Update to Consortium #162aee9, update scripts (#44)

* update icepack, rename snwITDrdg to snwitdrdg (CICE-Consortium#658) * Change max_blocks for rake tests on izumi (nothread). (CICE-Consortium#665) * Fix some raketests for izumi * fix some rake tests * Makefile: make Fortran object files depend on their dependency files (CICE-Consortium#667) When 'make' is invoked on the CICE Makefile, the first thing it does is to try to make the included dependency files (*.d) (which are in fact Makefiles themselves) [1], in alphabetical order. The rule to make the dep files have the dependency generator, 'makdep', as a prerequisite, so when processing the first dep file, make notices 'makdep' does not exist and proceeds to build it. If for whatever reason this compilation fails, make will then proceed to the second dep file, notice that it recently tried and failed to build its dependency 'makdep', give up on the second dep file, proceed to the third, and so on. In the end, no dep file is produced. Make then restarts itself and proceeds to build the code, which of course fails catastrophically because the Fortran source files are not compiled in the right order because the dependency files are missing. To avoid that, add a dependency on the dep file to the rules that make the object file out of the Fortran source files. Since old-fashioned suffix rules cannot have their own prerequisites [2], migrate the rules for the Fortran source files to use pattern rules [3] instead. While at it, also migrate the rule for the C source files. With this new dependency, the builds abort early, before trying to compile the Fortran sources, making it easier to understand what has gone wrong. Since we do not use suffix rules anymore, remove the '.SUFFIXES' line that indicates which extension to use suffix rules for (but keep the line that eliminates all default suffix rules). [1] https://www.gnu.org/software/make/manual/html_node/Remaking-Makefiles.html [2] https://www.gnu.org/software/make/manual/html_node/Suffix-Rules.html [3] https://www.gnu.org/software/make/manual/html_node/Pattern-Rules.html#Pattern-Rules * Fix multi-pe advection=none bug (CICE-Consortium#664) * update parsing scripts to improve robustness, fix multi-pe advection=none * Update cice script to improve performance including minor refactoring of parse_namelist and parse_settings to reduce cost and ability to use already setup ice_in file from a prior case in the suite. Added commented out timing ability in cice.setup. Change test default to PEND from FAIL. * fix cice.setup for case * add sedbak implementation to support Mac sed * s/spend/spent Co-authored-by: David A. Bailey <[email protected]> Co-authored-by: Philippe Blain <[email protected]>
apcraig · Nov 30, 2021 · 54e5c34 · 54e5c34
1 parent c2c0c4a
commit 54e5c34
Show file tree

Hide file tree

Showing 9 changed files with 99 additions and 44 deletions.
diff --git a/cice.setup b/cice.setup
@@ -1,5 +1,7 @@
 #!/bin/csh -f
 
+#set pd0 = `date -u "+%s%N"`
+
 set ICE_SANDBOX = `pwd`
 set ICE_VERSION = unknown
 if (-e cicecore/version.txt) then
@@ -824,8 +826,8 @@ EOF
     # set default test output as failure
     if (${docase} == 0) then
       echo "#---" >! test_output
-      echo "FAIL ${testname_noid} build" >> test_output
-      echo "FAIL ${testname_noid} run" >> test_output
+      echo "PEND ${testname_noid} build" >> test_output
+      echo "PEND ${testname_noid} run" >> test_output
     endif
 
     # from basic script dir to case
@@ -934,9 +936,21 @@ EOF
     if (-e ${fimods}) rm ${fimods}
     if (-e ${fsmods}) rm ${fsmods}
 
+    # Use an existing ice_in file from the suite if it exists
+    # to reduce time spent in parse_namelist
+    set skip_parse_namelist = spval
+    if (${dosuite} == 1) then
+      set iceinfn = ../ice_in_save_${grid}${soptions}
+      if (-e ${iceinfn}) then
+        echo "use ${iceinfn}"
+        cp ${iceinfn} ice_in
+        set skip_parse_namelist = true
+      endif
+    endif
+
+    # Set decomp info in namelist
     cat >! ${fimods} << EOF1
 # cice.setup settings
-
 nprocs            = ${task}
 nx_global         = ${ICE_DECOMP_NXGLOB}
 ny_global         = ${ICE_DECOMP_NYGLOB}
@@ -965,7 +979,6 @@ EOF1
 
     cat >! ${fsmods} << EOF1
 # cice.setup settings
-
 setenv ICE_SANDBOX  ${ICE_SANDBOX}
 setenv ICE_SCRIPTS  ${ICE_SCRIPTS}
 setenv ICE_CASENAME ${casename}
@@ -1034,44 +1047,57 @@ EOF1
 
     foreach name (${grid} $setsx)
       set found = 0
+
       if (-e ${ICE_SCRIPTS}/options/set_nml.${name}) then
         cat >> ${fimods} << EOF2
 
 # set_nml.${name}
-
 EOF2
-        cat ${ICE_SCRIPTS}/options/set_nml.${name} >> ${fimods}
-        cat >> ${fimods} << EOF2
-
+        if ("${skip_parse_namelist}" == "true") then
+          # need to make sure the decomp info from the set_nml is picked up.  each case
+          # has a slightly different decomp that is independent of the ice_in_save file.
+          # compute that then overwrite by set_nml as needed.
+          grep -i "distribution_type" ${ICE_SCRIPTS}/options/set_nml.${name} >> ${fimods}
+          grep -i "processor_shape"   ${ICE_SCRIPTS}/options/set_nml.${name} >> ${fimods}
+          cat >> ${fimods} << EOF2
+#   using saved ice_in
 EOF2
+        else
+          cat ${ICE_SCRIPTS}/options/set_nml.${name} >> ${fimods}
+          cat >> ${fimods} << EOF2
+EOF2
+        endif
         echo "adding namelist mods set_nml.${name}"
         echo "`date` ${0} adding namelist modes set_nml.${name}" >> ${casedir}/README.case
         set found = 1
       endif
+
       if (-e ${ICE_SCRIPTS}/options/set_env.${name}) then
 
         cat >> ${fsmods} << EOF2
 
 # set_env.${name}
-
 EOF2
         cat ${ICE_SCRIPTS}/options/set_env.${name} >> ${fsmods}
         cat >> ${fsmods} << EOF2
-
 EOF2
         echo "adding env mods set_env.${name}"
         echo "`date` ${0} adding namelist modes set_env.${name}" >> ${casedir}/README.case
         set found = 1
       endif
+
       if (${found} == 0) then
         echo "${0}: ERROR, ${ICE_SCRIPTS}/options/set_[nml,env].${name} not found"
         exit -1
       endif
     end
 
+#set pd1 = `date -u "+%s%N"`
+#@ pdd = ( $pd1 - $pd0 ) / 1000000
+#echo "tcxp b4 parse $pdd"
     ${casescr}/parse_settings.sh cice.settings ${fsmods}
     if ($status != 0) then
-      echo "${0}: ERROR, parse_namelist.sh aborted"
+      echo "${0}: ERROR, parse_settings.sh aborted"
       exit -1
     endif
     ${casescr}/parse_namelist.sh ice_in ${fimods}
@@ -1082,6 +1108,20 @@ EOF2
     source ./cice.settings
     source ./env.${machcomp} -nomodules || exit 2
     ${casescr}/parse_namelist_from_env.sh ice_in
+    if ($status != 0) then
+      echo "${0}: ERROR, parse_namelist_from_env.sh aborted"
+      exit -1
+    endif
+#set pd1 = `date -u "+%s%N"`
+#@ pdd = ( $pd1 - $pd0 ) / 1000000
+#echo "tcxp after parse $pdd"
+
+    # Save ice_in in the suite to reduce time spent in parse_namelist
+    if (${dosuite} == 1) then
+      if !(-e ${iceinfn}) then
+        cp ice_in ${iceinfn}
+      endif
+    endif
 
     #------------------------------------------------------------
     # Generate run script
@@ -1166,6 +1206,10 @@ EOF
       echo "" 
     endif
 
+#set pd1 = `date -u "+%s%N"`
+#@ pdd = ( $pd1 - $pd0 ) / 1000000
+#echo "tcxp case done $pdd"
+
    # This is the foreach end for the testsuite
   end
 # This is the foreach end for the envnames
@@ -1180,6 +1224,7 @@ if ( ${dosuite} == 1 ) then
   cat >> ${tsdir}/suite.submit << EOF0
 
 set nonomatch && rm -f ciceexe.* && unset nonomatch
+set nonomatch && rm -f ice_in_save* && unset nonomatch
 
 EOF0
 
@@ -1222,6 +1267,10 @@ endif
 
 #---------------------------------------------
 
+#set pd1 = `date -u "+%s%N"`
+#@ pdd = ( $pd1 - $pd0 ) / 1000000
+#echo "tcxp done $pdd"
+
 echo " "
 echo "${0} done"
 echo " "

diff --git a/configuration/scripts/Makefile b/configuration/scripts/Makefile
@@ -73,7 +73,6 @@ RM    := rm
 AR    := ar
 
 .SUFFIXES:
-.SUFFIXES: .F90 .F .c .o
 
 .PHONY: all cice libcice targets target db_files db_flags clean realclean helloworld calchk sumchk bcstchk gridavgchk
 all: $(EXEC)
@@ -169,13 +168,13 @@ libcice: $(OBJS)
 	@ echo "$(AR) -r $(EXEC) $(OBJS)"
 	$(AR) -r $(EXEC) $(OBJS)
 
-.c.o:
+%.o : %.c
 	$(CC) $(CFLAGS) $(CPPDEFS) $(INCLDIR) $<
 
-.F.o:
+%.o : %.F %.d
 	$(FC) -c $(FFLAGS) $(FIXEDFLAGS) $(CPPDEFS) $(INCLDIR) $<
 
-.F90.o:
+%.o : %.F90 %.d
 	$(FC) -c $(FFLAGS) $(FREEFLAGS) $(CPPDEFS) $(MODDIR) $(INCLDIR) $<
 
 clean:

diff --git a/...uration/scripts/options/set_nml.snwITDrdg → ...uration/scripts/options/set_nml.snwitdrdg b/...uration/scripts/options/set_nml.snwITDrdg → ...uration/scripts/options/set_nml.snwitdrdg
diff --git a/configuration/scripts/parse_namelist.sh b/configuration/scripts/parse_namelist.sh
@@ -10,7 +10,7 @@ filename=$1
 filemods=$2
 
 #echo "$0 $1 $2" 
-echo "running parse_namelist.sh"
+echo "running ${scriptname}"
 foundstring="FoundSTRING"
 vnamearray=()
 valuearray=()
@@ -43,29 +43,27 @@ do
       fi
     done
 
-    #sed -i 's|\(^\s*'"$vname"'\s*\=\s*\)\(.*$\)|\1'"$value"'|g' $filename
-    cp ${filename} ${filename}.check
-    sed -i.sedbak -e 's|\(^[[:space:]]*'"$vname"'[[:space:]]*=[[:space:]]*\)\(.*$\)|\1'"$foundstring"'|g' ${filename}.check
-    grep -q ${foundstring} ${filename}.check
-    if [ $? -eq 0 ]; then
+    grep -q "^[[:space:]]*${vname}[[:space:]]*=" $filename
+    grepout=$?
+    if [ ${grepout} -eq 0 ]; then
       sed -i.sedbak -e 's|\(^[[:space:]]*'"$vname"'[[:space:]]*=[[:space:]]*\)\(.*$\)|\1'"$value"'|g' ${filename}
       if [[ "${found}" == "${foundstring}" ]]; then
         vnamearray+=($vname)
         valuearray+=($value)
       else
         valuearray[$found]=${value}
       fi
-      if [[ -e "${filename}.sedbak" ]]; then
-        rm ${filename}.sedbak
-      fi
     else
       echo "${scriptname} ERROR: parsing error for ${vname}"
       exit -99
     fi
-    rm ${filename}.check ${filename}.check.sedbak
 
   fi
 
 done < "$filemods"
 
+if [[ -e "${filename}.sedbak" ]]; then
+  rm ${filename}.sedbak
+fi
+
 exit 0
diff --git a/configuration/scripts/parse_namelist_from_env.sh b/configuration/scripts/parse_namelist_from_env.sh
@@ -5,10 +5,11 @@ if [[ "$#" -ne 1 ]]; then
   exit -1
 fi
 
+scriptname=`basename "$0"`
 filename=$1
 
 #echo "$0 $1" 
-echo "running parse_namelist_from_env.sh"
+echo "running $scriptname"
 
 sed -i.sedbak -e 's|ICE_SANDBOX|'"${ICE_SANDBOX}"'|g' $filename
 sed -i.sedbak -e 's|ICE_MACHINE_INPUTDATA|'"${ICE_MACHINE_INPUTDATA}"'|g' $filename

diff --git a/configuration/scripts/parse_settings.sh b/configuration/scripts/parse_settings.sh
@@ -10,7 +10,7 @@ filename=$1
 filemods=$2
 
 #echo "$0 $1 $2" 
-echo "running parse_settings.sh"
+echo "running ${scriptname}"
 foundstring="FoundSTRING"
 vnamearray=()
 valuearray=()
@@ -23,8 +23,11 @@ do
   else
     #vname=`echo $line | sed "s|\(^\s*set\S*\)\s\{1,100\}\(\S*\)\s\{1,100\}\(\S*\).*$|\2|g"`
     #value=`echo $line | sed "s|\(^\s*set\S*\)\s\{1,100\}\(\S*\)\s\{1,100\}\(\S*\).*$|\3|g"`
-    vname=`echo $line | sed "s|\(^[[:space:]]*set[^[:space:]]*\)[[:space:]][[:space:]]*\([^[:space:]]*\)[[:space:]][[:space:]]*\([^[:space:]]*\).*$|\2|g"`
+    vname=`echo $line | sed "s|\(^[[:space:]]*set[^[:space:]]*\)[[:space:]][[:space:]]*\([^[:space:]]*\).*$|\2|g"`
     value=`echo $line | sed "s|\(^[[:space:]]*set[^[:space:]]*\)[[:space:]][[:space:]]*\([^[:space:]]*\)[[:space:]][[:space:]]*\([^[:space:]]*\).*$|\3|g"`
+    if [[ "${value}" == "${line}" ]]; then
+       value=""
+    fi
 #    echo "$line $vname $value"
 
     found=${foundstring}
@@ -43,22 +46,27 @@ do
       fi
     done
 
-    #sed -i 's|\(^\s*set.* '"$vname"' \)[^#]*\(#*.*$\)|\1 '"$value"'  \2|g' $filename
-    sed -i.sedbak -e 's|\(^[[:space:]]*set.* '"$vname"' \)[^#]*\(#*.*$\)|\1 '"$value"'  \2|g' $filename
-
-    if [[ "${found}" == "${foundstring}" ]]; then
-      vnamearray+=($vname)
-      valuearray+=($value)
+    grep -q "^[[:space:]]*set.* ${vname}[[:space:]]*" $filename
+    grepout=$?
+    if [ ${grepout} -eq 0 ]; then
+      sed -i.sedbak -e 's|\(^[[:space:]]*set.* '"$vname"' \)[^#]*\(#*.*$\)|\1 '"$value"'  \2|g' $filename
+      if [[ "${found}" == "${foundstring}" ]]; then
+        vnamearray+=($vname)
+        valuearray+=($value)
+      else
+        valuearray[$found]=${value}
+      fi
     else
-      valuearray[$found]=${value}
-    fi
-
-    if [[ -e "${filename}.sedbak" ]]; then
-      rm ${filename}.sedbak
+      echo "${scriptname} ERROR: parsing error for ${vname}"
+      exit -99
     fi
 
   fi
 
 done < "$filemods"
 
+if [[ -e "${filename}.sedbak" ]]; then
+  rm ${filename}.sedbak
+fi
+
 exit 0
diff --git a/configuration/scripts/tests/base_suite.ts b/configuration/scripts/tests/base_suite.ts
@@ -58,9 +58,9 @@ restart        gx3     4x2        fsd12,debug,short
 smoke          gx3     8x2        fsd12ww3,diag24,run1day
 smoke          gx3     4x1        isotope,debug
 restart        gx3     8x2        isotope
-smoke          gx3     4x1        snwITDrdg,snwgrain,icdefault,debug
+smoke          gx3     4x1        snwitdrdg,snwgrain,icdefault,debug
 smoke          gx3     4x1        snw30percent,icdefault,debug
-restart        gx3     8x2        snwITDrdg,icdefault,snwgrain
+restart        gx3     8x2        snwitdrdg,icdefault,snwgrain
 restart        gx3     4x4        gx3ncarbulk,iobinary
 restart        gx3     4x4        histall,precision8,cdf64
 smoke          gx3    30x1        bgcz,histall

diff --git a/configuration/scripts/tests/nothread_suite.ts b/configuration/scripts/tests/nothread_suite.ts
@@ -19,7 +19,7 @@ restart        gx3     16x1       gx3ncarbulk,iobinary
 restart        gx3     12x1       alt01
 restart        gx3     16x1       alt02
 restart        gx3     8x1        alt03
-restart        gx3     16x1       alt04
+restart        gx3     16x1x5x29x6 alt04
 restart        gx3     16x1       alt05
 restart        gx3     20x1       alt06
 restart        gx3     18x1       alt01,debug,short
@@ -66,7 +66,7 @@ restart        gx3     16x1x8x10x10  droundrobin        restart_gx3_8x1x25x29x2_
 restart        gx3     6x1x50x58x1   droundrobin        restart_gx3_8x1x25x29x2_dslenderX2
 restart        gx3     8x1x19x19x5   droundrobin        restart_gx3_8x1x25x29x2_dslenderX2
 restart        gx3     20x1x5x29x20  dsectrobin,short   restart_gx3_8x1x25x29x2_dslenderX2
-restart        gx3     32x1x5x10x10  drakeX2            restart_gx3_8x1x25x29x2_dslenderX2
+restart        gx3     32x1x5x10x12  drakeX2            restart_gx3_8x1x25x29x2_dslenderX2
 restart        gx3     16x1x8x10x10  droundrobin,maskhalo   restart_gx3_8x1x25x29x2_dslenderX2
 restart        gx3     4x1x25x29x4   droundrobin        restart_gx3_8x1x25x29x2_dslenderX2
 

diff --git a/icepack b/icepack
+2 −2		README.md
+4 −2		columnphysics/icepack_flux.F90
+1 −1		doc/source/icepack_index.rst
+11 −0		doc/source/master_list.bib
+1 −1		doc/source/user_guide/ug_troubleshooting.rst