Add wave-cice coupling; update to Consortium main (NOAA-EMC#51)

* add wave-ice fields
* initialize aicen_init, which turns up as NaN in calc of floediam
export
* add call to icepack_init_wave to initialize wavefreq and dwavefreq
* update to latest consortium main (PR 752)

add initializationsin ice_state

* initialize vsnon/vsnon_init and vicen/vicen_init

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
@@ -480,12 +482,14 @@ else
     exit -1
   endif
   cp -f ${ICE_SCRIPTS}/tests/report_results.csh ${tsdir}
+  cp -f ${ICE_SCRIPTS}/tests/create_fails.csh ${tsdir}
   cp -f ${ICE_SCRIPTS}/tests/poll_queue.csh ${tsdir}
 
   cat >! ${tsdir}/suite.submit << EOF0
 #!/bin/csh -f
 
 set nonomatch && rm -f ciceexe.* && unset nonomatch
+rm -f suite.jobs
 
 set dobuild  = true
 set doreuse  = true
@@ -634,7 +638,7 @@ EOF
     set bfbcomp_tmp = `echo $line | cut -d' ' -f5`
 
     # Append sets from .ts file to the $sets variable
-    set sets = "$sets_base,$sets_tmp"
+    set sets = "$sets_tmp,$sets_base"
 
     # Create a new bfbcomp_base variable to store bfbcomp passed to cice.setup
     # Use bfbcomp_base or bfbcomp_tmp
@@ -644,11 +648,6 @@ EOF
       set bfbcomp = "$bfbcomp_tmp"
     endif
 
-    set fbfbcomp = ${spval}
-    if ($bfbcomp != ${spval}) then
-      set fbfbcomp = ${machcomp}_${bfbcomp}
-    endif
-
     #------------------------------------------------------------
     # Parse pesx with strict checking, limit pes for machine
 
@@ -751,23 +750,46 @@ EOF
     endif
 
     set testname_noid = ${spval}
+
     # create case for test cases
+
+    set fbfbcomp = ${spval}
+    if ($bfbcomp != ${spval}) then
+      set fbfbcomp = ${machcomp}_${bfbcomp}
+    endif
+
     if (${docase} == 0) then
       set soptions = ""
       # Create sorted array and remove duplicates and "none"
-      set setsarray = `echo ${sets} | sed 's/,/ /g' | fmt -1 | sort -u`
+      set setsarray = `echo ${sets_tmp} | sed 's/,/ /g' | fmt -1 | sort -u`
       if ("${setsarray}" != "") then
         foreach field (${setsarray})
           if (${field} != "none") then
             set soptions = ${soptions}"_"${field}
           endif
         end
       endif
+      # Add options from command line, sort and remove duplicates
+      set soptions_base = ""
+      set setsarray_base = `echo ${sets_base} | sed 's/,/ /g' | fmt -1 | sort -u`
+      if ("${setsarray_base}" != "") then
+        foreach field (${setsarray_base})
+          set soptions = ${soptions}"_"${field}
+          set soptions_base = ${soptions_base}"_"${field}
+        end
+      endif
       # soptions starts with _
       set testname_noid = "${machcomp}_${test}_${grid}_${pesx}${soptions}"
       set testname_base = "${machcomp}_${test}_${grid}_${pesx}${soptions}.${testid}"
       set testname = "${tsdir}/${testname_base}"
       set case = ${testname}
+
+      if (${dosuite} == 1) then
+        # Add -s flags in cice.setup to bfbcomp name
+        if ($bfbcomp != ${spval}) then
+          set fbfbcomp = ${machcomp}_${bfbcomp}${soptions_base}
+        endif
+      endif
     endif
 
     if (-d ${case}) then
@@ -796,8 +818,8 @@ EOF
     # set default test output as failure
     if (${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
@@ -891,6 +913,9 @@ EOF
     echo "ICE_PES      = ${task}x${thrd}"
     echo "ICE_GRID     = ${grid} (${ICE_DECOMP_NXGLOB}x${ICE_DECOMP_NYGLOB}) blocksize=${ICE_DECOMP_BLCKX}x${ICE_DECOMP_BLCKY}x${ICE_DECOMP_MXBLCKS}"
     echo "ICE_DECOMP   = ${ICE_DECOMP_DECOMP} ${ICE_DECOMP_DSHAPE}"
+    if ($fbfbcomp != ${spval}) then
+      echo "ICE_BFBCOMP  = ${fbfbcomp}"
+    endif
 
     #------------------------------------------------------------
     # Copy in and update cice.settings and ice_in files
@@ -903,9 +928,21 @@ 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}
@@ -934,7 +971,6 @@ EOF1
 
     cat >! ${fsmods} << EOF1
 # cice.setup settings
-
 setenv ICE_SANDBOX  ${ICE_SANDBOX}
 setenv ICE_SCRIPTS  ${ICE_SCRIPTS}
 setenv ICE_CASENAME ${casename}
@@ -1003,42 +1039,59 @@ 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_settings.sh aborted"
+      exit -1
+    endif
     ${casescr}/parse_namelist.sh ice_in ${fimods}
     if ($status != 0) then
       echo "${0}: ERROR, parse_namelist.sh aborted"
@@ -1047,6 +1100,20 @@ EOF2
     source ./cice.settings
     source ./env.${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
@@ -1104,19 +1171,26 @@ echo "-------test--------------"
 echo "${testname_base}"
 cd ${testname_base}
 source ./cice.settings
+set bldstat = 0
 if (\${dobuild} == true) then
    if (\${doreuse} == true) then
      set ciceexe = "../ciceexe.\${ICE_TARGET}.\${ICE_ENVNAME}.\${ICE_COMMDIR}.\${ICE_BLDDEBUG}.\${ICE_THREADED}.\${ICE_IOTYPE}"
      ./cice.build --exe \${ciceexe}
+     set bldstat = \${status}
      if !(-e \${ciceexe}) cp -p \${ICE_RUNDIR}/cice \${ciceexe}
    else
      ./cice.build
+     set bldstat = \${status}
    endif
 endif
-if (\${dosubmit} == true) then
-  ./cice.submit | tee -a ../suite.jobs
-else if (\${dorun} == true) then
-  ./cice.test
+if (\$bldstat == 0) then
+  if (\${dosubmit} == true) then
+    set jobid = \`./cice.submit\`
+    echo "\$jobid"
+    echo "\$jobid  \${ICE_TESTNAME}  " >> ../suite.jobs
+  else if (\${dorun} == true) then
+    ./cice.test
+  endif
 endif
 cd ..
 EOF
@@ -1129,6 +1203,10 @@ 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
@@ -1143,6 +1221,7 @@ 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
 
@@ -1185,6 +1264,10 @@ endif
 
 #---------------------------------------------
 
+#set pd1 = `date -u "+%s%N"`
+#@ pdd = ( $pd1 - $pd0 ) / 1000000
+#echo "tcxp done $pdd"
+
 echo " "
 echo "${0} done"
 echo " "