From dc1269bcc1970bcc53bd1f95cd88cdac6e06fb68 Mon Sep 17 00:00:00 2001
From: apcraig <anthony.p.craig@gmail.com>
Date: Wed, 17 Nov 2021 19:54:20 -0700
Subject: [PATCH 1/5] update parsing scripts to improve robustness, fix
 multi-pe advection=none

---
 cice.setup                                    |  4 +++
 cicecore/cicedynB/general/ice_init.F90        |  7 ++--
 configuration/scripts/options/set_env.box2001 |  1 -
 configuration/scripts/parse_namelist.sh       |  2 +-
 configuration/scripts/parse_settings.sh       | 34 ++++++++++++-------
 5 files changed, 31 insertions(+), 17 deletions(-)
 delete mode 100644 configuration/scripts/options/set_env.box2001

diff --git a/cice.setup b/cice.setup
index be9266dd2..aae4319d4 100755
--- a/cice.setup
+++ b/cice.setup
@@ -1070,6 +1070,10 @@ EOF2
     end
 
     ${casescr}/parse_settings.sh cice.settings ${fsmods}
+    if ($status != 0) then
+      echo "${0}: ERROR, parse_namelist.sh aborted"
+      exit -1
+    endif
     ${casescr}/parse_namelist.sh ice_in ${fimods}
     if ($status != 0) then
       echo "${0}: ERROR, parse_namelist.sh aborted"
diff --git a/cicecore/cicedynB/general/ice_init.F90 b/cicecore/cicedynB/general/ice_init.F90
index b299ef77f..7485cbe23 100644
--- a/cicecore/cicedynB/general/ice_init.F90
+++ b/cicecore/cicedynB/general/ice_init.F90
@@ -958,6 +958,10 @@ subroutine input_data
          abort_list = trim(abort_list)//":1"
       endif
 
+      if (ktransport <= 0) then
+         advection = 'none'
+      endif
+
       if (ktransport > 0 .and. advection /= 'remap' .and. advection /= 'upwind') then
          if (my_task == master_task) write(nu_diag,*) subname//' ERROR: invalid advection=',trim(advection)
          abort_list = trim(abort_list)//":3"
@@ -1467,9 +1471,6 @@ subroutine input_data
             endif
             write(nu_diag,1030) ' ssh_stress       = ',trim(ssh_stress),trim(tmpstr2)
 
-            if (ktransport <= 0) then
-               advection = 'none'
-            endif
             if (trim(advection) == 'remap') then
                tmpstr2 = ' : linear remapping advection'
             elseif (trim(advection) == 'upwind') then
diff --git a/configuration/scripts/options/set_env.box2001 b/configuration/scripts/options/set_env.box2001
deleted file mode 100644
index a3f7c10f5..000000000
--- a/configuration/scripts/options/set_env.box2001
+++ /dev/null
@@ -1 +0,0 @@
-setenv NICELYR   1
diff --git a/configuration/scripts/parse_namelist.sh b/configuration/scripts/parse_namelist.sh
index ea539a2d0..6dbad45d6 100755
--- 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=()
diff --git a/configuration/scripts/parse_settings.sh b/configuration/scripts/parse_settings.sh
index d6ed31c15..fe7f87c1c 100755
--- 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}
@@ -44,18 +47,25 @@ do
     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)
+    cp ${filename} ${filename}.check
+    sed -i.sedbak -e 's|\(^[[:space:]]*set.* '"$vname"' \)[^#]*\(#*.*$\)|\1 '"$foundstring"' |g' $filename.check
+    grep -q ${foundstring} ${filename}.check
+    if [ $? -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]=${value}
+      fi
+      if [[ -e "${filename}.sedbak" ]]; then
+        rm ${filename}.sedbak
+      fi
     else
-      valuearray[$found]=${value}
-    fi
-
-    if [[ -e "${filename}.sedbak" ]]; then
-      rm ${filename}.sedbak
+      echo "${scriptname} ERROR: parsing error for ${vname}"
+      exit -99
     fi
+    rm ${filename}.check ${filename}.check.sedbak
 
   fi
 

From 60816b1f6ad0e92a5e25f762b982556a3c37d977 Mon Sep 17 00:00:00 2001
From: apcraig <anthony.p.craig@gmail.com>
Date: Mon, 22 Nov 2021 20:00:48 -0700
Subject: [PATCH 2/5] 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.
---
 cice.setup                                    | 71 ++++++++++++++++---
 configuration/scripts/parse_namelist.sh       | 14 ++--
 .../scripts/parse_namelist_from_env.sh        | 11 ++-
 configuration/scripts/parse_settings.sh       | 14 ++--
 4 files changed, 72 insertions(+), 38 deletions(-)

diff --git a/cice.setup b/cice.setup
index aae4319d4..a5cbbd468 100755
--- 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 spend in parse_namelist
+    set iceinfn = ../ice_in_save_${grid}${soptions}
+    set skip_parse_namelist = spval
+    if (${dosuite} == 1) then
+      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 $pdd"
+
+    # Save ice_in in the suite to reduce time spend in parse_namelist
+    if (${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/parse_namelist.sh b/configuration/scripts/parse_namelist.sh
index 6dbad45d6..f5ae8a406 100755
--- a/configuration/scripts/parse_namelist.sh
+++ b/configuration/scripts/parse_namelist.sh
@@ -43,26 +43,20 @@ 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
-      sed -i.sedbak -e 's|\(^[[:space:]]*'"$vname"'[[:space:]]*=[[:space:]]*\)\(.*$\)|\1'"$value"'|g' ${filename}
+    grep -q "^[[:space:]]*${vname}[[:space:]]*=" $filename
+    grepout=$?
+    if [ ${grepout} -eq 0 ]; then
+      sed -i -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
 
diff --git a/configuration/scripts/parse_namelist_from_env.sh b/configuration/scripts/parse_namelist_from_env.sh
index 4d829450f..08ca2154c 100755
--- a/configuration/scripts/parse_namelist_from_env.sh
+++ b/configuration/scripts/parse_namelist_from_env.sh
@@ -5,16 +5,13 @@ 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' $filename
-
-if [[ -e "${filename}.sedbak" ]]; then
-  rm ${filename}.sedbak
-fi
+sed -i -e 's|ICE_SANDBOX|'"${ICE_SANDBOX}"'|g' $filename
+sed -i -e 's|ICE_MACHINE_INPUTDATA|'"${ICE_MACHINE_INPUTDATA}"'|g' $filename
 
 exit 0
diff --git a/configuration/scripts/parse_settings.sh b/configuration/scripts/parse_settings.sh
index fe7f87c1c..a2aed53ce 100755
--- a/configuration/scripts/parse_settings.sh
+++ b/configuration/scripts/parse_settings.sh
@@ -46,26 +46,20 @@ do
       fi
     done
 
-    #sed -i 's|\(^\s*set.* '"$vname"' \)[^#]*\(#*.*$\)|\1 '"$value"'  \2|g' $filename
-    cp ${filename} ${filename}.check
-    sed -i.sedbak -e 's|\(^[[:space:]]*set.* '"$vname"' \)[^#]*\(#*.*$\)|\1 '"$foundstring"' |g' $filename.check
-    grep -q ${foundstring} ${filename}.check
-    if [ $? -eq 0 ]; then
-      sed -i.sedbak -e 's|\(^[[:space:]]*set.* '"$vname"' \)[^#]*\(#*.*$\)|\1 '"$value"'  \2|g' $filename
+    grep -q "^[[:space:]]*set.* ${vname}[[:space:]]*" $filename
+    grepout=$?
+    if [ ${grepout} -eq 0 ]; then
+      sed -i -e 's|\(^[[:space:]]*set.* '"$vname"' \)[^#]*\(#*.*$\)|\1 '"$value"'  \2|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
 

From 4c7987e42178762c1226590c0d28c02901dab148 Mon Sep 17 00:00:00 2001
From: apcraig <anthony.p.craig@gmail.com>
Date: Mon, 22 Nov 2021 22:31:00 -0700
Subject: [PATCH 3/5] fix cice.setup for case

---
 cice.setup | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cice.setup b/cice.setup
index a5cbbd468..ef08b3a7f 100755
--- a/cice.setup
+++ b/cice.setup
@@ -938,9 +938,9 @@ EOF
 
     # Use an existing ice_in file from the suite if it exists
     # to reduce time spend in parse_namelist
-    set iceinfn = ../ice_in_save_${grid}${soptions}
     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

From 14c436ee4958d4b8dd35900c0308389d70f243af Mon Sep 17 00:00:00 2001
From: apcraig <anthony.p.craig@gmail.com>
Date: Tue, 23 Nov 2021 14:46:58 -0700
Subject: [PATCH 4/5] add sedbak implementation to support Mac sed

---
 configuration/scripts/parse_namelist.sh          | 6 +++++-
 configuration/scripts/parse_namelist_from_env.sh | 8 ++++++--
 configuration/scripts/parse_settings.sh          | 6 +++++-
 3 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/configuration/scripts/parse_namelist.sh b/configuration/scripts/parse_namelist.sh
index f5ae8a406..dcb0d1ccc 100755
--- a/configuration/scripts/parse_namelist.sh
+++ b/configuration/scripts/parse_namelist.sh
@@ -46,7 +46,7 @@ do
     grep -q "^[[:space:]]*${vname}[[:space:]]*=" $filename
     grepout=$?
     if [ ${grepout} -eq 0 ]; then
-      sed -i -e 's|\(^[[:space:]]*'"$vname"'[[:space:]]*=[[:space:]]*\)\(.*$\)|\1'"$value"'|g' ${filename}
+      sed -i.sedbak -e 's|\(^[[:space:]]*'"$vname"'[[:space:]]*=[[:space:]]*\)\(.*$\)|\1'"$value"'|g' ${filename}
       if [[ "${found}" == "${foundstring}" ]]; then
         vnamearray+=($vname)
         valuearray+=($value)
@@ -62,4 +62,8 @@ do
 
 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
index 08ca2154c..4c25d358d 100755
--- a/configuration/scripts/parse_namelist_from_env.sh
+++ b/configuration/scripts/parse_namelist_from_env.sh
@@ -11,7 +11,11 @@ filename=$1
 #echo "$0 $1" 
 echo "running $scriptname"
 
-sed -i -e 's|ICE_SANDBOX|'"${ICE_SANDBOX}"'|g' $filename
-sed -i -e 's|ICE_MACHINE_INPUTDATA|'"${ICE_MACHINE_INPUTDATA}"'|g' $filename
+sed -i.sedbak -e 's|ICE_SANDBOX|'"${ICE_SANDBOX}"'|g' $filename
+sed -i.sedbak -e 's|ICE_MACHINE_INPUTDATA|'"${ICE_MACHINE_INPUTDATA}"'|g' $filename
+
+if [[ -e "${filename}.sedbak" ]]; then
+  rm ${filename}.sedbak
+fi
 
 exit 0
diff --git a/configuration/scripts/parse_settings.sh b/configuration/scripts/parse_settings.sh
index a2aed53ce..a3f432801 100755
--- a/configuration/scripts/parse_settings.sh
+++ b/configuration/scripts/parse_settings.sh
@@ -49,7 +49,7 @@ do
     grep -q "^[[:space:]]*set.* ${vname}[[:space:]]*" $filename
     grepout=$?
     if [ ${grepout} -eq 0 ]; then
-      sed -i -e 's|\(^[[:space:]]*set.* '"$vname"' \)[^#]*\(#*.*$\)|\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)
@@ -65,4 +65,8 @@ do
 
 done < "$filemods"
 
+if [[ -e "${filename}.sedbak" ]]; then
+  rm ${filename}.sedbak
+fi
+
 exit 0

From 80c407aebb28706e11aca77d1d1be64fc7b761a1 Mon Sep 17 00:00:00 2001
From: apcraig <anthony.p.craig@gmail.com>
Date: Wed, 24 Nov 2021 10:30:24 -0700
Subject: [PATCH 5/5] s/spend/spent

---
 cice.setup | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cice.setup b/cice.setup
index ef08b3a7f..60c56e5c2 100755
--- a/cice.setup
+++ b/cice.setup
@@ -937,7 +937,7 @@ EOF
     if (-e ${fsmods}) rm ${fsmods}
 
     # Use an existing ice_in file from the suite if it exists
-    # to reduce time spend in parse_namelist
+    # to reduce time spent in parse_namelist
     set skip_parse_namelist = spval
     if (${dosuite} == 1) then
       set iceinfn = ../ice_in_save_${grid}${soptions}
@@ -1116,7 +1116,7 @@ EOF2
 #@ pdd = ( $pd1 - $pd0 ) / 1000000
 #echo "tcxp after parse $pdd"
 
-    # Save ice_in in the suite to reduce time spend in parse_namelist
+    # 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}