`
  nat1c=`printf "%10.10i\n" $nat1`
-Line 165 
 nat2c=`printf "%10.10i\n" $nat2`
+Line 346 
 nat2c=`printf "%10.10i\n" $nat2`
  echo " Atm (rank_$rnkA):" $nat0  $nat1  $nat2
  echo "     " $nat0c $nat1c $nat2c
- listOc="pickup"
+ #----------------------------------------------------------------------
- listAt="pickup pickup_cpl pickup_ic pickup_land"
- #- dir where to put the results :
- dir1=res_2it
- dir2=res_1iA
- dir3=res_1iB
- #---- clean up current dir: rename pickup files and move output to temp_tst dir:
- if test $ksel = 0 ; then
-  /bin/rm -rf $tmpDir.0 $tmpDir.1 $tmpDir.2
-  mkdir $tmpDir.0 $tmpDir.1 $tmpDir.2
-  mv std_outp rank_0/*.clog rank_0/data $tmpDir.0
-  echo ' '
-  cd rank_$rnkO
-  for xx in $listOc
-  do rnp_loc $xx.ckptA $xx.$noc0c
-  done
-  move_outp ../$tmpDir.1
-  mv data ../$tmpDir.1
-  mv *.0001.clog ../$tmpDir.0
- #-- link back pickup files
-  sufx=$noc0c
-  listS=`ls ../$tmpDir.1/pickup*.${sufx}.* 2> /dev/null | head -1`
-  if test "x$listS" != x ; then
-    if [ $prt -ge 1 ] ; then echo ' link back:' ../$tmpDir'.1/pickup*.'${sufx}'*' ; fi
-    if test $action = 1 ; then ln -s ../$tmpDir.1/pickup*.${sufx}* . ; fi
-  fi
-  cd ..
-  cd rank_$rnkA
-  for xx in $listAt
-  do rnp_loc $xx.ckptA $xx.$nat0c
-  done
-  move_outp ../$tmpDir.2
-  mv data ../$tmpDir.2
-  mv *.0001.clog ../$tmpDir.0
- #-- link back pickup files
-  sufx=$nat0c
-  listS=`ls ../$tmpDir.2/pickup*.${sufx}.* 2> /dev/null | head -1`
-  if test "x$listS" != x ; then
-    if [ $prt -ge 1 ] ; then echo ' link back:' ../$tmpDir'.2/pickup*.'${sufx}'*' ; fi
-    if test $action = 1 ; then ln -s ../$tmpDir.2/pickup*.${sufx}* . ; fi
-  fi
-  cd ..
- #-- prepare for running Dbl
-  echo '=> prepare for running Dbl:'
-  Dbl=`expr $NiOc + $NiOc`
-  sed "1 s/[0-9]*/$Dbl/" input_cpl/data > rank_0/data
-  cp -p input_ocn/data.tst rank_$rnkO/data
-  cp -p input_atm/data.tst rank_$rnkA/data
-  echo 'rank_0/data:' `head -1 rank_0/data`
-  egrep 'nIter0|nTimeSteps' rank_$rnkO/data rank_$rnkA/data
- fi
  #-- run & post-process Dbl:
  if [ $ksel -eq 1 -o $kUp -le 1 ] ; then
-Line 228 
 if [ $ksel -eq 1 -o $kUp -le 1 ] ; then
+Line 357 
 if [ $ksel -eq 1 -o $kUp -le 1 ] ; then
     $CMD
   fi
  #-- after running Dbl:
+ #-  check for pickup
+  listOc=`ls -1 rank_$rnkO/$pickRef.ckptA*.data 2> /dev/null`
+  listAt=`ls -1 rank_$rnkA/$pickRef.ckptA*.data 2> /dev/null`
+  if test "x$listOc" = x -o "x$listAt" = x
+  then echo "==> RUN 2 x $NiOc it STOP without writing $pickRef => exit" ; exit 1
+  else echo "==>  END  RUN 2 x $NiOc it" ; fi
+ #-  move output
   rm -rf $dir1
   mkdir $dir1
   echo '=> move STDOUT to' $dir1
-Line 237 
 if [ $ksel -eq 1 -o $kUp -le 1 ] ; then
+Line 373 
 if [ $ksel -eq 1 -o $kUp -le 1 ] ; then
   mkdir $dir1/ocn
   cd rank_$rnkO
-  for xx in $listOc
+  listP=`ls pickup*.ckptA* | sed 's/\..*//g' | uniq`
-  do
+  echo ' listP=' $listP
-   rnp_loc $xx.ckptA $xx.$noc2c
+  for xx in $listP ; do rnp_loc $xx.ckptA $xx.$noc2c ; done
-  done
   echo 'move output to' $dir1/ocn
   move_outp  ../$dir1/ocn
   cd ..
   mkdir $dir1/atm
   cd rank_$rnkA
-  for xx in $listAt
+  listP=`ls pickup*.ckptA* | sed 's/\..*//g' | uniq`
-  do
+  echo ' listP=' $listP
-   rnp_loc $xx.ckptA $xx.$nat2c
+  for xx in $listP ; do rnp_loc $xx.ckptA $xx.$nat2c ; done
-  done
   echo 'move output to' $dir1/atm
   move_outp  ../$dir1/atm
   cd ..
  #-- prepare for running 1iA
   echo '=> prepare for running 1iA:'
-  Nit=$NiOc
+  nit=$NiOc ; Dbl=`expr $nit + $nit`
-  Dbl=`expr $Nit + $Nit`
+  sed "1 s/[0-9]*/$nit/" input_cpl/data > rank_0/data
-  sed "1 s/[0-9]*/$Nit/" input_cpl/data > rank_0/data
+  pFile=rank_$rnkO/data
-  sed "s/^ nTimeSteps=$Dbl/ nTimeSteps=$Nit/g" input_ocn/data.tst > rank_$rnkO/data
+  sed "s/^ nTimeSteps=$Dbl/ nTimeSteps=$nit/g" $pFile.tst > $pFile
-  Nit=$NiAt
+  nit=$NiAt ; Dbl=`expr $nit + $nit`
-  Dbl=`expr $Nit + $Nit`
+  pFile=rank_$rnkA/data
-  sed "s/^ nTimeSteps=$Dbl/ nTimeSteps=$Nit/g" input_atm/data.tst > rank_$rnkA/data
+  sed "s/^ nTimeSteps=$Dbl/ nTimeSteps=$nit/g" $pFile.tst > $pFile
   echo 'rank_0/data:' `head -1 rank_0/data`
   egrep 'nIter0|nTimeSteps' rank_$rnkO/data rank_$rnkA/data
  fi
-Line 277 
 if [ $ksel -eq 2 -o $kUp -le 2 ] ; then
+Line 411 
 if [ $ksel -eq 2 -o $kUp -le 2 ] ; then
     $CMD
   fi
  #-- after running 1iA
+ #-  check for pickup
+  listOc=`ls -1 rank_$rnkO/$pickRef.ckptA*.data 2> /dev/null`
+  listAt=`ls -1 rank_$rnkA/$pickRef.ckptA*.data 2> /dev/null`
+  if test "x$listOc" = x -o "x$listAt" = x
+  then echo "==> RUN 1iA STOP without writing $pickRef => exit" ; exit 2
+  else echo "==>  END  RUN 1iA" ; fi
+ #-  move output
   rm -rf $dir2
   mkdir $dir2
   echo '=> move STDOUT to' $dir2
-Line 286 
 if [ $ksel -eq 2 -o $kUp -le 2 ] ; then
+Line 427 
 if [ $ksel -eq 2 -o $kUp -le 2 ] ; then
   mkdir $dir2/ocn
   cd rank_$rnkO
-  for xx in $listOc
+  listP=`ls pickup*.ckptA* | sed 's/\..*//g' | uniq`
-  do
+  echo ' listP=' $listP
-   rnp_loc $xx.ckptA $xx.$noc1c
+  for xx in $listP ; do rnp_loc $xx.ckptA $xx.$noc1c ; done
-  done
  # remove pickup*.$noc0c* sym-link:
   find . ! -name . -prune -type l -name 'pickup*.'${noc0c}'*' -exec rm {} \;
   echo 'move output to' $dir2/ocn
-Line 298 
 if [ $ksel -eq 2 -o $kUp -le 2 ] ; then
+Line 438 
 if [ $ksel -eq 2 -o $kUp -le 2 ] ; then
   mkdir $dir2/atm
   cd rank_$rnkA
-  for xx in $listAt
+  listP=`ls pickup*.ckptA* | sed 's/\..*//g' | uniq`
-  do
+  echo ' listP=' $listP
-   rnp_loc $xx.ckptA $xx.$nat1c
+  for xx in $listP ; do rnp_loc $xx.ckptA $xx.$nat1c ; done
-  done
  # remove pickup*.$nat0c* sym-link:
   find . ! -name . -prune -type l -name 'pickup*.'${nat0c}'*' -exec rm {} \;
   echo 'move output to' $dir2/atm
-Line 312 
 if [ $ksel -eq 2 -o $kUp -le 2 ] ; then
+Line 451 
 if [ $ksel -eq 2 -o $kUp -le 2 ] ; then
   echo '=> prepare for running 1iB:'
   cd rank_$rnkO
   ln -s ../$dir2/ocn/pickup*.$noc1c.* .
-  sed "s/^ nIter0=$noc0/ nIter0=$noc1/g" data > data.tmp
+  sed "s/^ nIter0=$noc0/ nIter0=$noc1/g" data > data.tmp_$$
-  mv -f data.tmp data
+  mv -f data.tmp_$$ data
   cd ../rank_$rnkA
   ln -s ../$dir2/atm/pickup*.$nat1c.* .
-  sed "s/^ nIter0=$nat0/ nIter0=$nat1/g" data > data.tmp
+  sed "s/^ nIter0=$nat0/ nIter0=$nat1/g" data > data.tmp_$$
-  mv -f data.tmp data
+  mv -f data.tmp_$$ data
   cd ..
   echo 'rank_0/data:' `head -1 rank_0/data`
   egrep 'nIter0|nTimeSteps' rank_$rnkO/data rank_$rnkA/data
-Line 332 
 if [ $ksel -eq 3 -o $kUp -le 3 ] ; then
+Line 471 
 if [ $ksel -eq 3 -o $kUp -le 3 ] ; then
     $CMD
   fi
  #-- after running 1iB
+ #-  check for pickup
+  listOc=`ls -1 rank_$rnkO/$pickRef.ckptA*.data 2> /dev/null`
+  listAt=`ls -1 rank_$rnkA/$pickRef.ckptA*.data 2> /dev/null`
+  if test "x$listOc" = x -o "x$listAt" = x
+  then echo "==> RUN 1iB STOP without writing $pickRef => exit" ; exit 3
+  else echo "==>  END  RUN 1iB" ; fi
+ #-  move output
   rm -rf $dir3
   mkdir $dir3
   echo '=> move STDOUT to' $dir3
-Line 341 
 if [ $ksel -eq 3 -o $kUp -le 3 ] ; then
+Line 487 
 if [ $ksel -eq 3 -o $kUp -le 3 ] ; then
   mkdir $dir3/ocn
   cd rank_$rnkO
-  for xx in $listOc
+  listP=`ls pickup*.ckptA* | sed 's/\..*//g' | uniq`
-  do rnp_loc $xx.ckptA $xx.$noc2c
+  echo ' listP=' $listP
-  done
+  for xx in $listP ; do rnp_loc $xx.ckptA $xx.$noc2c ; done
  # remove pickup*.$noc1c* sym-link:
   find . ! -name . -prune -type l -name 'pickup*.'${noc1c}'*' -exec rm {} \;
   echo 'move output to' $dir3/ocn
-Line 352 
 if [ $ksel -eq 3 -o $kUp -le 3 ] ; then
+Line 498 
 if [ $ksel -eq 3 -o $kUp -le 3 ] ; then
   mkdir $dir3/atm
   cd rank_$rnkA
-  for xx in $listAt
+  listP=`ls pickup*.ckptA* | sed 's/\..*//g' | uniq`
-  do rnp_loc $xx.ckptA $xx.$nat2c
+  echo ' listP=' $listP
-  done
+  for xx in $listP ; do rnp_loc $xx.ckptA $xx.$nat2c ; done
  # remove pickup*.$nat1c* sym-link:
   find . ! -name . -prune -type l -name 'pickup*.'${nat1c}'*' -exec rm {} \;
   echo 'move output to' $dir3/atm
   move_outp  ../$dir3/atm
   cd ..
  fi
  #-- compare output:
-Line 368 
 if test $ksel = 4 ; then
+Line 515 
 if test $ksel = 4 ; then
   echo ' run 2it: ---------- ' > tmp1.txt
   grep "cg2d_init_res" $dir1/ocnSTDOUT.0000 \
        | sed 's/.* cg2d_init_res =//' >> tmp1.txt
-  Nit=`expr $NiOc + 2`
+  nit=`expr $NiOc + 2`
-  echo "NiOc= $NiOc ; Nit= $Nit"
+  #echo "NiOc= $NiOc ; nit= $nit"
-  sed "$Nit i \ ... 2it continue ..." tmp1.txt > tmp2.txt
+  sed "$nit i \ ... 2it continue ..." tmp1.txt > tmp2.txt
   rm -f tmp1.txt
   echo ' run 1iA: ---------- ' > tmp1.txt
   grep "cg2d_init_res" $dir2/ocnSTDOUT.0000 \
-Line 392 
 if test $ksel = 5 ; then
+Line 539 
 if test $ksel = 5 ; then
   echo ' run 2it: ---------- ' > tmp1.txt
   grep "cg2d_init_res" $dir1/atmSTDOUT.0000 \
        | sed 's/.* cg2d_init_res =//' >> tmp1.txt
-  Nit=`expr $NiAt + 2`
+  nit=`expr $NiAt + 2`
-  sed "$Nit i \ ... 2it continue ..." tmp1.txt > tmp2.txt
+  sed "$nit i \ ... 2it continue ..." tmp1.txt > tmp2.txt
   rm -f tmp1.txt
   echo ' run 1iA: ---------- ' > tmp1.txt
   grep "cg2d_init_res" $dir2/atmSTDOUT.0000 \
-Line 413 
 fi
+Line 560 
 fi
  #- compare pickup file:
  if test $ksel = 6 ; then
   echo ' ' ; echo '=== compare Ocn pickups: =============='
-  for xx in $listOc
+  listP=`( cd $dir1/ocn ; ls pickup*.$noc2c* | sed 's/\..*//g' | uniq )`
+  for xx in $listP
   do
     dif_tiles $dir1/ocn $dir3/ocn $xx.$noc2c
   done
   echo ' ' ; echo '=== compare Atm pickups: =============='
-  for xx in $listAt
+  listP=`( cd $dir1/atm ; ls pickup*.$nat2c* | sed 's/\..*//g' | uniq )`
+  for xx in $listP
   do
     dif_tiles $dir1/atm $dir3/atm $xx.$nat2c
   done
-Line 428 
 fi
+Line 577 
 fi
  #- clean-up and reset:
  if test $ksel = 7 ; then
   echo "== clean-up and reset :"
- #echo '--> remove pickup*.'$noc0c'* sym-links:'
+  cd rank_$rnkO
- #cd rank_$rnkO
+  listS=`find . ! -name . -prune -type l -name 'pickup*.'${noc0c}'*'`
- #  listS=`find . ! -name . -prune -type l -name 'pickup*.'${noc0c}'*'`
+  if test "x$listS" != x ; then
- #  if [ $prt -ge 2 ] ; then echo " in rank_$rnkO: rm" $listS ; fi
+    echo '--> remove pickup*.'$noc0c'* sym-links:'
- #  rm -f $listS
+    if [ $prt -ge 2 ] ; then echo " in rank_$rnkO: rm" $listS ; fi
- #echo '--> remove pickup*.'$nat0c'* sym-links:'
+    rm -f $listS
- #cd ../rank_$rnkA
+  fi
- #  listS=`find . ! -name . -prune -type l -name 'pickup*.'${nat0c}'*'`
+  cd ../rank_$rnkA
- #  if [ $prt -ge 2 ] ; then echo " in rank_$rnkA: rm" $listS ; fi
+  listS=`find . ! -name . -prune -type l -name 'pickup*.'${nat0c}'*'`
- #  rm -f $listS
+  if test "x$listS" != x ; then
- #cd ..
+    echo '--> remove pickup*.'$nat0c'* sym-links:'
+    if [ $prt -ge 2 ] ; then echo " in rank_$rnkA: rm" $listS ; fi
+    rm -f $listS
+  fi
+  cd ..
  #- move back files from temp_tst dir:
   echo '=> restore std data files'
-  rm -f rank_0/data  rank_$rnkO/data rank_$rnkA/data
+  rm -f rank_{0,$rnkO,$rnkA}/data
+  rm -f rank_{$rnkO,$rnkA}/data.tst
+  rm -f rank_{$rnkO,$rnkA}/data.pkg
   mv $tmpDir.0/*Ocean.0001.clog $tmpDir.1/* rank_$rnkO
   mv $tmpDir.0/*Atmos.0001.clog $tmpDir.2/* rank_$rnkA
   mv $tmpDir.0/std_outp .
-Line 450 
 if test $ksel = 7 ; then
+Line 605 
 if test $ksel = 7 ; then
  #echo '--> remove output dir and output files:'
  #echo ' rm -rf' $dir1 $dir2 $dir3
  #rm -rf $dir1 $dir2 $dir3
- #rm -f atm.txt ocn.txt
+  rm -f atm.txt ocn.txt
   exit
  fi

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-Removed from v.1.9
+Added in v.1.10

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