merge latest master (NOAA-EMC#4)

* Isotopes for CICE (CICE-Consortium#423) Co-authored-by: apcraig <[email protected]> Co-authored-by: David Bailey <[email protected]> Co-authored-by: Elizabeth Hunke <[email protected]> Convergence on ustar for CICE. (CICE-Consortium#452) (NOAA-EMC#5) * Add atmiter_conv to CICE * Add documentation * trigger build the docs Co-authored-by: David A. Bailey <[email protected]> update icepack submodule Add restart_coszen namelist option updated orbital calculations needed for cesm fixed problems in updated orbital calculations needed for cesm update CICE6 to support coupling with UFS put in changes so that both ufsatm and cesm requirements for potential temperature and density are satisfied Fix threading problem in init_bgc Fix additional OMP problems Fix logging issues for NUOPC Move the forapps directory update icepack submodule update comp_ice.backend with temporary ice_timers fix changes for coldstart running remove cesmcoupled ifdefs removal of many cpp-ifdefs fix compile errors fixes to get cesm working fixed white space issue change Orion to orion in backend remove duplicate print lines from ice_transport_driver add -link_mpi=dbg to debug flags (NOAA-EMC#8) cice6 compile (NOAA-EMC#6) * enable debug build. fix to remove errors * fix an error in comp_ice.backend.libcice * change Orion to orion for machine identification changes for consistency w/ current emc-cice5 (NOAA-EMC#13) Update to emc/develop fork to current CICE consortium Co-authored-by: David A. Bailey <[email protected]> Co-authored-by: Tony Craig <[email protected]> Co-authored-by: Elizabeth Hunke <[email protected]> Co-authored-by: Mariana Vertenstein <[email protected]> Co-authored-by: apcraig <[email protected]> Co-authored-by: Philippe Blain <[email protected]> Fixcommit (NOAA-EMC#14) Align commit history between emc/develop and cice-consortium/master Update CICE6 for integration to S2S * add wcoss_dell_p3 compiler macro * update to icepack w/ debug fix * replace SITE with MACHINE_ID * update compile scripts Support TACC stampede (NOAA-EMC#19)
DeniseWorthen · May 10, 2024 · d3f2e61 · d3f2e61
1 parent 0af031d
commit d3f2e61
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diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "icepack"]
 	path = icepack
-	url = https://github.com/cice-consortium/icepack
+	url = https://github.com/NOAA-EMC/Icepack
diff --git a/LICENSE.pdf b/LICENSE.pdf
diff --git a/README.md b/README.md
@@ -1,6 +1,5 @@
-<!--- [![Travis-CI](https://travis-ci.org/CICE-Consortium/CICE.svg?branch=main)](https://travis-ci.org/CICE-Consortium/CICE) --->
-[![GHActions](https://github.com/CICE-Consortium/CICE/workflows/GHActions/badge.svg)](https://github.com/CICE-Consortium/CICE/actions)
-[![Documentation Status](https://readthedocs.org/projects/cice-consortium-cice/badge/?version=main)](http://cice-consortium-cice.readthedocs.io/en/main/?badge=main)
+[![Build Status](https://travis-ci.org/CICE-Consortium/CICE.svg?branch=master)](https://travis-ci.org/CICE-Consortium/CICE)
+[![Documentation Status](https://readthedocs.org/projects/cice-consortium-cice/badge/?version=master)](http://cice-consortium-cice.readthedocs.io/en/master/?badge=master)
 [![lcov](https://img.shields.io/endpoint?url=https://apcraig.github.io/coverage.json)](https://apcraig.github.io)
 
 <!--- [![codecov](https://codecov.io/gh/apcraig/Test_CICE_Icepack/branch/master/graph/badge.svg)](https://codecov.io/gh/apcraig/Test_CICE_Icepack) --->

diff --git a/cice.setup b/cice.setup
@@ -1,7 +1,5 @@
 #!/bin/csh -f
 
-#set pd0 = `date -u "+%s%N"`
-
 set ICE_SANDBOX = `pwd`
 set ICE_VERSION = unknown
 if (-e cicecore/version.txt) then
@@ -392,18 +390,6 @@ if ((${dosuite} == 1 || ${dotest} == 1) && ${testid} == ${spval}) then
   exit -1
 endif
 
-# This creates a new sandbox and modifies the source code for "improved" lcov analysis
-# Turn this if block off if you don't want coverage to do that
-if ($coverage == 1) then
-  set sandbox_lcov = ${ICE_SANDBOX}/../cice_lcov_${sdate}-${stime}
-  cp -p -r ${ICE_SANDBOX} ${sandbox_lcov}
-  echo "shifting to sandbox = ${sandbox_lcov}"
-  set ICE_SANDBOX = ${sandbox_lcov}
-  set ICE_SCRIPTS = "${ICE_SANDBOX}/configuration/scripts"
-  cd ${ICE_SANDBOX}
-  ${ICE_SCRIPTS}/tests/lcov_modify_source.sh
-endif
-
 #---------------------------------------------------------------------
 # Setup tsfile and test suite support stuff
 
@@ -455,22 +441,7 @@ if ( ${dosuite} == 0 ) then
   set sets = ""
 
 else
-  # generate unique set of suites in tarrays in order they are set
-  set tarrays0 = `echo ${testsuite} | sed 's/,/ /g' | fmt -1 `
-  #echo "${0}: tarrays0 = ${tarrays0}"
-  set tarrays = $tarrays0[1]
-  foreach t1 ( ${tarrays0} )
-    set found = 0
-    foreach t2 ( ${tarrays} )
-      if ( ${t1} == ${t2} ) then
-         set found = 1
-      endif
-    end
-    if ( ${found} == 0 ) then
-       set tarrays = ( ${tarrays} ${t1} )
-    endif
-  end
-  #echo "${0}: tarrays = ${tarrays}"
+  set tarrays = `echo ${testsuite} | sed 's/,/ /g' | fmt -1 | sort -u`
   set testsuitecnt = 0
   foreach tarray ( ${tarrays} )
     @ testsuitecnt = ${testsuitecnt} + 1
@@ -497,14 +468,12 @@ 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
@@ -653,7 +622,7 @@ EOF
     set bfbcomp_tmp = `echo $line | cut -d' ' -f5`
 
     # Append sets from .ts file to the $sets variable
-    set sets = "$sets_tmp,$sets_base"
+    set sets = "$sets_base,$sets_tmp"
 
     # Create a new bfbcomp_base variable to store bfbcomp passed to cice.setup
     # Use bfbcomp_base or bfbcomp_tmp
@@ -663,6 +632,11 @@ 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
 
@@ -765,46 +739,23 @@ 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_tmp} | sed 's/,/ /g' | fmt -1 | sort -u`
+      set setsarray = `echo ${sets} | sed 's/,/ /g' | fmt -1 | sort -u`
       if ("${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 ${case}) then
@@ -833,8 +784,8 @@ EOF
     # set default test output as failure
     if (${docase} == 0) then
       echo "#---" >! test_output
-      echo "PEND ${testname_noid} build" >> test_output
-      echo "PEND ${testname_noid} run" >> test_output
+      echo "FAIL ${testname_noid} build" >> test_output
+      echo "FAIL ${testname_noid} run" >> test_output
     endif
 
     # from basic script dir to case
@@ -928,9 +879,6 @@ 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
@@ -943,21 +891,9 @@ 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}
@@ -986,6 +922,7 @@ EOF1
 
     cat >! ${fsmods} << EOF1
 # cice.setup settings
+
 setenv ICE_SANDBOX  ${ICE_SANDBOX}
 setenv ICE_SCRIPTS  ${ICE_SCRIPTS}
 setenv ICE_CASENAME ${casename}
@@ -1054,59 +991,42 @@ EOF1
 
     foreach name (${grid} $setsx)
       set found = 0
-
       if (-e ${ICE_SCRIPTS}/options/set_nml.${name}) then
         cat >> ${fimods} << EOF2
 
 # set_nml.${name}
+
 EOF2
-        if ("${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
+        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 "${0}: ERROR, parse_namelist.sh aborted"
@@ -1115,20 +1035,6 @@ EOF2
     source ./cice.settings
     source ./env.${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
@@ -1186,26 +1092,19 @@ 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}.\${ICE_SNICARHC}"
+     set ciceexe = "../ciceexe.\${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 (\$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
+if (\${dosubmit} == true) then
+  ./cice.submit | tee -a ../suite.jobs
+else if (\${dorun} == true) then
+  ./cice.test
 endif
 cd ..
 EOF
@@ -1218,10 +1117,6 @@ 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
@@ -1236,7 +1131,6 @@ 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
 
@@ -1279,10 +1173,6 @@ endif
 
 #---------------------------------------------
 
-#set pd1 = `date -u "+%s%N"`
-#@ pdd = ( $pd1 - $pd0 ) / 1000000
-#echo "tcxp done $pdd"
-
 echo " "
 echo "${0} done"
 echo " "