/[MITgcm]/MITgcm/verification/cpl_aim+ocn/run_cpl_test
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revision 1.5 by jmc, Thu Oct 28 20:46:45 2004 UTC revision 1.20 by jmc, Wed Jan 16 13:40:04 2013 UTC
# Line 3  Line 3 
3  # $Header$  # $Header$
4  # $Name$  # $Name$
5    
6  Np=3  #- default:
7  Opt=' '   Npr=3 ; NpOc=1 ;
8  Opt='-ieee'  #Npr=25; NpOc=12;
9  if [ $# -lt 1 ]  MTH=
10  then  MTHo=
11    echo 'Usage:'`basename $0`' step '  MTHa=
12    echo ' => test coupled set-up on myrinet cluster'  GMKopt='-devel'
13    echo 'step = 0 : clean all directories'  #GMKopt='-ieee'
14    echo 'step = 1 : compile the 3 executables (cpl,ocn,atm)'  #GMKopt=
15    echo 'step = 2 : copy input files and dir(s)'  rnkO=1 ; rnkA=`expr $rnkO + $NpOc`
16    echo "step = 3 : run on $Np processor"  
17    echo 'step = 4 : check the results'  #- parse options:
18    if [ $# -ge 1 ] ; then if test $1 = '-mth' ; then
19      MTH='-omp' ; shift
20      if test -f input_ocn/eedata.mth ; then MTHo=$MTH ; fi
21      if test -f input_atm/eedata.mth ; then MTHa=$MTH ; fi
22    fi ; fi
23    #- allows more argument for building step (step=1)
24    chkArg=$# ; if [ $# -gt 1 ]; then chkArg=$1 ; fi
25    if [ $chkArg -ne 1 ]; then
26      echo 'Usage:'`basename $0`' [opt] step [bld-arg]'
27      echo ' => test coupled set-up on linux box (1.cpu)'
28      echo 'opt = -mth : compile and run (if eedata.mth) 2-threads for ocn & atm'
29      echo ' step = 0 : clean all directories'
30      echo ' step = 1 : compile the 3 executables (cpl,ocn,atm); optional arg:'
31      echo '       -of Optfile_Name : using option-file "Optfile_Name"'
32      echo ' step = 2 : copy input files and dir(s)'
33      echo " step = 3 : run with $Npr mpi processes"
34      echo ' step = 4 : check the results'
35      echo ' step = 5 : remove output files in rank_0,1,2 dir.'
36    exit    exit
37  fi  fi
38  kpr=$1  kpr=$1
39  dir=`pwd`  dir=`pwd`
40    
 #- only works from a 3 nodes PBS bach session ( qsub -I -l nodes=3:p4 )  
 #  on myrinet cluster:  
 xx=`hostname | sed 's/[0-9]/X/g'`  
 if test $xx != 'myrinet-X-XX'  
 then  
   echo ' hostname='`hostname`  
   echo 'for now, works only on myrinet cluster'  
   exit 9  
 fi  
 if test 'dummy'$PBS_NODEFILE = 'dummy'  
 then  
   echo ' $PBS_NODEFILE not defined'  
   echo "for now, works only from a $Np nodes PBS bach session"  
   exit 8  
 else ncpus=`wc -l $PBS_NODEFILE | awk '{print $1}'`  
  if test $ncpus != $Np ; then  
   echo ' Nb of nodes from $PBS_NODEFILE =' $ncpus  
   echo "for now, works only from a $Np nodes PBS bach session"  
   exit 8  
  fi  
 fi  
   
41  #============================================================================  #============================================================================
42    
43  if test $kpr = 0  if test $kpr = 0
44  then  then
45   rm -f genmake_optfile pr_group std_outp Coupler.0000.clog   rm -f pr_group std_outp comp_res.{ocn,atm,land,sice}
46   rm -f build_???/TTT.*make.* build_???/TTT.mkdepend.*   rm -f build_???/TTT.*make.* build_???/TTT.mkdepend.*
47   /bin/rm -r -f rank_0 rank_1 rank_2   /bin/rm -r -f rank_? rank_1? rank_2?
48   if test -f build_cpl/Makefile ; then cd build_cpl ; make CLEAN ; cd .. ; fi   if test -f build_cpl/Makefile ; then cd build_cpl ; make Clean ; cd .. ; fi
49   if test -f build_ocn/Makefile ; then cd build_ocn ; make CLEAN ; cd .. ; fi   if test -f build_ocn/Makefile ; then cd build_ocn ; make Clean ; cd .. ; fi
50   if test -f build_atm/Makefile ; then cd build_atm ; make CLEAN ; cd .. ; fi   if test -f build_atm/Makefile ; then cd build_atm ; make Clean ; cd .. ; fi
51    fi
52    if test $kpr = 5
53    then
54     echo 'remove output files in rank_0,1,2 dir.'
55     rm -f pr_group std_outp comp_res.{ocn,atm,land,sice}
56     if test -d rank_0 ; then cd rank_0 ; rm -f Coupler.0000.clog ; cd .. ; fi
57     if test -d rank_$rnkO
58     then cd rank_$rnkO ; rm -f *.data *.meta STD???.0000 UV-*.0001.clog ; cd .. ; fi
59     if test -d rank_$rnkA
60     then cd rank_$rnkA ; rm -f *.data *.meta STD???.0000 UV-*.0001.clog ; cd .. ; fi
61  fi  fi
62    
63  if test $kpr = 1  if test $kpr = 1
64  then  then
65    
66   cp -p ../../tools/build_options/linux_ia32_ifc+mpi_cg01 genmake_optfile  #- choice of the optfile:
67    #  default: take a local one in dir verification with sufix '+mpi'
68     nbOpF=`ls ../linux_* | grep '+mpi' 2> /dev/null | wc -l`
69    #  or take the one given as argument:
70     if [ $# -ge 3 ]; then
71       if test $2 = '-of' -a -f $3 ; then nbOpF=-1 ; OPTFILE=$3 ; fi
72     fi
73     if test $nbOpF = 1 ; then
74       OPTFILE=`ls ../linux_* | grep '+mpi'`
75     elif [ $nbOpF -ge 2 ] ; then
76       echo "pick the 1rst of these ( $nbOpF ) optfiles:"
77       ls ../linux_* | grep '+mpi'
78       OPTFILE=`ls ../linux_* | grep '+mpi' | head -1`
79     elif [ $nbOpF -ne -1 ] ; then
80       echo "Pb in finding optfile: found $nbOpF :"
81       ls ../linux_* | grep '+mpi' ; exit
82     fi
83     zz=`grep '^ *FC=' $OPTFILE | tail -1`
84     echo " Using optfile: $OPTFILE  (compiler: $zz) $MTH"
85     zz=`echo $OPTFILE | grep -c '^\/'`
86     if test $zz = 0 ; then OPTFILE="../$OPTFILE" ; fi
87    #---
88   echo '==== compile coupler:'   echo '==== compile coupler:'
89   cd build_cpl   cd build_cpl
90   echo ' --- genmake2 (cpl):'   echo ' --- genmake2 (cpl):'
91   ../../../tools/genmake2 -of ../genmake_optfile $Opt >  TTT.genmake.$$   ../../../tools/genmake2 -of $OPTFILE -mpi $GMKopt >  TTT.genmake.$$
92   tail -5 TTT.genmake.$$   tail -5 TTT.genmake.$$
93   echo ' --- make depend (cpl):'   echo ' --- make depend (cpl):'
94   make depend > TTT.mkdepend.$$   make depend > TTT.mkdepend.$$
# Line 74  then Line 101  then
101   echo '==== compile OGCM:'   echo '==== compile OGCM:'
102   cd build_ocn   cd build_ocn
103   echo ' --- genmake2 (ocn):'   echo ' --- genmake2 (ocn):'
104   ../../../tools/genmake2 -of ../genmake_optfile $Opt >  TTT.genmake.$$   ../../../tools/genmake2 -of $OPTFILE -mpi $MTHo $GMKopt >  TTT.genmake.$$
105   tail -5 TTT.genmake.$$   tail -5 TTT.genmake.$$
106   echo ' --- make depend (ocn):'   echo ' --- make depend (ocn):'
107   make depend > TTT.mkdepend.$$   make depend > TTT.mkdepend.$$
# Line 87  then Line 114  then
114   echo '==== compile AGCM:'   echo '==== compile AGCM:'
115   cd build_atm   cd build_atm
116   echo ' --- genmake2 (atm):'   echo ' --- genmake2 (atm):'
117   ../../../tools/genmake2 -of ../genmake_optfile $Opt >  TTT.genmake.$$   ../../../tools/genmake2 -of $OPTFILE -mpi $MTHa $GMKopt >  TTT.genmake.$$
118   tail -5 TTT.genmake.$$   tail -5 TTT.genmake.$$
119   echo ' --- make depend (atm):'   echo ' --- make depend (atm):'
120   make depend > TTT.mkdepend.$$   make depend > TTT.mkdepend.$$
# Line 103  fi Line 130  fi
130    
131  if test $kpr = 2  if test $kpr = 2
132  then  then
133    cp -p -r input_cpl rank_0    echo 'rm dir:' rank_? rank_1? rank_2?
134    cp -p -r input_ocn rank_1    /bin/rm -r -f rank_? rank_1? rank_2?
135    cp -p -r input_atm rank_2    echo 'Link files from dir:' input_cpl '->' rank_0
136      mkdir rank_0
137    cd rank_1    ( cd rank_0 ; ln -s ../input_cpl/* . )
138    ./IMPORT_INPUT_FILES  
139      n=$rnkO
140      echo 'Link files from dir:' input_ocn '->' rank_$n
141      mkdir rank_$n
142      cd rank_$n
143      ln -s ../input_ocn/* .
144      if test -x prepare_run ; then ./prepare_run ; fi
145      if test "x$MTHo" != x ; then
146        echo " MTH run: mv -f eedata.mth eedata"
147        if test -h eedata ; then rm -f eedata ; fi
148        mv -f eedata.mth eedata
149      fi
150    cd $dir    cd $dir
151      n=`expr $n + 1`
152    cd rank_2    while [ $n -le $NpOc ] ; do
153    ./SHARE_OCN_GRID '../rank_1'      ln -s rank_$rnkO rank_$n
154        n=`expr $n + 1`
155      done
156    
157      n=$rnkA
158      echo 'Link files from dir:' input_atm '->' rank_$n
159      mkdir rank_$n
160      cd rank_$n
161      ln -s ../input_atm/* .
162      if test -x prepare_run ; then ./prepare_run ; fi
163      if test "x$MTHa" != x ; then
164        echo " MTH run: mv -f eedata.mth eedata"
165        if test -h eedata ; then rm -f eedata ; fi
166        mv -f eedata.mth eedata
167      fi
168    cd $dir    cd $dir
169      n=`expr $n + 1`
170      while [ $n -lt $Npr ] ; do
171        ln -s rank_$rnkA rank_$n
172        n=`expr $n + 1`
173      done
174    
175  fi  fi
176    
177  if test $kpr = 3  if test $kpr = 3
178  then  then
179   ROOTDIR=$dir    ROOTDIR=$dir
180   rm -f rank_?/pickup*.ckptA.00?.00?.??ta  # rm -f rank_?/pickup*.ckptA.00?.00?.??ta
181   echo $ROOTDIR    echo $ROOTDIR
182   tmpfil=TTT.$$    tmpfil=TTT.$$
183    
184   echo $PBS_NODEFILE  #--- running on the same node:
185   list=`cat $PBS_NODEFILE`    list='' ; nc=0; xx=`hostname`
186   rm -f pr_group ; touch pr_group    while [ $nc -lt $Npr ] ; do list="$list $xx" ; nc=`expr $nc + 1` ; done
187   nc=0 ; dd1=cpl ;  #-- On darwin cluster node (from qrsh session):
188   for xx in $list  # JOB_ID=`qstat | sed -n '3,$ p' | grep " $USER " | awk '{print $1}'`
189   do  # NODEFILE="/tmp/$JOB_ID.1.darwin/machines"
190    echo $xx $nc $dir/build_$dd1/mitgcmuv >> pr_group  # echo " JOB_ID = '$JOB_ID' ; NODEFILE = '$NODEFILE'"
191    if test $nc = 0 ; then dd1=ocn ; else dd1=atm ; fi  #-- On ACES cluster (in PBS batch job):
192    nc=1  # NODEFILE=$PBS_NODEFILE
193   done  #--- running on different nodes:
194    # ls -l $NODEFILE
195   cd $ROOTDIR  # nprc=`cat $NODEFILE | uniq | wc -l`
196   #  -wd $ROOTDIR  # if [ $nprc -ge $Npr ] ; then
197   /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/pgi/bin/mpirun.ch_gm -pg pr_group --gm-kill 5 -v  ./build_cpl/mitgcmuv > std_outp 2>&1  #   list=`cat $NODEFILE | uniq | head -$Npr`
198   tail -20 std_outp  # else
199   ls -l rank_?/pickup*.ckptA.001.001.data  #   list=`cat $NODEFILE | head -$Npr`
200    # fi
201    
202      nc=0; nn=0; dd1=cpl ;
203      rm -f pr_group ; touch pr_group
204      for xx in $list
205      do
206        echo $xx $nn $dir/build_$dd1/mitgcmuv >> pr_group
207        nc=`expr $nc + 1`
208        if [ $nc -le $NpOc ] ; then dd1=ocn ; else dd1=atm ; fi
209        nn=1
210      done
211      NpAt=`expr $Npr - 1 - $NpOc`
212      RunOpt="-np 1 ./build_cpl/mitgcmuv"
213      RunOpt="$RunOpt : -np $NpOc ./build_ocn/mitgcmuv"
214      RunOpt="$RunOpt : -np $NpAt ./build_atm/mitgcmuv"
215    
216      cd $ROOTDIR
217      if test "x$MTH" != x ; then
218        export OMP_NUM_THREADS=2 ; export KMP_STACKSIZE=400m
219        if test "x$MTHo" != x ; then
220          echo -n " run OCN ($MTHo) with $OMP_NUM_THREADS threads ;"
221        fi
222        if test "x$MTHa" != x ; then
223          echo -n " run ATM ($MTHa) with $OMP_NUM_THREADS threads ;"
224        fi
225        echo ""
226      fi
227      mpich=`which mpirun`
228      echo $mpich | grep 'mpich-mx' > /dev/null 2>&1
229      mpichmx=$?
230      echo $mpich | grep 'mpich2' > /dev/null 2>&1
231      mpich2=$?
232      echo $mpich | grep 'openmpi' > /dev/null 2>&1
233      opnmpi=$?
234      if test $mpich2 == 0 -o $opnmpi == 0 ; then
235      #- with Hydra mpich2 (on baudelaire) or with openmpi:
236        echo "execute 'mpirun $RunOpt' :"
237        mpirun $RunOpt  > std_outp 2>&1
238      elif test $mpichmx == 0 ; then
239      #- with mpich-mx (on beagle):
240        echo "execute 'mpirun -pg pr_group -v ./build_cpl/mitgcmuv' :"
241        mpirun -pg pr_group -v ./build_cpl/mitgcmuv > std_outp 2>&1
242      else
243      # /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/pgi/bin/mpirun.ch_gm -pg pr_group -wd $ROOTDIR --gm-kill 5 -v  ./build_cpl/mitgcmuv > std_outp 2>&1
244      #- with mpich-1 (on danton, ACES):
245        echo "execute 'mpirun -p4pg pr_group -v ./build_cpl/mitgcmuv' :"
246        mpirun -p4pg pr_group -v ./build_cpl/mitgcmuv > std_outp 2>&1
247      fi
248      tail -20 std_outp
249      ls -l rank_$rnkO/pickup*.ckptA.001.001.data
250      ls -l rank_$rnkA/pickup*.ckptA.001.001.data
251    
252  fi  fi
253    
254  if test $kpr = 4  if test $kpr = 4
255  then  then
256     CompRes="$HOME/bin/comp_res"
257    
258   if test -f rank_1/STDOUT.0000   if test -f rank_$rnkO/STDOUT.0000
259   then echo '==> check Ocean output:'   then echo '==> check Ocean output:'
260      /home/jmc/bin/comp_res rank_1/STDOUT.0000 results/ocnSTDOUT.0000      $CompRes rank_$rnkO/STDOUT.0000 results/ocnSTDOUT.0000
261     echo ' '      mv -f comp_res.log comp_res.ocn
262   else echo 'No Ocean output file in rank_1' ; fi      echo ' '
263     else echo "No Ocean output file in rank_$rnkO" ; fi
264    
265   if test -f rank_2/STDOUT.0000   if test -f rank_$rnkA/STDOUT.0000
266   then   then
267      echo '==> check Atmos output:'      echo '==> check Atmos output:'
268      /home/jmc/bin/comp_res rank_2/STDOUT.0000 results/atmSTDOUT.0000      $CompRes rank_$rnkA/STDOUT.0000 results/atmSTDOUT.0000
269        mv -f comp_res.log comp_res.atm
270      echo '==> check Land output:'      echo '==> check Land output:'
271      /home/jmc/bin/comp_res rank_2/STDOUT.0000 results/atmSTDOUT.0000 L      $CompRes rank_$rnkA/STDOUT.0000 results/atmSTDOUT.0000 L
272        mv -f comp_res.log comp_res.land
273      echo '==> check thSIce output:'      echo '==> check thSIce output:'
274      /home/jmc/bin/comp_res rank_2/STDOUT.0000 results/atmSTDOUT.0000 I      $CompRes rank_$rnkA/STDOUT.0000 results/atmSTDOUT.0000 I
275     echo ' '      mv -f comp_res.log comp_res.sice
276   else echo 'No Atmos output file in rank_1' ; fi      echo ' '
277     else echo "No Atmos output file in rank_$rnkA" ; fi
278    
279  fi  fi
280    
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