From 095f3bf6484c660886682d9970a330a95b17a76d Mon Sep 17 00:00:00 2001
From: turner <matthew.turner.ctr@nrlmry.navy.mil>
Date: Mon, 12 Jun 2017 15:35:54 +0000
Subject: [PATCH 01/29] Test scripts now write to README.case instead of a
 separate README.test.  Replace the cice.<test_name>.csh scripts with
 cice.test.csh.

---
 configuration/scripts/tests/cice.10day.csh  | 173 --------------------
 configuration/scripts/tests/cice.annual.csh | 173 --------------------
 configuration/scripts/tests/cice.smoke.csh  | 173 --------------------
 create.case                                 |   6 +-
 4 files changed, 3 insertions(+), 522 deletions(-)
 delete mode 100755 configuration/scripts/tests/cice.10day.csh
 delete mode 100755 configuration/scripts/tests/cice.annual.csh
 delete mode 100755 configuration/scripts/tests/cice.smoke.csh

diff --git a/configuration/scripts/tests/cice.10day.csh b/configuration/scripts/tests/cice.10day.csh
deleted file mode 100755
index 06d95d340..000000000
--- a/configuration/scripts/tests/cice.10day.csh
+++ /dev/null
@@ -1,173 +0,0 @@
-#! /bin/csh -f
-
-echo ${0}
-
-source ./cice.settings
-source ${CICE_CASEDIR}/env.${CICE_MACHINE} || exit 2
-
-set jobfile = cice.10day
-set subfile = cice.submit
-
-set ntasks = ${CICE_NTASKS}
-set nthrds = ${CICE_NTHRDS}
-set maxtpn = ${CICE_MACHINE_TPNODE}
-set acct   = ${CICE_MACHINE_ACCT}
-
-@ taskpernode = ${maxtpn} / $nthrds
-@ nnodes = ${ntasks} / ${taskpernode}
-if (${nnodes} * ${taskpernode} < ${ntasks}) @ nnodes = $nnodes + 1
-set taskpernodelimit = ${taskpernode}
-if (${taskpernodelimit} > ${ntasks}) set taskpernodelimit = ${ntasks}
-
-set ptile = $taskpernode
-if ($ptile > ${maxtpn} / 2) @ ptile = ${maxtpn} / 2
-
-#==========================================
-
-# Create test script that runs cice.build, cice.run, and validates
-#==========================================
-
-cat >! ${jobfile} << EOF0
-#!/bin/csh -f 
-EOF0
-
-#==========================================
-
-if (${CICE_MACHINE} =~ yellowstone*) then
-cat >> ${jobfile} << EOFB
-#BSUB -n ${ntasks}
-#BSUB -R "span[ptile=${ptile}]"
-#BSUB -q caldera
-#BSUB -N
-###BSUB -x
-#BSUB -a poe
-#BSUB -o poe.stdout.%J
-#BSUB -e poe.stderr.%J
-#BSUB -J ${CICE_CASENAME}
-#BSUB -W 0:10
-#BSUB -P ${acct}
-EOFB
-
-else if (${CICE_MACHINE} =~ thunder* || ${CICE_MACHINE} =~ gordon* || ${CICE_MACHINE} =~ conrad*) then
-cat >> ${jobfile} << EOFB
-#PBS -N ${CICE_CASENAME}
-#PBS -q debug
-#PBS -A ${acct}
-#PBS -l select=${nnodes}:ncpus=${maxtpn}:mpiprocs=${taskpernode}
-#PBS -l walltime=0:10:00
-#PBS -j oe
-###PBS -M username@domain.com
-###PBS -m be
-EOFB
-
-else if (${CICE_MACHINE} =~ cori*) then
-cat >> ${jobfile} << EOFB
-#SBATCH -J ${CICE_CASENAME}
-#SBATCH -p debug
-###SBATCH -A ${acct}
-#SBATCH -N ${nnodes}
-#SBATCH -t 0:10:00
-#SBATCH -L SCRATCH
-#SBATCH -C haswell
-###SBATCH -e filename
-###SBATCH -o filename
-###SBATCH --mail-type FAIL
-###SBATCH --mail-user username@domain.com
-EOFB
-
-else if (${CICE_MACHINE} =~ wolf*) then
-cat >> ${jobfile} << EOFB
-#MSUB -A climateacme
-#MSUB -l walltime=01:00:00
-#MSUB -l nodes=1:ppn=4
-#MSUB -N cice
-EOFB
-#cat >> ${jobfile} << EOFB
-##SBATCH -J ${CICE_CASENAME}
-####SBATCH -p tossdev
-##SBATCH -t 0:45:00
-##SBATCH -A ${acct}
-##SBATCH -N ${nnodes}
-####SBATCH -L SCRATCH
-####SBATCH -C haswell
-##SBATCH -e slurm%j.err
-##SBATCH -o slurm%j.out
-####SBATCH --mail-type FAIL
-####SBATCH --mail-user username@domain.com
-#EOFB
-
-endif
-
-cat >> ${jobfile} << EOF2
-cd ${CICE_CASEDIR}
-source ./cice.settings || exit 2
-source ./env.\${CICE_MACHINE} || exit 2
-
-# Compile the CICE code
-./cice.build
-set rc_build = \$?
-
-# Run the CICE model
-./cice.run
-set rc_run = \$?
-
-EOF2
-
-if ($1 != "") then
-cat >> ${jobfile} << EOF3
-  # Get the final output filename
-  foreach file (\${CICE_RUNDIR}/restart/*)
-    set test_data = \$file
-  end
-  
-  set baseline_data = $1/\$test_data:t
-
-  if ( { cmp -s \$test_data \$baseline_data } ) then
-    set rc_valid = 0
-  else
-    set rc_valid = 1
-  endif
-EOF3
-endif
-
-cat >> ${jobfile} << EOF4
-
-if (\$rc_build == 0) then
-  echo "Build:      PASS"
-else
-  echo "Build:      FAIL"
-endif
-
-if (\$rc_run == 0) then
-  echo "Run:        PASS"
-else
-  echo "Run:        FAIL"
-endif
-EOF4
-
-if ($1 != "") then
-cat >> ${jobfile} << EOF5
-
-if (\$rc_valid == 0) then
-  echo "Validation: PASS"
-else
-  echo "Validation: FAIL"
-endif
-EOF5
-endif
-
-#==========================================
-
-chmod +x ${jobfile}
-
-#==========================================
-
-cat >! ${subfile} << EOFS
-#!/bin/csh -f 
-
-${CICE_MACHINE_SUBMIT} ${jobfile}
-echo "\`date\` \${0}: ${CICE_CASENAME} job submitted"  >> ${CICE_CASEDIR}/README.test
-
-EOFS
-
-chmod +x ${subfile}
diff --git a/configuration/scripts/tests/cice.annual.csh b/configuration/scripts/tests/cice.annual.csh
deleted file mode 100755
index 04e256c90..000000000
--- a/configuration/scripts/tests/cice.annual.csh
+++ /dev/null
@@ -1,173 +0,0 @@
-#! /bin/csh -f
-
-echo ${0}
-
-source ./cice.settings
-source ${CICE_CASEDIR}/env.${CICE_MACHINE} || exit 2
-
-set jobfile = cice.annual
-set subfile = cice.submit
-
-set ntasks = ${CICE_NTASKS}
-set nthrds = ${CICE_NTHRDS}
-set maxtpn = ${CICE_MACHINE_TPNODE}
-set acct   = ${CICE_MACHINE_ACCT}
-
-@ taskpernode = ${maxtpn} / $nthrds
-@ nnodes = ${ntasks} / ${taskpernode}
-if (${nnodes} * ${taskpernode} < ${ntasks}) @ nnodes = $nnodes + 1
-set taskpernodelimit = ${taskpernode}
-if (${taskpernodelimit} > ${ntasks}) set taskpernodelimit = ${ntasks}
-
-set ptile = $taskpernode
-if ($ptile > ${maxtpn} / 2) @ ptile = ${maxtpn} / 2
-
-#==========================================
-
-# Create test script that runs cice.build, cice.run, and validates
-#==========================================
-
-cat >! ${jobfile} << EOF0
-#!/bin/csh -f 
-EOF0
-
-#==========================================
-
-if (${CICE_MACHINE} =~ yellowstone*) then
-cat >> ${jobfile} << EOFB
-#BSUB -n ${ntasks}
-#BSUB -R "span[ptile=${ptile}]"
-#BSUB -q caldera
-#BSUB -N
-###BSUB -x
-#BSUB -a poe
-#BSUB -o poe.stdout.%J
-#BSUB -e poe.stderr.%J
-#BSUB -J ${CICE_CASENAME}
-#BSUB -W 0:10
-#BSUB -P ${acct}
-EOFB
-
-else if (${CICE_MACHINE} =~ thunder* || ${CICE_MACHINE} =~ gordon* || ${CICE_MACHINE} =~ conrad*) then
-cat >> ${jobfile} << EOFB
-#PBS -N ${CICE_CASENAME}
-#PBS -q debug
-#PBS -A ${acct}
-#PBS -l select=${nnodes}:ncpus=${maxtpn}:mpiprocs=${taskpernode}
-#PBS -l walltime=0:10:00
-#PBS -j oe
-###PBS -M username@domain.com
-###PBS -m be
-EOFB
-
-else if (${CICE_MACHINE} =~ cori*) then
-cat >> ${jobfile} << EOFB
-#SBATCH -J ${CICE_CASENAME}
-#SBATCH -p debug
-###SBATCH -A ${acct}
-#SBATCH -N ${nnodes}
-#SBATCH -t 0:10:00
-#SBATCH -L SCRATCH
-#SBATCH -C haswell
-###SBATCH -e filename
-###SBATCH -o filename
-###SBATCH --mail-type FAIL
-###SBATCH --mail-user username@domain.com
-EOFB
-
-else if (${CICE_MACHINE} =~ wolf*) then
-cat >> ${jobfile} << EOFB
-#MSUB -A climateacme
-#MSUB -l walltime=01:00:00
-#MSUB -l nodes=1:ppn=4
-#MSUB -N cice
-EOFB
-#cat >> ${jobfile} << EOFB
-##SBATCH -J ${CICE_CASENAME}
-####SBATCH -p tossdev
-##SBATCH -t 0:45:00
-##SBATCH -A ${acct}
-##SBATCH -N ${nnodes}
-####SBATCH -L SCRATCH
-####SBATCH -C haswell
-##SBATCH -e slurm%j.err
-##SBATCH -o slurm%j.out
-####SBATCH --mail-type FAIL
-####SBATCH --mail-user username@domain.com
-#EOFB
-
-endif
-
-cat >> ${jobfile} << EOF2
-cd ${CICE_CASEDIR}
-source ./cice.settings || exit 2
-source ./env.\${CICE_MACHINE} || exit 2
-
-# Compile the CICE code
-./cice.build
-set rc_build = \$?
-
-# Run the CICE model
-./cice.run
-set rc_run = \$?
-
-EOF2
-
-if ($1 != "") then
-cat >> ${jobfile} << EOF3
-  # Get the final output filename
-  foreach file (\${CICE_RUNDIR}/restart/*)
-    set test_data = \$file
-  end
-  
-  set baseline_data = $1/\$test_data:t
-
-  if ( { cmp -s \$test_data \$baseline_data } ) then
-    set rc_valid = 0
-  else
-    set rc_valid = 1
-  endif
-EOF3
-endif
-
-cat >> ${jobfile} << EOF4
-
-if (\$rc_build == 0) then
-  echo "Build:      PASS"
-else
-  echo "Build:      FAIL"
-endif
-
-if (\$rc_run == 0) then
-  echo "Run:        PASS"
-else
-  echo "Run:        FAIL"
-endif
-EOF4
-
-if ($1 != "") then
-cat >> ${jobfile} << EOF5
-
-if (\$rc_valid == 0) then
-  echo "Validation: PASS"
-else
-  echo "Validation: FAIL"
-endif
-EOF5
-endif
-
-#==========================================
-
-chmod +x ${jobfile}
-
-#==========================================
-
-cat >! ${subfile} << EOFS
-#!/bin/csh -f 
-
-${CICE_MACHINE_SUBMIT} ${jobfile}
-echo "\`date\` \${0}: ${CICE_CASENAME} job submitted"  >> ${CICE_CASEDIR}/README.test
-
-EOFS
-
-chmod +x ${subfile}
diff --git a/configuration/scripts/tests/cice.smoke.csh b/configuration/scripts/tests/cice.smoke.csh
deleted file mode 100755
index d44240e80..000000000
--- a/configuration/scripts/tests/cice.smoke.csh
+++ /dev/null
@@ -1,173 +0,0 @@
-#! /bin/csh -f
-
-echo ${0}
-
-source ./cice.settings
-source ${CICE_CASEDIR}/env.${CICE_MACHINE} || exit 2
-
-set jobfile = cice.smoke
-set subfile = cice.submit
-
-set ntasks = ${CICE_NTASKS}
-set nthrds = ${CICE_NTHRDS}
-set maxtpn = ${CICE_MACHINE_TPNODE}
-set acct   = ${CICE_MACHINE_ACCT}
-
-@ taskpernode = ${maxtpn} / $nthrds
-@ nnodes = ${ntasks} / ${taskpernode}
-if (${nnodes} * ${taskpernode} < ${ntasks}) @ nnodes = $nnodes + 1
-set taskpernodelimit = ${taskpernode}
-if (${taskpernodelimit} > ${ntasks}) set taskpernodelimit = ${ntasks}
-
-set ptile = $taskpernode
-if ($ptile > ${maxtpn} / 2) @ ptile = ${maxtpn} / 2
-
-#==========================================
-
-# Create test script that runs cice.build, cice.run, and validates
-#==========================================
-
-cat >! ${jobfile} << EOF0
-#!/bin/csh -f 
-EOF0
-
-#==========================================
-
-if (${CICE_MACHINE} =~ yellowstone*) then
-cat >> ${jobfile} << EOFB
-#BSUB -n ${ntasks}
-#BSUB -R "span[ptile=${ptile}]"
-#BSUB -q caldera
-#BSUB -N
-###BSUB -x
-#BSUB -a poe
-#BSUB -o poe.stdout.%J
-#BSUB -e poe.stderr.%J
-#BSUB -J ${CICE_CASENAME}
-#BSUB -W 0:10
-#BSUB -P ${acct}
-EOFB
-
-else if (${CICE_MACHINE} =~ thunder* || ${CICE_MACHINE} =~ gordon* || ${CICE_MACHINE} =~ conrad*) then
-cat >> ${jobfile} << EOFB
-#PBS -N ${CICE_CASENAME}
-#PBS -q debug
-#PBS -A ${acct}
-#PBS -l select=${nnodes}:ncpus=${maxtpn}:mpiprocs=${taskpernode}
-#PBS -l walltime=0:10:00
-#PBS -j oe
-###PBS -M username@domain.com
-###PBS -m be
-EOFB
-
-else if (${CICE_MACHINE} =~ cori*) then
-cat >> ${jobfile} << EOFB
-#SBATCH -J ${CICE_CASENAME}
-#SBATCH -p debug
-###SBATCH -A ${acct}
-#SBATCH -N ${nnodes}
-#SBATCH -t 0:10:00
-#SBATCH -L SCRATCH
-#SBATCH -C haswell
-###SBATCH -e filename
-###SBATCH -o filename
-###SBATCH --mail-type FAIL
-###SBATCH --mail-user username@domain.com
-EOFB
-
-else if (${CICE_MACHINE} =~ wolf*) then
-cat >> ${jobfile} << EOFB
-#MSUB -A climateacme
-#MSUB -l walltime=01:00:00
-#MSUB -l nodes=1:ppn=4
-#MSUB -N cice
-EOFB
-#cat >> ${jobfile} << EOFB
-##SBATCH -J ${CICE_CASENAME}
-####SBATCH -p tossdev
-##SBATCH -t 0:45:00
-##SBATCH -A ${acct}
-##SBATCH -N ${nnodes}
-####SBATCH -L SCRATCH
-####SBATCH -C haswell
-##SBATCH -e slurm%j.err
-##SBATCH -o slurm%j.out
-####SBATCH --mail-type FAIL
-####SBATCH --mail-user username@domain.com
-#EOFB
-
-endif
-
-cat >> ${jobfile} << EOF2
-cd ${CICE_CASEDIR}
-source ./cice.settings || exit 2
-source ./env.\${CICE_MACHINE} || exit 2
-
-# Compile the CICE code
-./cice.build
-set rc_build = \$?
-
-# Run the CICE model
-./cice.run
-set rc_run = \$?
-
-EOF2
-
-if ($1 != "") then
-cat >> ${jobfile} << EOF3
-  # Get the final output filename
-  foreach file (\${CICE_RUNDIR}/restart/*)
-    set test_data = \$file
-  end
-  
-  set baseline_data = $1/\$test_data:t
-
-  if ( { cmp -s \$test_data \$baseline_data } ) then
-    set rc_valid = 0
-  else
-    set rc_valid = 1
-  endif
-EOF3
-endif
-
-cat >> ${jobfile} << EOF4
-
-if (\$rc_build == 0) then
-  echo "Build:      PASS"
-else
-  echo "Build:      FAIL"
-endif
-
-if (\$rc_run == 0) then
-  echo "Run:        PASS"
-else
-  echo "Run:        FAIL"
-endif
-EOF4
-
-if ($1 != "") then
-cat >> ${jobfile} << EOF5
-
-if (\$rc_valid == 0) then
-  echo "Validation: PASS"
-else
-  echo "Validation: FAIL"
-endif
-EOF5
-endif
-
-#==========================================
-
-chmod +x ${jobfile}
-
-#==========================================
-
-cat >! ${subfile} << EOFS
-#!/bin/csh -f 
-
-${CICE_MACHINE_SUBMIT} ${jobfile}
-echo "\`date\` \${0}: ${CICE_CASENAME} job submitted"  >> ${CICE_CASEDIR}/README.test
-
-EOFS
-
-chmod +x ${subfile}
diff --git a/create.case b/create.case
index c8c1c7fa3..7d723ecdb 100755
--- a/create.case
+++ b/create.case
@@ -176,7 +176,7 @@ else
     exit -1
   endif
   mkdir -p $testname
-  echo "`date`${0} $initargv[*]" > $testname/README.test
+  echo "`date`${0} $initargv[*]" > $testname/README.case
   set case = $testname
 endif
 
@@ -330,10 +330,10 @@ if ($test != $spval) then
   source ./env.${mach} || exit 2
 
   if ($baseline == 0) then
-    ${CICE_SCRDIR}/tests/cice.${test}.csh $bdir
+    ${CICE_SCRDIR}/tests/cice.test.csh $bdir
   else
     # Generate baseline dataset
-    ${CICE_SCRDIR}/tests/cice.${test}.csh
+    ${CICE_SCRDIR}/tests/cice.test.csh
   endif
 endif
 

From 34cd5f05fdd2c464148902ae9e1e3058176489d6 Mon Sep 17 00:00:00 2001
From: turner <matthew.turner.ctr@nrlmry.navy.mil>
Date: Mon, 12 Jun 2017 15:37:17 +0000
Subject: [PATCH 02/29] when checking for compile success, write PASS/FAIL to
 new test_output file if the CICE_TEST variable is defined

---
 configuration/scripts/cice.build | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/configuration/scripts/cice.build b/configuration/scripts/cice.build
index d71d1fd6b..2c684c769 100755
--- a/configuration/scripts/cice.build
+++ b/configuration/scripts/cice.build
@@ -80,6 +80,10 @@ gmake -j ${CICE_MACHINE_BLDTHRDS} VPFILE=Filepath EXEC=${CICE_RUNDIR}/cice CICE_
 if ($status != 0) then
   echo "${0}: COMPILE FAILED, see"
   echo "  cat ${CICE_OBJDIR}/${CICE_BLDLOG_FILE}"
+  if ( $?CICE_TEST ) then
+    # This is a test case.  Write output to test_output file
+    echo "FAIL $CICE_CASENAME build" >> ${CICE_CASEDIR}/test_output
+  endif
   exit 99
 endif
 
@@ -87,4 +91,7 @@ if !(-d ${CICE_LOGDIR}) mkdir -p ${CICE_LOGDIR}
 cp -p ${CICE_BLDLOG_FILE} ${CICE_LOGDIR}/
 echo "`date` ${0}:${CICE_CASENAME} build completed ${CICE_BLDLOG_FILE}"  >> ${CICE_CASEDIR}/README.case
 echo "${0}: COMPILE SUCCESSFUL, ${CICE_LOGDIR}/${CICE_BLDLOG_FILE}"
+if ( $?CICE_TEST ) then
+  echo "PASS $CICE_CASENAME build" >> ${CICE_CASEDIR}/test_output
+endif
 

From cfabe1530daa330e78b1861bf02b7480711a7a0d Mon Sep 17 00:00:00 2001
From: turner <matthew.turner.ctr@nrlmry.navy.mil>
Date: Mon, 12 Jun 2017 15:38:33 +0000
Subject: [PATCH 03/29] update cice.run.setup.csh to add the option to write
 PASS/FAIL information to the test_output file (only if CICE_TEST is defined)

---
 configuration/scripts/cice.run.setup.csh | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/configuration/scripts/cice.run.setup.csh b/configuration/scripts/cice.run.setup.csh
index 1735720c7..9a5297823 100755
--- a/configuration/scripts/cice.run.setup.csh
+++ b/configuration/scripts/cice.run.setup.csh
@@ -205,11 +205,22 @@ echo " "
 if !(-d \${CICE_LOGDIR}) mkdir -p \${CICE_LOGDIR}
 cp -p \${CICE_RUNLOG_FILE} \${CICE_LOGDIR}
 
-grep ' CICE COMPLETED SUCCESSFULLY' \${CICE_RUNLOG_FILE}  || echo "CICE run did not complete - see \${CICE_LOGDIR}/\${CICE_RUNLOG_FILE}" && exit -1
+grep ' CICE COMPLETED SUCCESSFULLY' \${CICE_RUNLOG_FILE}
+if ( \$? != 0 ) then
+  echo "CICE run did not complete - see \${CICE_LOGDIR}/\${CICE_RUNLOG_FILE}"
+  if ( \$?CICE_TEST ) then
+    echo "FAIL \${CICE_CASENAME} run" >> \${CICE_CASEDIR}/test_output
+  endif
+  exit -1
+endif
 
 echo "\`date\` \${0}: \${CICE_CASENAME} run completed \${CICE_RUNLOG_FILE}"  >> \${CICE_CASEDIR}/README.case
 echo "done \${0}"
 
+if ( \$?CICE_TEST ) then
+  echo "PASS \${CICE_CASENAME} run" >> \${CICE_CASEDIR}/test_output
+endif
+
 EOFE
 
 #==========================================

From 0c8766135d27883e2351155c3774d55270044cca Mon Sep 17 00:00:00 2001
From: turner <matthew.turner.ctr@nrlmry.navy.mil>
Date: Mon, 12 Jun 2017 15:40:41 +0000
Subject: [PATCH 04/29] delete old cice.<test_nae>.csh scripts and replace with
 cice.test.csh script.  The cice.test.csh script adds a new environment
 variable (CICE_TEST) to cice.settings.  The build process has been removed
 from cice.test.csh, and replaced with a check to see if the executable
 exists.  If not, the script prints an error message and exits.

---
 configuration/scripts/tests/cice.test.csh | 159 ++++++++++++++++++++++
 1 file changed, 159 insertions(+)
 create mode 100755 configuration/scripts/tests/cice.test.csh

diff --git a/configuration/scripts/tests/cice.test.csh b/configuration/scripts/tests/cice.test.csh
new file mode 100755
index 000000000..953baf4e3
--- /dev/null
+++ b/configuration/scripts/tests/cice.test.csh
@@ -0,0 +1,159 @@
+#! /bin/csh -f
+
+echo ${0}
+
+# Define this as a test case in the cice.settings file
+cat >> ./cice.settings << EOF
+
+# Add variable defining this case_dir as a test
+setenv CICE_TEST true
+EOF
+
+source ./cice.settings
+source ${CICE_CASEDIR}/env.${CICE_MACHINE} || exit 2
+
+set jobfile = cice.test
+set subfile = cice.submit
+
+set ntasks = ${CICE_NTASKS}
+set nthrds = ${CICE_NTHRDS}
+set maxtpn = ${CICE_MACHINE_TPNODE}
+set acct   = ${CICE_MACHINE_ACCT}
+
+@ taskpernode = ${maxtpn} / $nthrds
+@ nnodes = ${ntasks} / ${taskpernode}
+if (${nnodes} * ${taskpernode} < ${ntasks}) @ nnodes = $nnodes + 1
+set taskpernodelimit = ${taskpernode}
+if (${taskpernodelimit} > ${ntasks}) set taskpernodelimit = ${ntasks}
+
+set ptile = $taskpernode
+if ($ptile > ${maxtpn} / 2) @ ptile = ${maxtpn} / 2
+
+#==========================================
+
+# Create test script that runs cice.run, and validates
+#==========================================
+
+cat >! ${jobfile} << EOF0
+#!/bin/csh -f 
+EOF0
+
+#==========================================
+
+if (${CICE_MACHINE} =~ yellowstone*) then
+cat >> ${jobfile} << EOFB
+#BSUB -n ${ntasks}
+#BSUB -R "span[ptile=${ptile}]"
+#BSUB -q caldera
+#BSUB -N
+###BSUB -x
+#BSUB -a poe
+#BSUB -o poe.stdout.%J
+#BSUB -e poe.stderr.%J
+#BSUB -J ${CICE_CASENAME}
+#BSUB -W 0:10
+#BSUB -P ${acct}
+EOFB
+
+else if (${CICE_MACHINE} =~ thunder* || ${CICE_MACHINE} =~ gordon* || ${CICE_MACHINE} =~ conrad*) then
+cat >> ${jobfile} << EOFB
+#PBS -N ${CICE_CASENAME}
+#PBS -q debug
+#PBS -A ${acct}
+#PBS -l select=${nnodes}:ncpus=${maxtpn}:mpiprocs=${taskpernode}
+#PBS -l walltime=0:10:00
+#PBS -j oe
+###PBS -M username@domain.com
+###PBS -m be
+EOFB
+
+else if (${CICE_MACHINE} =~ cori*) then
+cat >> ${jobfile} << EOFB
+#SBATCH -J ${CICE_CASENAME}
+#SBATCH -p debug
+###SBATCH -A ${acct}
+#SBATCH -N ${nnodes}
+#SBATCH -t 0:10:00
+#SBATCH -L SCRATCH
+#SBATCH -C haswell
+###SBATCH -e filename
+###SBATCH -o filename
+###SBATCH --mail-type FAIL
+###SBATCH --mail-user username@domain.com
+EOFB
+
+else if (${CICE_MACHINE} =~ wolf*) then
+cat >> ${jobfile} << EOFB
+#MSUB -A climateacme
+#MSUB -l walltime=01:00:00
+#MSUB -l nodes=1:ppn=4
+#MSUB -N cice
+EOFB
+#cat >> ${jobfile} << EOFB
+##SBATCH -J ${CICE_CASENAME}
+####SBATCH -p tossdev
+##SBATCH -t 0:45:00
+##SBATCH -A ${acct}
+##SBATCH -N ${nnodes}
+####SBATCH -L SCRATCH
+####SBATCH -C haswell
+##SBATCH -e slurm%j.err
+##SBATCH -o slurm%j.out
+####SBATCH --mail-type FAIL
+####SBATCH --mail-user username@domain.com
+#EOFB
+
+endif
+
+cat >> ${jobfile} << EOF2
+cd ${CICE_CASEDIR}
+source ./cice.settings || exit 2
+source ./env.\${CICE_MACHINE} || exit 2
+
+# Check to see if executable exists in CICE_RUNDIR
+if ( ! -f \${CICE_RUNDIR}/cice ) then
+  echo "cice executable does not exist in \${CICE_RUNDIR}.  "
+  echo "Please run cice.build before this test."
+  exit 99
+endif
+
+# Run the CICE model
+./cice.run
+
+EOF2
+
+if ($1 != "") then
+cat >> ${jobfile} << EOF3
+  # Get the final output filename
+  foreach file (\${CICE_RUNDIR}/restart/*)
+    set test_data = \$file
+  end
+  
+  set baseline_data = $1/\$test_data:t
+
+  echo "Performing binary comparison between files:"
+  echo "baseline: \$baseline_data"
+  echo "test:     \$test_data"
+  if ( { cmp -s \$test_data \$baseline_data } ) then
+    echo "PASS \${CICE_CASENAME} test" >> ${CICE_CASEDIR}/test_output
+  else
+    echo "FAIL \${CICE_CASENAME} test" >> ${CICE_CASEDIR}/test_output
+  endif
+EOF3
+endif
+
+#==========================================
+
+chmod +x ${jobfile}
+
+#==========================================
+
+cat >! ${subfile} << EOFS
+#!/bin/csh -f 
+
+${CICE_MACHINE_SUBMIT} ${jobfile}
+echo "\`date\` \${0}: ${CICE_CASENAME} job submitted"  >> ${CICE_CASEDIR}/README.case
+
+EOFS
+
+chmod +x ${subfile}

From b2aafa274fb5f3dd648ad94267476f083e5369f3 Mon Sep 17 00:00:00 2001
From: turner <matthew.turner.ctr@nrlmry.navy.mil>
Date: Mon, 12 Jun 2017 16:32:04 +0000
Subject: [PATCH 05/29] Move batch logic from cice.run.setup.csh and
 cice.test.csh to new cice.batch.csh.  Move job launch logic from
 cice.run.setup.csh and cice.test.csh to cice.launch.csh.

---
 .../{tests/cice.smoke.csh => cice.batch.csh}  | 111 ++++--------
 configuration/scripts/cice.launch.csh         |  53 ++++++
 configuration/scripts/cice.run.setup.csh      | 145 +--------------
 configuration/scripts/tests/cice.annual.csh   | 165 ------------------
 configuration/scripts/tests/cice.test.csh     |  80 +--------
 create.case                                   |   6 +-
 6 files changed, 94 insertions(+), 466 deletions(-)
 rename configuration/scripts/{tests/cice.smoke.csh => cice.batch.csh} (56%)
 create mode 100755 configuration/scripts/cice.launch.csh
 delete mode 100755 configuration/scripts/tests/cice.annual.csh

diff --git a/configuration/scripts/tests/cice.smoke.csh b/configuration/scripts/cice.batch.csh
similarity index 56%
rename from configuration/scripts/tests/cice.smoke.csh
rename to configuration/scripts/cice.batch.csh
index a4be7df39..3aac1056f 100755
--- a/configuration/scripts/tests/cice.smoke.csh
+++ b/configuration/scripts/cice.batch.csh
@@ -5,8 +5,7 @@ echo ${0}
 source ./cice.settings
 source ${CICE_CASEDIR}/env.${CICE_MACHINE} || exit 2
 
-set jobfile = cice.smoke
-set subfile = cice.submit
+set jobfile = $1
 
 set ntasks = ${CICE_NTASKS}
 set nthrds = ${CICE_NTHRDS}
@@ -24,9 +23,6 @@ if ($ptile > ${maxtpn} / 2) @ ptile = ${maxtpn} / 2
 
 #==========================================
 
-# Create test script that runs cice.build, cice.run, and validates
-#==========================================
-
 cat >! ${jobfile} << EOF0
 #!/bin/csh -f 
 EOF0
@@ -48,6 +44,20 @@ cat >> ${jobfile} << EOFB
 #BSUB -P ${acct}
 EOFB
 
+#==========================================
+
+elseif (${CICE_MACHINE} =~ cheyenne*) then
+cat >> ${jobfile} << EOFB
+#PBS -j oe 
+#PBS -m ae 
+#PBS -V
+#PBS -q regular
+#PBS -N ${CICE_CASENAME}
+#PBS -A ${CICE_ACCT}
+#PBS -l select=${nnodes}:ncpus=${ntasks}:mpiprocs=${ntasks}
+#PBS -l walltime=02:00:00
+EOFB
+
 else if (${CICE_MACHINE} =~ thunder* || ${CICE_MACHINE} =~ gordon* || ${CICE_MACHINE} =~ conrad*) then
 cat >> ${jobfile} << EOFB
 #PBS -N ${CICE_CASENAME}
@@ -78,88 +88,27 @@ EOFB
 else if (${CICE_MACHINE} =~ wolf*) then
 cat >> ${jobfile} << EOFB
 #SBATCH -J ${CICE_CASENAME}
-#SBATCH -t 0:10:00
+#SBATCH -t 0:45:00
 #SBATCH -A ${acct}
 #SBATCH -N ${nnodes}
 #SBATCH -e slurm%j.err
 #SBATCH -o slurm%j.out
-#SBATCH --mail-type FAIL
-#SBATCH --mail-user=eclare@lanl.gov
+###SBATCH --mail-type END,FAIL
+###SBATCH --mail-user=eclare@lanl.gov
 #SBATCH --qos=low
 EOFB
 
-endif
-
-cat >> ${jobfile} << EOF2
-cd ${CICE_CASEDIR}
-source ./cice.settings || exit 2
-source ./env.\${CICE_MACHINE} || exit 2
-
-# Compile the CICE code
-./cice.build
-set rc_build = \$?
-
-# Run the CICE model
-./cice.run
-set rc_run = \$?
-
-EOF2
-
-if ($1 != "") then
-cat >> ${jobfile} << EOF3
-  # Get the final output filename
-  foreach file (\${CICE_RUNDIR}/restart/*)
-    set test_data = \$file
-  end
-  
-  set baseline_data = $1/\$test_data:t
-
-  if ( { cmp -s \$test_data \$baseline_data } ) then
-    set rc_valid = 0
-  else
-    set rc_valid = 1
-  endif
-EOF3
-endif
-
-cat >> ${jobfile} << EOF4
-
-if (\$rc_build == 0) then
-  echo "Build:      PASS"
-else
-  echo "Build:      FAIL"
-endif
-
-if (\$rc_run == 0) then
-  echo "Run:        PASS"
-else
-  echo "Run:        FAIL"
-endif
-EOF4
-
-if ($1 != "") then
-cat >> ${jobfile} << EOF5
+else if (${CICE_MACHINE} =~ pinto*) then
+cat >> ${jobfile} << EOFB
+#SBATCH -J ${CICE_CASENAME}
+#SBATCH -t 0:45:00
+#SBATCH -A ${acct}
+#SBATCH -N ${nnodes}
+#SBATCH -e slurm%j.err
+#SBATCH -o slurm%j.out
+###SBATCH --mail-type END,FAIL
+###SBATCH --mail-user=eclare@lanl.gov
+#SBATCH --qos=standby
+EOFB
 
-if (\$rc_valid == 0) then
-  echo "Validation: PASS"
-else
-  echo "Validation: FAIL"
 endif
-EOF5
-endif
-
-#==========================================
-
-chmod +x ${jobfile}
-
-#==========================================
-
-cat >! ${subfile} << EOFS
-#!/bin/csh -f 
-
-${CICE_MACHINE_SUBMIT} ${jobfile}
-echo "\`date\` \${0}: ${CICE_CASENAME} job submitted"  >> ${CICE_CASEDIR}/README.test
-
-EOFS
-
-chmod +x ${subfile}
diff --git a/configuration/scripts/cice.launch.csh b/configuration/scripts/cice.launch.csh
new file mode 100755
index 000000000..4ee2805af
--- /dev/null
+++ b/configuration/scripts/cice.launch.csh
@@ -0,0 +1,53 @@
+#! /bin/csh -f
+
+echo ${0}
+
+source ./cice.settings
+
+set jobfile = $1
+
+set ntasks = ${CICE_NTASKS}
+set nthrds = ${CICE_NTHRDS}
+
+#==========================================
+
+if (${CICE_MACHINE} =~ yellowstone*) then
+cat >> ${jobfile} << EOFR
+setenv MP_TASK_AFFINITY core:\${OMP_NUM_THREADS}
+mpirun.lsf ./cice >&! \$CICE_RUNLOG_FILE
+EOFR
+
+elseif (${CICE_MACHINE} =~ cheyenne*) then
+cat >> ${jobfile} << EOFR
+mpiexec_mpt -n ${ntasks} ./cice >&! \$CICE_RUNLOG_FILE
+EOFR
+
+else if (${CICE_MACHINE} =~ thunder*) then
+cat >> ${jobfile} << EOFR
+mpiexec_mpt -np ${ntasks} omplace ./cice >&! \$CICE_RUNLOG_FILE
+EOFR
+
+else if (${CICE_MACHINE} =~ gordon* || ${CICE_MACHINE} =~ conrad*) then
+cat >> ${jobfile} << EOFR
+aprun -n ${ntasks} -N ${ntasks} -d ${nthrds} ./cice >&! \$CICE_RUNLOG_FILE
+EOFR
+
+else if (${CICE_MACHINE} =~ cori*) then
+cat >> ${jobfile} << EOFR
+srun -n ${ntasks} -c ${nthrds} ./cice >&! \$CICE_RUNLOG_FILE
+EOFR
+
+else if (${CICE_MACHINE} =~ wolf*) then
+cat >> ${jobfile} << EOFR
+mpirun -np ${ntasks} ./cice >&! \$CICE_RUNLOG_FILE
+EOFR
+
+else if (${CICE_MACHINE} =~ pinto*) then
+cat >> ${jobfile} << EOFR
+mpirun -np ${ntasks} ./cice >&! \$CICE_RUNLOG_FILE
+EOFR
+#cat >> ${jobfile} << EOFR
+#srun -n ${ntasks} -c ${nthrds} ./cice >&! \$CICE_RUNLOG_FILE
+#EOFR
+
+endif
diff --git a/configuration/scripts/cice.run.setup.csh b/configuration/scripts/cice.run.setup.csh
index 9a5297823..08db5d956 100755
--- a/configuration/scripts/cice.run.setup.csh
+++ b/configuration/scripts/cice.run.setup.csh
@@ -8,111 +8,12 @@ source ${CICE_CASEDIR}/env.${CICE_MACHINE} || exit 2
 set jobfile = cice.run
 set subfile = cice.submit
 
-set ntasks = ${CICE_NTASKS}
 set nthrds = ${CICE_NTHRDS}
-set maxtpn = ${CICE_MACHINE_TPNODE}
-set acct   = ${CICE_MACHINE_ACCT}
-
-@ taskpernode = ${maxtpn} / $nthrds
-@ nnodes = ${ntasks} / ${taskpernode}
-if (${nnodes} * ${taskpernode} < ${ntasks}) @ nnodes = $nnodes + 1
-set taskpernodelimit = ${taskpernode}
-if (${taskpernodelimit} > ${ntasks}) set taskpernodelimit = ${ntasks}
-
-set ptile = $taskpernode
-if ($ptile > ${maxtpn} / 2) @ ptile = ${maxtpn} / 2
 
 #==========================================
 
-cat >! ${jobfile} << EOF0
-#!/bin/csh -f 
-EOF0
-
-#==========================================
-
-if (${CICE_MACHINE} =~ yellowstone*) then
-cat >> ${jobfile} << EOFB
-#BSUB -n ${ntasks}
-#BSUB -R "span[ptile=${ptile}]"
-#BSUB -q caldera
-#BSUB -N
-###BSUB -x
-#BSUB -a poe
-#BSUB -o poe.stdout.%J
-#BSUB -e poe.stderr.%J
-#BSUB -J ${CICE_CASENAME}
-#BSUB -W 0:10
-#BSUB -P ${acct}
-EOFB
-
-#==========================================
-
-elseif (${CICE_MACHINE} =~ cheyenne*) then
-cat >> ${jobfile} << EOFB
-#PBS -j oe 
-#PBS -m ae 
-#PBS -V
-#PBS -q regular
-#PBS -N ${CICE_CASENAME}
-#PBS -A ${CICE_ACCT}
-#PBS -l select=${nnodes}:ncpus=${ntasks}:mpiprocs=${ntasks}
-#PBS -l walltime=02:00:00
-EOFB
-
-else if (${CICE_MACHINE} =~ thunder* || ${CICE_MACHINE} =~ gordon* || ${CICE_MACHINE} =~ conrad*) then
-cat >> ${jobfile} << EOFB
-#PBS -N ${CICE_CASENAME}
-#PBS -q debug
-#PBS -A ${acct}
-#PBS -l select=${nnodes}:ncpus=${maxtpn}:mpiprocs=${taskpernode}
-#PBS -l walltime=0:10:00
-#PBS -j oe
-###PBS -M username@domain.com
-###PBS -m be
-EOFB
-
-else if (${CICE_MACHINE} =~ cori*) then
-cat >> ${jobfile} << EOFB
-#SBATCH -J ${CICE_CASENAME}
-#SBATCH -p debug
-###SBATCH -A ${acct}
-#SBATCH -N ${nnodes}
-#SBATCH -t 0:10:00
-#SBATCH -L SCRATCH
-#SBATCH -C haswell
-###SBATCH -e filename
-###SBATCH -o filename
-###SBATCH --mail-type FAIL
-###SBATCH --mail-user username@domain.com
-EOFB
-
-else if (${CICE_MACHINE} =~ wolf*) then
-cat >> ${jobfile} << EOFB
-#SBATCH -J ${CICE_CASENAME}
-#SBATCH -t 0:45:00
-#SBATCH -A ${acct}
-#SBATCH -N ${nnodes}
-#SBATCH -e slurm%j.err
-#SBATCH -o slurm%j.out
-#SBATCH --mail-type END,FAIL
-#SBATCH --mail-user=eclare@lanl.gov
-#SBATCH --qos=low
-EOFB
-
-else if (${CICE_MACHINE} =~ pinto*) then
-cat >> ${jobfile} << EOFB
-#SBATCH -J ${CICE_CASENAME}
-#SBATCH -t 0:45:00
-#SBATCH -A ${acct}
-#SBATCH -N ${nnodes}
-#SBATCH -e slurm%j.err
-#SBATCH -o slurm%j.out
-###SBATCH --mail-type END,FAIL
-###SBATCH --mail-user=eclare@lanl.gov
-#SBATCH --qos=standby
-EOFB
-
-endif
+# Write the batch code into the job file
+$1/cice.batch.csh ${jobfile}
 
 #==========================================
 
@@ -153,46 +54,8 @@ EOF1
 
 #==========================================
 
-if (${CICE_MACHINE} =~ yellowstone*) then
-cat >> ${jobfile} << EOFR
-setenv MP_TASK_AFFINITY core:\${OMP_NUM_THREADS}
-mpirun.lsf ./cice >&! \$CICE_RUNLOG_FILE
-EOFR
-
-elseif (${CICE_MACHINE} =~ cheyenne*) then
-cat >> ${jobfile} << EOFR
-mpiexec_mpt -n ${ntasks} ./cice >&! \$CICE_RUNLOG_FILE
-EOFR
-
-else if (${CICE_MACHINE} =~ thunder*) then
-cat >> ${jobfile} << EOFR
-mpiexec_mpt -np ${ntasks} omplace ./cice >&! \$CICE_RUNLOG_FILE
-EOFR
-
-else if (${CICE_MACHINE} =~ gordon* || ${CICE_MACHINE} =~ conrad*) then
-cat >> ${jobfile} << EOFR
-aprun -n ${ntasks} -N ${ntasks} -d ${nthrds} ./cice >&! \$CICE_RUNLOG_FILE
-EOFR
-
-else if (${CICE_MACHINE} =~ cori*) then
-cat >> ${jobfile} << EOFR
-srun -n ${ntasks} -c ${nthrds} ./cice >&! \$CICE_RUNLOG_FILE
-EOFR
-
-else if (${CICE_MACHINE} =~ wolf*) then
-cat >> ${jobfile} << EOFR
-mpirun -np ${ntasks} ./cice >&! \$CICE_RUNLOG_FILE
-EOFR
-
-else if (${CICE_MACHINE} =~ pinto*) then
-cat >> ${jobfile} << EOFR
-mpirun -np ${ntasks} ./cice >&! \$CICE_RUNLOG_FILE
-EOFR
-#cat >> ${jobfile} << EOFR
-#srun -n ${ntasks} -c ${nthrds} ./cice >&! \$CICE_RUNLOG_FILE
-#EOFR
-
-endif
+# Write the job launching logic into the job file
+$1/cice.launch.csh ${jobfile}
 
 #==========================================
 
diff --git a/configuration/scripts/tests/cice.annual.csh b/configuration/scripts/tests/cice.annual.csh
deleted file mode 100755
index 45717964e..000000000
--- a/configuration/scripts/tests/cice.annual.csh
+++ /dev/null
@@ -1,165 +0,0 @@
-#! /bin/csh -f
-
-echo ${0}
-
-source ./cice.settings
-source ${CICE_CASEDIR}/env.${CICE_MACHINE} || exit 2
-
-set jobfile = cice.annual
-set subfile = cice.submit
-
-set ntasks = ${CICE_NTASKS}
-set nthrds = ${CICE_NTHRDS}
-set maxtpn = ${CICE_MACHINE_TPNODE}
-set acct   = ${CICE_MACHINE_ACCT}
-
-@ taskpernode = ${maxtpn} / $nthrds
-@ nnodes = ${ntasks} / ${taskpernode}
-if (${nnodes} * ${taskpernode} < ${ntasks}) @ nnodes = $nnodes + 1
-set taskpernodelimit = ${taskpernode}
-if (${taskpernodelimit} > ${ntasks}) set taskpernodelimit = ${ntasks}
-
-set ptile = $taskpernode
-if ($ptile > ${maxtpn} / 2) @ ptile = ${maxtpn} / 2
-
-#==========================================
-
-# Create test script that runs cice.build, cice.run, and validates
-#==========================================
-
-cat >! ${jobfile} << EOF0
-#!/bin/csh -f 
-EOF0
-
-#==========================================
-
-if (${CICE_MACHINE} =~ yellowstone*) then
-cat >> ${jobfile} << EOFB
-#BSUB -n ${ntasks}
-#BSUB -R "span[ptile=${ptile}]"
-#BSUB -q caldera
-#BSUB -N
-###BSUB -x
-#BSUB -a poe
-#BSUB -o poe.stdout.%J
-#BSUB -e poe.stderr.%J
-#BSUB -J ${CICE_CASENAME}
-#BSUB -W 0:10
-#BSUB -P ${acct}
-EOFB
-
-else if (${CICE_MACHINE} =~ thunder* || ${CICE_MACHINE} =~ gordon* || ${CICE_MACHINE} =~ conrad*) then
-cat >> ${jobfile} << EOFB
-#PBS -N ${CICE_CASENAME}
-#PBS -q debug
-#PBS -A ${acct}
-#PBS -l select=${nnodes}:ncpus=${maxtpn}:mpiprocs=${taskpernode}
-#PBS -l walltime=0:10:00
-#PBS -j oe
-###PBS -M username@domain.com
-###PBS -m be
-EOFB
-
-else if (${CICE_MACHINE} =~ cori*) then
-cat >> ${jobfile} << EOFB
-#SBATCH -J ${CICE_CASENAME}
-#SBATCH -p debug
-###SBATCH -A ${acct}
-#SBATCH -N ${nnodes}
-#SBATCH -t 0:10:00
-#SBATCH -L SCRATCH
-#SBATCH -C haswell
-###SBATCH -e filename
-###SBATCH -o filename
-###SBATCH --mail-type FAIL
-###SBATCH --mail-user username@domain.com
-EOFB
-
-else if (${CICE_MACHINE} =~ wolf*) then
-cat >> ${jobfile} << EOFB
-#SBATCH -J ${CICE_CASENAME}
-#SBATCH -t 0:10:00
-#SBATCH -A ${acct}
-#SBATCH -N ${nnodes}
-#SBATCH -e slurm%j.err
-#SBATCH -o slurm%j.out
-#SBATCH --mail-type FAIL
-#SBATCH --mail-user=eclare@lanl.gov
-#SBATCH --qos=low
-EOFB
-
-endif
-
-cat >> ${jobfile} << EOF2
-cd ${CICE_CASEDIR}
-source ./cice.settings || exit 2
-source ./env.\${CICE_MACHINE} || exit 2
-
-# Compile the CICE code
-./cice.build
-set rc_build = \$?
-
-# Run the CICE model
-./cice.run
-set rc_run = \$?
-
-EOF2
-
-if ($1 != "") then
-cat >> ${jobfile} << EOF3
-  # Get the final output filename
-  foreach file (\${CICE_RUNDIR}/restart/*)
-    set test_data = \$file
-  end
-  
-  set baseline_data = $1/\$test_data:t
-
-  if ( { cmp -s \$test_data \$baseline_data } ) then
-    set rc_valid = 0
-  else
-    set rc_valid = 1
-  endif
-EOF3
-endif
-
-cat >> ${jobfile} << EOF4
-
-if (\$rc_build == 0) then
-  echo "Build:      PASS"
-else
-  echo "Build:      FAIL"
-endif
-
-if (\$rc_run == 0) then
-  echo "Run:        PASS"
-else
-  echo "Run:        FAIL"
-endif
-EOF4
-
-if ($1 != "") then
-cat >> ${jobfile} << EOF5
-
-if (\$rc_valid == 0) then
-  echo "Validation: PASS"
-else
-  echo "Validation: FAIL"
-endif
-EOF5
-endif
-
-#==========================================
-
-chmod +x ${jobfile}
-
-#==========================================
-
-cat >! ${subfile} << EOFS
-#!/bin/csh -f 
-
-${CICE_MACHINE_SUBMIT} ${jobfile}
-echo "\`date\` \${0}: ${CICE_CASENAME} job submitted"  >> ${CICE_CASEDIR}/README.test
-
-EOFS
-
-chmod +x ${subfile}
diff --git a/configuration/scripts/tests/cice.test.csh b/configuration/scripts/tests/cice.test.csh
index 1c35940e8..8319572cd 100755
--- a/configuration/scripts/tests/cice.test.csh
+++ b/configuration/scripts/tests/cice.test.csh
@@ -15,87 +15,15 @@ source ${CICE_CASEDIR}/env.${CICE_MACHINE} || exit 2
 set jobfile = cice.test
 set subfile = cice.submit
 
-set ntasks = ${CICE_NTASKS}
 set nthrds = ${CICE_NTHRDS}
-set maxtpn = ${CICE_MACHINE_TPNODE}
-set acct   = ${CICE_MACHINE_ACCT}
-
-@ taskpernode = ${maxtpn} / $nthrds
-@ nnodes = ${ntasks} / ${taskpernode}
-if (${nnodes} * ${taskpernode} < ${ntasks}) @ nnodes = $nnodes + 1
-set taskpernodelimit = ${taskpernode}
-if (${taskpernodelimit} > ${ntasks}) set taskpernodelimit = ${ntasks}
-
-set ptile = $taskpernode
-if ($ptile > ${maxtpn} / 2) @ ptile = ${maxtpn} / 2
 
 #==========================================
 
 # Create test script that runs cice.run, and validates
 #==========================================
 
-cat >! ${jobfile} << EOF0
-#!/bin/csh -f 
-EOF0
-
-#==========================================
-
-if (${CICE_MACHINE} =~ yellowstone*) then
-cat >> ${jobfile} << EOFB
-#BSUB -n ${ntasks}
-#BSUB -R "span[ptile=${ptile}]"
-#BSUB -q caldera
-#BSUB -N
-###BSUB -x
-#BSUB -a poe
-#BSUB -o poe.stdout.%J
-#BSUB -e poe.stderr.%J
-#BSUB -J ${CICE_CASENAME}
-#BSUB -W 0:10
-#BSUB -P ${acct}
-EOFB
-
-else if (${CICE_MACHINE} =~ thunder* || ${CICE_MACHINE} =~ gordon* || ${CICE_MACHINE} =~ conrad*) then
-cat >> ${jobfile} << EOFB
-#PBS -N ${CICE_CASENAME}
-#PBS -q debug
-#PBS -A ${acct}
-#PBS -l select=${nnodes}:ncpus=${maxtpn}:mpiprocs=${taskpernode}
-#PBS -l walltime=0:10:00
-#PBS -j oe
-###PBS -M username@domain.com
-###PBS -m be
-EOFB
-
-else if (${CICE_MACHINE} =~ cori*) then
-cat >> ${jobfile} << EOFB
-#SBATCH -J ${CICE_CASENAME}
-#SBATCH -p debug
-###SBATCH -A ${acct}
-#SBATCH -N ${nnodes}
-#SBATCH -t 0:10:00
-#SBATCH -L SCRATCH
-#SBATCH -C haswell
-###SBATCH -e filename
-###SBATCH -o filename
-###SBATCH --mail-type FAIL
-###SBATCH --mail-user username@domain.com
-EOFB
-
-else if (${CICE_MACHINE} =~ wolf*) then
-cat >> ${jobfile} << EOFB
-#SBATCH -J ${CICE_CASENAME}
-#SBATCH -t 0:10:00
-#SBATCH -A ${acct}
-#SBATCH -N ${nnodes}
-#SBATCH -e slurm%j.err
-#SBATCH -o slurm%j.out
-#SBATCH --mail-type FAIL
-#SBATCH --mail-user=eclare@lanl.gov
-#SBATCH --qos=low
-EOFB
-
-endif
+# Write the batch code into the job file
+$1/cice.batch.csh ${jobfile}
 
 cat >> ${jobfile} << EOF2
 cd ${CICE_CASEDIR}
@@ -114,14 +42,14 @@ endif
 
 EOF2
 
-if ($1 != "") then
+if ($2 != "") then
 cat >> ${jobfile} << EOF3
   # Get the final output filename
   foreach file (\${CICE_RUNDIR}/restart/*)
     set test_data = \$file
   end
   
-  set baseline_data = $1/\$test_data:t
+  set baseline_data = $2/\$test_data:t
 
   echo "Performing binary comparison between files:"
   echo "baseline: \$baseline_data"
diff --git a/create.case b/create.case
index 7d723ecdb..ca9e96b66 100755
--- a/create.case
+++ b/create.case
@@ -320,7 +320,7 @@ ${casescr}/parse_namelist.sh ice_in ${fimods}
 source ./cice.settings
 source ./env.${mach} || exit 2
 
-${casescr}/cice.run.setup.csh
+${casescr}/cice.run.setup.csh ${CICE_SCRDIR}
 
 #------------------------------------------------------------
 
@@ -330,10 +330,10 @@ if ($test != $spval) then
   source ./env.${mach} || exit 2
 
   if ($baseline == 0) then
-    ${CICE_SCRDIR}/tests/cice.test.csh $bdir
+    ${CICE_SCRDIR}/tests/cice.test.csh ${CICE_SCRDIR} $bdir
   else
     # Generate baseline dataset
-    ${CICE_SCRDIR}/tests/cice.test.csh
+    ${CICE_SCRDIR}/tests/cice.test.csh ${CICE_SCRDIR}
   endif
 endif
 

From 56686688998f0e272ad4ea4f8c08463951b73aba Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Mon, 12 Jun 2017 16:42:27 +0000
Subject: [PATCH 06/29] Remove the requirement for -b or -bd to be provided
 when using create.case to generate a test

---
 create.case | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/create.case b/create.case
index ca9e96b66..ad42ce2d5 100755
--- a/create.case
+++ b/create.case
@@ -135,11 +135,6 @@ if ($case != $spval && $test != $spval) then
   exit -1
 endif
 
-if ($test != $spval && $baseline == 0 && $bdir == $spval) then
-  echo "${0}: ERROR in arguments, when using -t either -b or -bd required"
-  exit -1
-endif
-
 set chck = `echo ${pesx} | sed 's/^[0-9]\+x[0-9]\+$/OK/'`
 if (${chck} == OK) then
   set task = `echo ${pesx} | sed s/x.\*//`

From 17d722dff2defc108a8631b30d872e2cc3647098 Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Mon, 12 Jun 2017 16:47:56 +0000
Subject: [PATCH 07/29] Add the option to pass a test ID to create.case, which
 gets included in the case_dir name

---
 create.case | 31 ++++++++++++++++++++++++++-----
 1 file changed, 26 insertions(+), 5 deletions(-)

diff --git a/create.case b/create.case
index ad42ce2d5..f0a2466cf 100755
--- a/create.case
+++ b/create.case
@@ -18,6 +18,7 @@ set pesx = 4x1
 set sets = ""
 set baseline = 0
 set bdir = $spval
+set testid = $spval
 
 if ($#argv < 1) then
   set helpheader = 1
@@ -55,7 +56,8 @@ NAME
              - "annual": Compiles code and performs annual run
              - "restart": Compiles code and performs an exact restart test
         -b baseline, generate baseline data
-        -bd baseline dir, location of baseline dataset (required if -t is used without -b)
+        -bd baseline dir, location of baseline dataset
+        -testid test ID, user-defined indentifier for test
 
       EXAMPLES:
       create.case -h
@@ -112,6 +114,9 @@ while (1)
     case "-bd":
       set bdir = $argv[1]
       breaksw
+    case "-testid":
+      set testid = $argv[1]
+      breaksw
     default:
       echo "${0}: ERROR unknown option $option, use -h for help"
       exit -1
@@ -155,15 +160,31 @@ else
   if ($sets != "") then
     set soptions = `echo $sets | sed 's/,/_/g'`
     if ($baseline == 1) then
-      set testname = "${test}_baseline_${grid}_${mach}_${pesx}_$soptions"
+      if ( $testid != $spval ) then
+        set testname = "${test}_baseline_${grid}_${mach}_${pesx}_${soptions}.${testid}"
+      else
+        set testname = "${test}_baseline_${grid}_${mach}_${pesx}_$soptions"
+      endif
     else
-      set testname = "${test}_${grid}_${mach}_${pesx}_$soptions"
+      if ( $testid != $spval ) then
+        set testname = "${test}_${grid}_${mach}_${pesx}_${soptions}.${testid}"
+      else
+        set testname = "${test}_${grid}_${mach}_${pesx}_$soptions"
+      endif
     endif
   else
     if ($baseline == 1) then
-      set testname = "${test}_baseline_${grid}_${mach}_$pesx"
+      if ( $testid != $spval ) then
+        set testname = "${test}_baseline_${grid}_${mach}_${pesx}.${testid}"
+      else
+        set testname = "${test}_baseline_${grid}_${mach}_$pesx"
+      endif
     else
-      set testname = "${test}_${grid}_${mach}_$pesx"
+      if ( $testid != $spval ) then
+        set testname = "${test}_${grid}_${mach}_${pesx}.${testid}"
+      else
+        set testname = "${test}_${grid}_${mach}_$pesx"
+      endif
     endif
   endif
   if (-d $testname) then

From f52288db18732639234744901a901e7dc7f62f0a Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Mon, 12 Jun 2017 17:02:24 +0000
Subject: [PATCH 08/29] Modification to create.case to properly handle running
 tests where -b and -bd are not specified

---
 configuration/scripts/cice.batch.csh | 6 +++++-
 create.case                          | 3 +--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/configuration/scripts/cice.batch.csh b/configuration/scripts/cice.batch.csh
index 3aac1056f..eea17c863 100755
--- a/configuration/scripts/cice.batch.csh
+++ b/configuration/scripts/cice.batch.csh
@@ -1,6 +1,10 @@
 #! /bin/csh -f
 
-echo ${0}
+if ( $1 != "" ) then
+  echo ${0} ${1}
+else
+  echo ${0}
+endif
 
 source ./cice.settings
 source ${CICE_CASEDIR}/env.${CICE_MACHINE} || exit 2
diff --git a/create.case b/create.case
index f0a2466cf..621761a4d 100755
--- a/create.case
+++ b/create.case
@@ -345,10 +345,9 @@ if ($test != $spval) then
   source ./cice.settings
   source ./env.${mach} || exit 2
 
-  if ($baseline == 0) then
+  if ($bdir != $spval) then
     ${CICE_SCRDIR}/tests/cice.test.csh ${CICE_SCRDIR} $bdir
   else
-    # Generate baseline dataset
     ${CICE_SCRDIR}/tests/cice.test.csh ${CICE_SCRDIR}
   endif
 endif

From d2dbf285f8b83d5187c64c390c066a6fd3a10c6e Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Mon, 12 Jun 2017 17:07:38 +0000
Subject: [PATCH 09/29] Add a check in create.case to ensure that the test
 requested is one of smoke, 10day, annual, or restart

---
 create.case | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/create.case b/create.case
index 621761a4d..13bd79576 100755
--- a/create.case
+++ b/create.case
@@ -140,6 +140,12 @@ if ($case != $spval && $test != $spval) then
   exit -1
 endif
 
+if ($test != $spval && $test != 'smoke' && $test != '10day' && $test != 'annual' \
+ && $test != 'restart') then
+  echo "${0}: ERROR in arguments.  $test is not a valid test"
+  exit -1
+endif
+
 set chck = `echo ${pesx} | sed 's/^[0-9]\+x[0-9]\+$/OK/'`
 if (${chck} == OK) then
   set task = `echo ${pesx} | sed s/x.\*//`

From 0db5c737a285bdb0293e35459601f0b076307c7e Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Tue, 13 Jun 2017 13:52:17 +0000
Subject: [PATCH 10/29] Update cice.run.setup.csh to not overwrite the
 ice.restart_file pointer file.  This is necessary for the exact restart test

---
 configuration/scripts/cice.run.setup.csh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/configuration/scripts/cice.run.setup.csh b/configuration/scripts/cice.run.setup.csh
index 08db5d956..3f341a24c 100755
--- a/configuration/scripts/cice.run.setup.csh
+++ b/configuration/scripts/cice.run.setup.csh
@@ -37,7 +37,7 @@ if !(-d \${CICE_RUNDIR}) mkdir -p \${CICE_RUNDIR}
 if !(-d \${CICE_HSTDIR}) mkdir -p \${CICE_HSTDIR}
 if !(-d \${CICE_RSTDIR}) mkdir -p \${CICE_RSTDIR}
 
-if !(-e ice.restart_file) cp \${CICE_RSTPFILE} \${CICE_RUNDIR}
+if !(-e \${CICE_RUNDIR}/ice.restart_file) cp \${CICE_RSTPFILE} \${CICE_RUNDIR}
 
 #--------------------------------------------
 cd \${CICE_RUNDIR}

From d224516479f79a3a358abd02afe4e1db2ea3a6bc Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Tue, 13 Jun 2017 13:53:32 +0000
Subject: [PATCH 11/29] Create new exact restart test case.

---
 .../scripts/options/test_nml.restart          |  7 ++
 configuration/scripts/tests/cice.restart.csh  | 95 +++++++++++++++++++
 create.case                                   |  7 +-
 3 files changed, 105 insertions(+), 4 deletions(-)
 create mode 100644 configuration/scripts/options/test_nml.restart
 create mode 100755 configuration/scripts/tests/cice.restart.csh

diff --git a/configuration/scripts/options/test_nml.restart b/configuration/scripts/options/test_nml.restart
new file mode 100644
index 000000000..0682417d2
--- /dev/null
+++ b/configuration/scripts/options/test_nml.restart
@@ -0,0 +1,7 @@
+npt            = 48
+dumpfreq       = 'd'
+dumpfreq_n     = 1
+bfbflag        = .true.
+diag_type      = 'stdout'
+print_global   = .true.
+histfreq       = 'd','x','x','x','x'
diff --git a/configuration/scripts/tests/cice.restart.csh b/configuration/scripts/tests/cice.restart.csh
new file mode 100755
index 000000000..ab1e43d97
--- /dev/null
+++ b/configuration/scripts/tests/cice.restart.csh
@@ -0,0 +1,95 @@
+#! /bin/csh -f
+
+echo ${0}
+
+# Define this as a test case in the cice.settings file
+cat >> ./cice.settings << EOF
+
+# Add variable defining this case_dir as a test
+setenv CICE_TEST true
+EOF
+
+source ./cice.settings
+source ${CICE_CASEDIR}/env.${CICE_MACHINE} || exit 2
+
+set jobfile = cice.test
+set subfile = cice.submit
+
+set nthrds = ${CICE_NTHRDS}
+
+#==========================================
+
+# Create test script that runs cice.run, and validates
+#==========================================
+
+# Write the batch code into the job file
+$1/cice.batch.csh ${jobfile}
+
+cat >> ${jobfile} << EOF2
+cd ${CICE_CASEDIR}
+source ./cice.settings || exit 2
+source ./env.\${CICE_MACHINE} || exit 2
+
+# Check to see if executable exists in CICE_RUNDIR
+if ( ! -f \${CICE_RUNDIR}/cice ) then
+  echo "cice executable does not exist in \${CICE_RUNDIR}.  "
+  echo "Please run cice.build before this test."
+  exit 99
+endif
+
+# Run the CICE model for the 2-day simulation
+./cice.run
+if ( \$? != 0 ) then
+  exit 99
+endif
+
+# Prepend 'baseline_' to the final restart file to save for comparison
+foreach file (\${CICE_RUNDIR}/restart/*)
+  set test_data = \$file
+end
+set baseline_data = \${CICE_RUNDIR}/restart/baseline_\$test_data:t
+mv \$test_data \$baseline_data
+
+# Modify the contents of the pointer file for restart
+perl -i -pe's/(\d{4})-(\d{2})-(\d{2})/sprintf("%04d-%02d-%02d",\$1,\$2,\$3-1)/e' \${CICE_RUNDIR}/ice.restart_file
+
+# Modify the namelist for the restart simulation
+cp ice_in ice_in.restart_full
+perl -i -pe"s/(npt\s+=)\s(\d+)/\1 24/" ice_in  # replace npt = 48 with npt = 24
+perl -i -pe"s/(dumpfreq_n\s+=)\s(\d+)/\1 1/" ice_in   # replace dump freq with 1
+perl -i -pe"s/(runtype\s+=)\s(\S+)/\1 'continue'/" ice_in   # runtype with continuation
+
+# Run the CICE model for the restart simulation
+./cice.run
+if ( \$? != 0 ) then
+  exit 99
+endif
+
+EOF2
+
+cat >> ${jobfile} << EOF3
+echo "Performing binary comparison between files:"
+echo "baseline: \$baseline_data"
+echo "test:     \$test_data"
+if ( { cmp -s \$test_data \$baseline_data } ) then
+  echo "PASS \${CICE_CASENAME} test" >> ${CICE_CASEDIR}/test_output
+else
+  echo "FAIL \${CICE_CASENAME} test" >> ${CICE_CASEDIR}/test_output
+endif
+EOF3
+
+#==========================================
+
+chmod +x ${jobfile}
+
+#==========================================
+
+cat >! ${subfile} << EOFS
+#!/bin/csh -f 
+
+${CICE_MACHINE_SUBMIT} ${jobfile}
+echo "\`date\` \${0}: ${CICE_CASENAME} job submitted"  >> ${CICE_CASEDIR}/README.case
+
+EOFS
+
+chmod +x ${subfile}
diff --git a/create.case b/create.case
index 13bd79576..e462ddbd7 100755
--- a/create.case
+++ b/create.case
@@ -348,10 +348,9 @@ ${casescr}/cice.run.setup.csh ${CICE_SCRDIR}
 
 if ($test != $spval) then
   # Generate test script
-  source ./cice.settings
-  source ./env.${mach} || exit 2
-
-  if ($bdir != $spval) then
+  if ($test == 'restart') then
+    ${CICE_SCRDIR}/tests/cice.restart.csh ${CICE_SCRDIR}
+  else if ($bdir != $spval) then
     ${CICE_SCRDIR}/tests/cice.test.csh ${CICE_SCRDIR} $bdir
   else
     ${CICE_SCRDIR}/tests/cice.test.csh ${CICE_SCRDIR}

From 2ddbdd937e5c476eebe8d4ba83a91386e3864a36 Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Tue, 13 Jun 2017 14:24:42 +0000
Subject: [PATCH 12/29] Add new README.test file that gives instructions on
 running the test cases.  Also add the testid field to README_v6

---
 README.test | 55 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 README_v6   |  1 +
 2 files changed, 56 insertions(+)
 create mode 100644 README.test

diff --git a/README.test b/README.test
new file mode 100644
index 000000000..513caac9a
--- /dev/null
+++ b/README.test
@@ -0,0 +1,55 @@
+CICE version 6 testing
+  June 2017
+
+This README file documents how to use the testing suite developed for the
+CICE Consortium sea ice model.  The tests currently supported are:
+  1. "Smoke" test  - Ensures that the model compiles successfully and runs
+                     to completion for a 1 day simulation.  Validation is
+                     determined by performing a binary comparison on restart
+                     files to a baseline dataset.
+  2. 10-day test   - Ensures that the model compiles successfully and runs
+                     to completion for a 10 day simulation.  Validation is
+                     determined by performing a binary comparison on restart
+                     files to a baseline dataset.
+  3. Exact restart - Ensures that the output from a cold-start simulation
+                     and a restart simulation provide bit-for-bit identical
+                     results.
+  4. Annual test   - Ensures that the model compiles successfully and runs
+                     to completion for an annual simulation.  Validation is
+                     determined by performing a binary comparison on restart
+                     files to a baseline dataset.
+
+--- To generate a baseline dataset for a test case ---
+
+Quickstart (example):
+
+./create.case -t smoke -m conrad -b
+cd smoke_baseline_gx3_conrad_4x1
+./cice.build
+./cice.submit
+# After job finishes, check output
+cat test_output
+
+
+--- To run a test case and compare to a baseline dataset ---
+
+Quickstart (example):
+
+./create.case -t smoke -m conrad -bd /path/to/baseline/restart
+cd smoke_gx3_conrad_4x1
+./cice.build
+./cice.submit
+# After job finishes, check output
+cat test_output
+
+
+--- To run a test case without comparing to a baseline ---
+
+Quickstart (example):
+
+./create.case -t smoke -m conrad
+cd smoke_gx3_conrad_4x1
+./cice.build
+./cice.submit
+# After job finishes, check output
+cat test_output
diff --git a/README_v6 b/README_v6
index eb9efbea8..cee0f26fe 100644
--- a/README_v6
+++ b/README_v6
@@ -30,6 +30,7 @@ create.case generates a case, use "create.case -h" for help with the tool.
   -t is the test name and location (cannot be used with -c).
   -b is used to specify that a baseline dataset is to be generated (only used with -t)
   -bd is used to specify the location of the baseline datasets (only used with -t)
+  -testid is used to specify a test ID (used only with -t)
 
 Several files are placed in the case directory
  - env.${machine} defines the environment

From 4b7b976f32f903146b185b63ac1015d07b1cb5ff Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 15 Jun 2017 15:26:22 +0000
Subject: [PATCH 13/29] add CICE_MACHINE_BASELINE default baseline directory to
 env.<machine> files

---
 configuration/scripts/machines/env.cheyenne    | 1 +
 configuration/scripts/machines/env.conrad      | 1 +
 configuration/scripts/machines/env.cori        | 1 +
 configuration/scripts/machines/env.gordon      | 1 +
 configuration/scripts/machines/env.pinto       | 1 +
 configuration/scripts/machines/env.thunder     | 1 +
 configuration/scripts/machines/env.wolf        | 1 +
 configuration/scripts/machines/env.yellowstone | 1 +
 8 files changed, 8 insertions(+)
 mode change 100644 => 100755 configuration/scripts/machines/env.cheyenne
 mode change 100644 => 100755 configuration/scripts/machines/env.cori
 mode change 100644 => 100755 configuration/scripts/machines/env.gordon
 mode change 100644 => 100755 configuration/scripts/machines/env.pinto
 mode change 100644 => 100755 configuration/scripts/machines/env.thunder
 mode change 100644 => 100755 configuration/scripts/machines/env.wolf
 mode change 100644 => 100755 configuration/scripts/machines/env.yellowstone

diff --git a/configuration/scripts/machines/env.cheyenne b/configuration/scripts/machines/env.cheyenne
old mode 100644
new mode 100755
index df082e551..ff4809d03
--- a/configuration/scripts/machines/env.cheyenne
+++ b/configuration/scripts/machines/env.cheyenne
@@ -12,6 +12,7 @@ module load pio/2.2.0
 setenv CICE_MACHINE_ENVNAME cheyenne
 setenv CICE_MACHINE_WKDIR /glade/scratch/$user/CICE_RUNS
 setenv CICE_MACHINE_INPUTDATA /glade/p/work/dbailey/atm/gx3v2m/NCAR_bulk
+setenv CICE_MACHINE_BASELINE /glade/scratch/$user/CICE_BASELINE
 setenv CICE_MACHINE_SUBMIT "qsub"
 setenv CICE_MACHINE_TPNODE 36
 setenv CICE_MACHINE_ACCT P0000000
diff --git a/configuration/scripts/machines/env.conrad b/configuration/scripts/machines/env.conrad
index 4b7064307..83f65c490 100755
--- a/configuration/scripts/machines/env.conrad
+++ b/configuration/scripts/machines/env.conrad
@@ -34,6 +34,7 @@ limit stacksize unlimited
 setenv CICE_MACHINE_ENVNAME conrad
 setenv CICE_MACHINE_WKDIR $WORKDIR/CICE_RUNS
 setenv CICE_MACHINE_INPUTDATA /p/home/turner/CICE/atm/
+setenv CICE_MACHINE_BASELINE $WORKDIR/CICE_BASELINE
 setenv CICE_MACHINE_SUBMIT "qsub "
 setenv CICE_MACHINE_ACCT ARLAP96070PET
 setenv CICE_MACHINE_TPNODE 32    # tasks per node
diff --git a/configuration/scripts/machines/env.cori b/configuration/scripts/machines/env.cori
old mode 100644
new mode 100755
index b639a5b20..83cb9ba4c
--- a/configuration/scripts/machines/env.cori
+++ b/configuration/scripts/machines/env.cori
@@ -36,6 +36,7 @@ limit stacksize unlimited
 setenv CICE_MACHINE_ENVNAME cori
 setenv CICE_MACHINE_WKDIR $SCRATCH/CICE_RUNS
 setenv CICE_MACHINE_INPUTDATA /global/homes/t/tcraig/cice_data/
+setenv CICE_MACHINE_BASELINE $SCRATCH/CICE_BASELINE
 setenv CICE_MACHINE_SUBMIT "sbatch "
 setenv CICE_MACHINE_ACCT P00000000
 setenv CICE_MACHINE_TPNODE 32    # tasks per node
diff --git a/configuration/scripts/machines/env.gordon b/configuration/scripts/machines/env.gordon
old mode 100644
new mode 100755
index 067e7210b..48412836d
--- a/configuration/scripts/machines/env.gordon
+++ b/configuration/scripts/machines/env.gordon
@@ -34,6 +34,7 @@ limit stacksize unlimited
 setenv CICE_MACHINE_ENVNAME gordon
 setenv CICE_MACHINE_WKDIR $WORKDIR/CICE_RUNS
 setenv CICE_MACHINE_INPUTDATA /p/work1/RASM_data/cice_data/
+setenv CICE_MACHINE_BASELINE $WORKDIR/CICE_BASELINE
 setenv CICE_MACHINE_SUBMIT "qsub "
 setenv CICE_MACHINE_ACCT P00000000
 setenv CICE_MACHINE_TPNODE 32    # tasks per node
diff --git a/configuration/scripts/machines/env.pinto b/configuration/scripts/machines/env.pinto
old mode 100644
new mode 100755
index 185b8c3e2..a2d17135c
--- a/configuration/scripts/machines/env.pinto
+++ b/configuration/scripts/machines/env.pinto
@@ -20,6 +20,7 @@ setenv PNETCDF_PATH /usr/projects/climate/SHARED_CLIMATE/software/conejo/paralle
 setenv CICE_MACHINE_ENVNAME pinto
 setenv CICE_MACHINE_WKDIR /net/scratch3/$user/CICE_RUNS
 setenv CICE_MACHINE_INPUTDATA /usr/projects/climate/eclare/DATA/atm/gx3v2m/NCAR_bulk/
+setenv CICE_MACHINE_BASELINE /net/scratch3/$user/CICE_BASELINE
 setenv CICE_MACHINE_SUBMIT "sbatch "
 setenv CICE_MACHINE_ACCT climateacme
 setenv CICE_MACHINE_TPNODE 16
diff --git a/configuration/scripts/machines/env.thunder b/configuration/scripts/machines/env.thunder
old mode 100644
new mode 100755
index a8b8f0ffc..915e6e379
--- a/configuration/scripts/machines/env.thunder
+++ b/configuration/scripts/machines/env.thunder
@@ -28,6 +28,7 @@ setenv NETCDF_PATH /app/COST/netcdf-fortran/4.4.2/intel
 setenv CICE_MACHINE_ENVNAME thunder
 setenv CICE_MACHINE_WKDIR $WORKDIR/CICE_RUNS
 setenv CICE_MACHINE_INPUTDATA /p/work2/projects/rasm/cice_data/
+setenv CICE_MACHINE_BASELINE $WORKDIR/CICE_BASELINE
 setenv CICE_MACHINE_SUBMIT "qsub "
 setenv CICE_MACHINE_ACCT P00000000
 setenv CICE_MACHINE_TPNODE 36    # tasks per node
diff --git a/configuration/scripts/machines/env.wolf b/configuration/scripts/machines/env.wolf
old mode 100644
new mode 100755
index 5f63134ea..c0247722a
--- a/configuration/scripts/machines/env.wolf
+++ b/configuration/scripts/machines/env.wolf
@@ -20,6 +20,7 @@ setenv PNETCDF_PATH /usr/projects/climate/SHARED_CLIMATE/software/conejo/paralle
 setenv CICE_MACHINE_ENVNAME wolf
 setenv CICE_MACHINE_WKDIR /net/scratch3/$user/CICE_RUNS
 setenv CICE_MACHINE_INPUTDATA /usr/projects/climate/eclare/DATA/atm/gx3v2m/NCAR_bulk/
+setenv CICE_MACHINE_BASELINE /net/scratch3/$user/CICE_BASELINE
 setenv CICE_MACHINE_SUBMIT "sbatch "
 setenv CICE_MACHINE_ACCT climateacme
 setenv CICE_MACHINE_TPNODE 16
diff --git a/configuration/scripts/machines/env.yellowstone b/configuration/scripts/machines/env.yellowstone
old mode 100644
new mode 100755
index c93668966..d5dc9312b
--- a/configuration/scripts/machines/env.yellowstone
+++ b/configuration/scripts/machines/env.yellowstone
@@ -24,6 +24,7 @@ setenv LAPACK_LIBDIR /glade/apps/opt/lapack/3.4.2/intel/12.1.5/lib
 setenv CICE_MACHINE_ENVNAME yellowstone
 setenv CICE_MACHINE_WKDIR /glade/scratch/$user/CICE_RUNS
 setenv CICE_MACHINE_INPUTDATA /glade/u/home/tcraig/cice_data/
+setenv CICE_MACHINE_BASELINE /glade/scratch/$user/CICE_BASELINE
 setenv CICE_MACHINE_SUBMIT "bsub < "
 setenv CICE_MACHINE_ACCT P00000000
 setenv CICE_MACHINE_TPNODE 32

From a3c6c857785f7dbb9bb17e44160939b262259f41 Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 15 Jun 2017 15:27:08 +0000
Subject: [PATCH 14/29] bugfix for cheyenne machine.  Also added error if using
 unknown machine

---
 configuration/scripts/cice.batch.csh  | 5 ++++-
 configuration/scripts/cice.launch.csh | 5 ++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/configuration/scripts/cice.batch.csh b/configuration/scripts/cice.batch.csh
index eea17c863..38105cbfb 100755
--- a/configuration/scripts/cice.batch.csh
+++ b/configuration/scripts/cice.batch.csh
@@ -50,7 +50,7 @@ EOFB
 
 #==========================================
 
-elseif (${CICE_MACHINE} =~ cheyenne*) then
+else if (${CICE_MACHINE} =~ cheyenne*) then
 cat >> ${jobfile} << EOFB
 #PBS -j oe 
 #PBS -m ae 
@@ -115,4 +115,7 @@ cat >> ${jobfile} << EOFB
 #SBATCH --qos=standby
 EOFB
 
+else
+  echo "${0} ERROR ${CICE_MACHINE} unknown"
+  exit -1
 endif
diff --git a/configuration/scripts/cice.launch.csh b/configuration/scripts/cice.launch.csh
index 4ee2805af..fbdeb9a02 100755
--- a/configuration/scripts/cice.launch.csh
+++ b/configuration/scripts/cice.launch.csh
@@ -17,7 +17,7 @@ setenv MP_TASK_AFFINITY core:\${OMP_NUM_THREADS}
 mpirun.lsf ./cice >&! \$CICE_RUNLOG_FILE
 EOFR
 
-elseif (${CICE_MACHINE} =~ cheyenne*) then
+else if (${CICE_MACHINE} =~ cheyenne*) then
 cat >> ${jobfile} << EOFR
 mpiexec_mpt -n ${ntasks} ./cice >&! \$CICE_RUNLOG_FILE
 EOFR
@@ -50,4 +50,7 @@ EOFR
 #srun -n ${ntasks} -c ${nthrds} ./cice >&! \$CICE_RUNLOG_FILE
 #EOFR
 
+else
+  echo "${0} ERROR ${CICE_MACHINE} unknown"
+  exit -1
 endif

From 473d158e478accc426d9d90390544caae616e10d Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 15 Jun 2017 15:27:52 +0000
Subject: [PATCH 15/29] Check return status of calls to cice.launch.csh and
 cice.batch.csh.  Remove writing to test_output from cice.run.setup.csh

---
 configuration/scripts/cice.run.setup.csh | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/configuration/scripts/cice.run.setup.csh b/configuration/scripts/cice.run.setup.csh
index 3f341a24c..e189d7576 100755
--- a/configuration/scripts/cice.run.setup.csh
+++ b/configuration/scripts/cice.run.setup.csh
@@ -14,6 +14,9 @@ set nthrds = ${CICE_NTHRDS}
 
 # Write the batch code into the job file
 $1/cice.batch.csh ${jobfile}
+if ($? == -1) then
+  exit -1
+endif
 
 #==========================================
 
@@ -56,6 +59,9 @@ EOF1
 
 # Write the job launching logic into the job file
 $1/cice.launch.csh ${jobfile}
+if ($? == -1) then
+  exit -1
+endif
 
 #==========================================
 
@@ -71,19 +77,12 @@ cp -p \${CICE_RUNLOG_FILE} \${CICE_LOGDIR}
 grep ' CICE COMPLETED SUCCESSFULLY' \${CICE_RUNLOG_FILE}
 if ( \$? != 0 ) then
   echo "CICE run did not complete - see \${CICE_LOGDIR}/\${CICE_RUNLOG_FILE}"
-  if ( \$?CICE_TEST ) then
-    echo "FAIL \${CICE_CASENAME} run" >> \${CICE_CASEDIR}/test_output
-  endif
   exit -1
 endif
 
 echo "\`date\` \${0}: \${CICE_CASENAME} run completed \${CICE_RUNLOG_FILE}"  >> \${CICE_CASEDIR}/README.case
 echo "done \${0}"
 
-if ( \$?CICE_TEST ) then
-  echo "PASS \${CICE_CASENAME} run" >> \${CICE_CASEDIR}/test_output
-endif
-
 EOFE
 
 #==========================================

From 91e432f317ab5a37838618968a8319935ee77356 Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 15 Jun 2017 15:28:25 +0000
Subject: [PATCH 16/29] Update the documentation for the recent modifications
 to create.case

---
 README_v6 | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/README_v6 b/README_v6
index cee0f26fe..1a6ad2440 100644
--- a/README_v6
+++ b/README_v6
@@ -22,7 +22,7 @@ cd ~/mycase1
 A bit more information:
 
 create.case generates a case, use "create.case -h" for help with the tool.
-  -c is the case name and location (required)
+  -c is the case name and location
   -m is the machine name (required)
   -g is the resolution (default is gx3)
   -p is the task x thread/task values (default is 4x1)
@@ -30,6 +30,8 @@ create.case generates a case, use "create.case -h" for help with the tool.
   -t is the test name and location (cannot be used with -c).
   -b is used to specify that a baseline dataset is to be generated (only used with -t)
   -bd is used to specify the location of the baseline datasets (only used with -t)
+  -bg is used to specify the cice version name for generating baseline datasets (only used with -t)
+  -bc is used to specify the cice versoin name for comparison. I.e., the version name for the baseline dataset (only used with -t)
   -testid is used to specify a test ID (used only with -t)
 
 Several files are placed in the case directory

From 16b7c4b904eab4469c29a3cf983c85b68e42f973 Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 15 Jun 2017 15:30:42 +0000
Subject: [PATCH 17/29] Add output to beginning of cice.tests.csh that prints
 information about the test (baseline generating?  baseline directory, etc.). 
 Add output to test_output after call to cice.run.  Add conditional to check
 for output data if the test is a baseline-generating test, and write
 PASS/FAIL to test_output

---
 configuration/scripts/tests/cice.test.csh | 51 +++++++++++++++++++----
 1 file changed, 44 insertions(+), 7 deletions(-)

diff --git a/configuration/scripts/tests/cice.test.csh b/configuration/scripts/tests/cice.test.csh
index 8319572cd..1de419768 100755
--- a/configuration/scripts/tests/cice.test.csh
+++ b/configuration/scripts/tests/cice.test.csh
@@ -2,12 +2,9 @@
 
 echo ${0}
 
-# Define this as a test case in the cice.settings file
-cat >> ./cice.settings << EOF
-
-# Add variable defining this case_dir as a test
-setenv CICE_TEST true
-EOF
+# $1 = ${CICE_SCRDIR}
+# $2 = $baseline
+# $3 = baseline (compare) directory
 
 source ./cice.settings
 source ${CICE_CASEDIR}/env.${CICE_MACHINE} || exit 2
@@ -19,11 +16,27 @@ set nthrds = ${CICE_NTHRDS}
 
 #==========================================
 
+# Print information about this test to stdout
+echo ""
+echo "Test case directory: ${CICE_CASEDIR}"
+if ($2 == 1) then
+  # This is a baseline generating run
+  echo "This is a baseline-generating test."
+  echo "Baseline datasets will be stored in: ${CICE_RUNDIR}"
+else
+  # This is not a baseline-generating run
+  echo "This is not a baseline-generating run."
+  echo "Test data will be compared to data in $3"
+endif
+
 # Create test script that runs cice.run, and validates
 #==========================================
 
 # Write the batch code into the job file
 $1/cice.batch.csh ${jobfile}
+if ($? == -1) then
+  exit -1
+endif
 
 cat >> ${jobfile} << EOF2
 cd ${CICE_CASEDIR}
@@ -39,10 +52,19 @@ endif
 
 # Run the CICE model
 ./cice.run
+if ( \$? != 0 ) then
+  # Run failed
+  echo "FAIL \${CICE_CASENAME} run" >> \${CICE_CASEDIR}/test_output
+  exit 99
+else
+  # Run succeeded
+  echo "PASS \${CICE_CASENAME} run" >> \${CICE_CASEDIR}/test_output
+endif
 
 EOF2
 
-if ($2 != "") then
+if ($2 == 0) then
+  # Not a baseline-generating test
 cat >> ${jobfile} << EOF3
   # Get the final output filename
   foreach file (\${CICE_RUNDIR}/restart/*)
@@ -60,6 +82,21 @@ cat >> ${jobfile} << EOF3
     echo "FAIL \${CICE_CASENAME} test" >> ${CICE_CASEDIR}/test_output
   endif
 EOF3
+else
+  # Baseline generating run
+cat >> ${jobfile} << EOF3
+  # Get the final output filename
+  foreach file (\${CICE_RUNDIR}/restart/*)
+    set test_data = \$file
+  end
+  
+  if ( \$test_data != "" ) then
+    echo "PASS \${CICE_CASENAME} generate" >> ${CICE_CASEDIR}/test_output
+  else
+    echo "FAIL \${CICE_CASENAME} generate" >> ${CICE_CASEDIR}/test_output
+  endif
+EOF3
+
 endif
 
 #==========================================

From ff71bdbc72ba7c6a62a93ac56a3b2d047bcdbfb9 Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 15 Jun 2017 15:31:14 +0000
Subject: [PATCH 18/29] add default CICE_TEST and CICE_BASELINE variables to
 cice.settings file

---
 configuration/scripts/cice.settings | 2 ++
 1 file changed, 2 insertions(+)
 mode change 100644 => 100755 configuration/scripts/cice.settings

diff --git a/configuration/scripts/cice.settings b/configuration/scripts/cice.settings
old mode 100644
new mode 100755
index 6c0d080ba..e578cfa38
--- a/configuration/scripts/cice.settings
+++ b/configuration/scripts/cice.settings
@@ -24,6 +24,8 @@ setenv CICE_BLCKY      29
 setenv CICE_MXBLCKS    4
 setenv CICE_DECOMP     cartesian
 setenv CICE_DSHAPE     slenderX2
+setenv CICE_TEST       false       # Define if this is a test case
+setenv CICE_BASELINE   undefined
 
 #======================================================
 

From 5729c9506b4a5ffaf584aaffc60220d376ee09fe Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 15 Jun 2017 15:34:14 +0000
Subject: [PATCH 19/29] Assign a default testid.  Add new baseCom (-bc) and
 baseGen (-bg) arguments.  Remove 'baseline' from casename.  Always add testid
 to casename if running a test and not generating a baseline dataset.  Add new
 code to modify CICE_RUNDIR to the baseline directory if generating a baseline
 dataset.  Add new code to modify CICE_BASELINE to the baseline directory if
 not generating a baseline dataset.  Modification to how cice.test.csh is
 called.

---
 create.case | 100 ++++++++++++++++++++++++++++++++++++----------------
 1 file changed, 69 insertions(+), 31 deletions(-)

diff --git a/create.case b/create.case
index e462ddbd7..f686a28ab 100755
--- a/create.case
+++ b/create.case
@@ -18,7 +18,9 @@ set pesx = 4x1
 set sets = ""
 set baseline = 0
 set bdir = $spval
-set testid = $spval
+set testid = "t00"
+set baseCom = $spval  # Baseline compare
+set baseGen = $spval  # Baseline generate
 
 if ($#argv < 1) then
   set helpheader = 1
@@ -42,7 +44,7 @@ cat << EOF1
 NAME   
       create.case - creates a CICE case directory
         -h help
-        -c case, case directory/name (required)
+        -c case, case directory/name
         -m machine, machine name (required)
         -p tasks x threads, mxn (default is 4x1)
         -g grid, grid (default = gx3)
@@ -55,15 +57,19 @@ NAME
              - "10day": Compiles code and performs 10 day run
              - "annual": Compiles code and performs annual run
              - "restart": Compiles code and performs an exact restart test
-        -b baseline, generate baseline data
-        -bd baseline dir, location of baseline dataset
-        -testid test ID, user-defined indentifier for test
+        -b generate baseline data (this does NOT take an argument)
+        -bd baseline directory, high level directory where baselines are stored
+        -bg cice version name for generate, directory under the baseline directory where baselines are stored
+        -bc cice version name for compare, directory under the baseline directory where baselines are stored
+        -testid test ID, user-defined indentifier for test (default = t00)
 
       EXAMPLES:
       create.case -h
       create.case -c ~/caseA -m yellowstone 
       create.case -p 32x4 -g gx1 -m gordon -c caseB
       create.case -c ~/caseC -m spirit -s diag1,writeicf
+   
+      For testing instructions, please view README.test
 
 EOF1
 exit -1
@@ -114,6 +120,12 @@ while (1)
     case "-bd":
       set bdir = $argv[1]
       breaksw
+    case "-bc":
+      set baseCom = $argv[1]
+      breaksw
+    case "-bg":
+      set baseGen = $argv[1]
+      breaksw
     case "-testid":
       set testid = $argv[1]
       breaksw
@@ -165,32 +177,17 @@ if ($case != $spval) then
 else
   if ($sets != "") then
     set soptions = `echo $sets | sed 's/,/_/g'`
-    if ($baseline == 1) then
-      if ( $testid != $spval ) then
-        set testname = "${test}_baseline_${grid}_${mach}_${pesx}_${soptions}.${testid}"
-      else
-        set testname = "${test}_baseline_${grid}_${mach}_${pesx}_$soptions"
-      endif
+    # Only include $testid in testname if this is not a baseline-generating run
+    if ($baseline == 0) then
+      set testname = "${test}_${grid}_${mach}_${pesx}_${soptions}.${testid}"
     else
-      if ( $testid != $spval ) then
-        set testname = "${test}_${grid}_${mach}_${pesx}_${soptions}.${testid}"
-      else
-        set testname = "${test}_${grid}_${mach}_${pesx}_$soptions"
-      endif
+      set testname = "${test}_${grid}_${mach}_${pesx}_${soptions}"
     endif
   else
-    if ($baseline == 1) then
-      if ( $testid != $spval ) then
-        set testname = "${test}_baseline_${grid}_${mach}_${pesx}.${testid}"
-      else
-        set testname = "${test}_baseline_${grid}_${mach}_$pesx"
-      endif
+    if ($baseline == 0) then
+      set testname = "${test}_${grid}_${mach}_${pesx}.${testid}"
     else
-      if ( $testid != $spval ) then
-        set testname = "${test}_${grid}_${mach}_${pesx}.${testid}"
-      else
-        set testname = "${test}_${grid}_${mach}_$pesx"
-      endif
+      set testname = "${test}_${grid}_${mach}_${pesx}"
     endif
   endif
   if (-d $testname) then
@@ -281,12 +278,48 @@ grid_file         = '${CICE_DECOMP_GRIDFILE}'
 kmt_file          = '${CICE_DECOMP_KMTFILE}'
 EOF1
 
+# If this is a baseline generating test, and baseGen is passed, modify CICE_RUNDIR
+if ($test != $spval && $baseline == 1) then
+  if ($baseGen != $spval) then
+    if ($bdir != $spval) then
+      setenv rundir_tmp ${bdir}/$baseGen
+    else
+      setenv rundir_tmp ${CICE_MACHINE_BASELINE}/$baseGen
+    endif
+  else
+    if ($bdir != $spval) then
+      setenv rundir_tmp ${bdir}
+    else
+      setenv rundir_tmp ${CICE_MACHINE_BASELINE}
+    endif
+  endif
+else
+  setenv rundir_tmp ${CICE_MACHINE_WKDIR}
+endif
+
+# If this is a baseline-compare test, modify CICE_RUNDIR
+if ($test != $spval && $baseline == 0) then
+  if ($baseCom != $spval)then
+    if ($bdir != $spval) then
+      setenv basedir_tmp ${bdir}/$baseCom
+    else
+      setenv basedir_tmp ${CICE_MACHINE_BASELINE}/$baseCom
+    endif
+  else
+    if ($bdir != $spval) then
+      setenv basedir_tmp ${bdir}
+    else
+      setenv basedir_tmp ${CICE_MACHINE_BASELINE}
+    endif
+  endif
+endif
+
 cat >! ${fsmods} << EOF1
 setenv CICE_SANDBOX  ${CICE_SANDBOX}
 setenv CICE_CASENAME ${casename}
 setenv CICE_CASEDIR  ${casedir}
 setenv CICE_MACHINE  ${mach}
-setenv CICE_RUNDIR   ${CICE_MACHINE_WKDIR}/${casename}
+setenv CICE_RUNDIR   ${rundir_tmp}/${casename}
 setenv CICE_GRID     ${grid}
 setenv CICE_NXGLOB   ${CICE_DECOMP_NXGLOB}
 setenv CICE_NYGLOB   ${CICE_DECOMP_NYGLOB}
@@ -298,6 +331,7 @@ setenv CICE_MXBLCKS  ${CICE_DECOMP_MXBLCKS}
 setenv CICE_BLCKX    ${CICE_DECOMP_BLCKX}
 setenv CICE_BLCKY    ${CICE_DECOMP_BLCKY}
 setenv CICE_RSTPFILE ${CICE_DECOMP_RSTPFILE}
+setenv CICE_BASELINE ${basedir_tmp}
 EOF1
 
 if ($#sets > 0) then
@@ -327,6 +361,8 @@ if ($test != $spval) then
     echo "adding namelist mods test_nml.${test}"
     set found = 1
   endif
+  # Define this as a test case
+  echo "setenv CICE_TEST true" >> ${fsmods}
   if (${found} == 0) then
     echo "${0}: ERROR, ${CICE_SCRDIR}/options/test_nml.${name} not found"
     exit -1
@@ -347,16 +383,18 @@ ${casescr}/cice.run.setup.csh ${CICE_SCRDIR}
 #------------------------------------------------------------
 
 if ($test != $spval) then
+  # Print information to stdout
+  echo "Creating scripts for $test test"
+
   # Generate test script
   if ($test == 'restart') then
     ${CICE_SCRDIR}/tests/cice.restart.csh ${CICE_SCRDIR}
-  else if ($bdir != $spval) then
-    ${CICE_SCRDIR}/tests/cice.test.csh ${CICE_SCRDIR} $bdir
   else
-    ${CICE_SCRDIR}/tests/cice.test.csh ${CICE_SCRDIR}
+    ${CICE_SCRDIR}/tests/cice.test.csh ${CICE_SCRDIR} $baseline ${CICE_BASELINE}/$casename
   endif
 endif
 
+echo " "
 echo "${0} done"
 echo " "
 

From 648209034558f54b6fa6f321abcfa142fb618abf Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 15 Jun 2017 16:32:52 +0000
Subject: [PATCH 20/29] Add PASS/FAIL commands to cice.restart.csh after calls
 to cice.run.  Replace calls to perl (when modifying namelists) with a call to
 parse_namelist.sh.  Slight modifications to allow for the restart case to be
 re-run successfully.

---
 configuration/scripts/tests/cice.restart.csh | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/configuration/scripts/tests/cice.restart.csh b/configuration/scripts/tests/cice.restart.csh
index ab1e43d97..d1338db9c 100755
--- a/configuration/scripts/tests/cice.restart.csh
+++ b/configuration/scripts/tests/cice.restart.csh
@@ -40,7 +40,10 @@ endif
 # Run the CICE model for the 2-day simulation
 ./cice.run
 if ( \$? != 0 ) then
+  echo "FAIL \${CICE_CASENAME} 2-day-run" >> \${CICE_CASEDIR}/test_output
   exit 99
+else
+  echo "PASS \${CICE_CASENAME} 2-day-run" >> \${CICE_CASEDIR}/test_output
 endif
 
 # Prepend 'baseline_' to the final restart file to save for comparison
@@ -54,15 +57,18 @@ mv \$test_data \$baseline_data
 perl -i -pe's/(\d{4})-(\d{2})-(\d{2})/sprintf("%04d-%02d-%02d",\$1,\$2,\$3-1)/e' \${CICE_RUNDIR}/ice.restart_file
 
 # Modify the namelist for the restart simulation
-cp ice_in ice_in.restart_full
-perl -i -pe"s/(npt\s+=)\s(\d+)/\1 24/" ice_in  # replace npt = 48 with npt = 24
-perl -i -pe"s/(dumpfreq_n\s+=)\s(\d+)/\1 1/" ice_in   # replace dump freq with 1
-perl -i -pe"s/(runtype\s+=)\s(\S+)/\1 'continue'/" ice_in   # runtype with continuation
+cp ice_in ice_in.2-day
+\${CICE_CASEDIR}/casescripts/parse_namelist.sh ice_in \${CICE_CASEDIR}/casescripts/test_nml.restart2
 
 # Run the CICE model for the restart simulation
 ./cice.run
+cp ice_in ice_in.restart
+cp ice_in.2-day ice_in
 if ( \$? != 0 ) then
+  echo "FAIL \${CICE_CASENAME} restart-run" >> \${CICE_CASEDIR}/test_output
   exit 99
+else
+  echo "PASS \${CICE_CASENAME} restart-run" >> \${CICE_CASEDIR}/test_output
 endif
 
 EOF2
@@ -72,9 +78,9 @@ echo "Performing binary comparison between files:"
 echo "baseline: \$baseline_data"
 echo "test:     \$test_data"
 if ( { cmp -s \$test_data \$baseline_data } ) then
-  echo "PASS \${CICE_CASENAME} test" >> ${CICE_CASEDIR}/test_output
+  echo "PASS \${CICE_CASENAME} compare" >> ${CICE_CASEDIR}/test_output
 else
-  echo "FAIL \${CICE_CASENAME} test" >> ${CICE_CASEDIR}/test_output
+  echo "FAIL \${CICE_CASENAME} compare" >> ${CICE_CASEDIR}/test_output
 endif
 EOF3
 

From f5e45431775d55efc5b94e388b29e6f6439af05c Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 15 Jun 2017 16:40:25 +0000
Subject: [PATCH 21/29] For restart test case, create.case now copies new
 test_nml.restart2 file to casescripts directory

---
 create.case | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/create.case b/create.case
index f686a28ab..1f88cbf4e 100755
--- a/create.case
+++ b/create.case
@@ -215,6 +215,15 @@ foreach file (cice.build cice.settings Makefile ice_in makdep.c)
   endif
   cp -f -p ${CICE_SCRDIR}/$file ${casedir}
 end
+# For restart test case, copy extra namelist modification file to casedir
+if ($test == 'restart') then
+  set file = "options/test_nml.restart2"
+  if !(-e ${CICE_SCRDIR}/$file) then
+    echo "${0}: ERROR, ${CICE_SCRDIR}/$file not found"
+    exit -1
+  endif
+  cp -f -p ${CICE_SCRDIR}/$file ${casescr}
+endif
 
 # from machines dir to case
 foreach file (env.${mach} Macros.${mach})

From 374955d3b7be3f52c524664e6671856ae8b2180b Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 15 Jun 2017 16:40:48 +0000
Subject: [PATCH 22/29] add new test_nml.restart2 options file

---
 configuration/scripts/options/test_nml.restart2 | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 configuration/scripts/options/test_nml.restart2

diff --git a/configuration/scripts/options/test_nml.restart2 b/configuration/scripts/options/test_nml.restart2
new file mode 100644
index 000000000..4eefa9f10
--- /dev/null
+++ b/configuration/scripts/options/test_nml.restart2
@@ -0,0 +1,8 @@
+npt            = 24
+dumpfreq       = 'd'
+dumpfreq_n     = 1
+bfbflag        = .true.
+diag_type      = 'stdout'
+print_global   = .true.
+histfreq       = 'd','x','x','x','x'
+runtype        = 'continue'

From 356f958c314dd07958ba0c5819ab6d1bea8e0dc3 Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 15 Jun 2017 20:50:49 +0000
Subject: [PATCH 23/29] Modify README.test to account for the recent updates to
 the testing suite

---
 README.test | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/README.test b/README.test
index 513caac9a..f76619a59 100644
--- a/README.test
+++ b/README.test
@@ -35,7 +35,7 @@ cat test_output
 
 Quickstart (example):
 
-./create.case -t smoke -m conrad -bd /path/to/baseline/restart
+./create.case -t smoke -m conrad
 cd smoke_gx3_conrad_4x1
 ./cice.build
 ./cice.submit
@@ -43,13 +43,27 @@ cd smoke_gx3_conrad_4x1
 cat test_output
 
 
---- To run a test case without comparing to a baseline ---
+--- To run a regression test (compare cicev6.0.1 output to cicev6.0.0 output) ---
 
 Quickstart (example):
 
-./create.case -t smoke -m conrad
+./create.case -t smoke -m conrad -b -bg cicev6.0.1 -bc cicev6.0.0
 cd smoke_gx3_conrad_4x1
 ./cice.build
 ./cice.submit
 # After job finishes, check output
 cat test_output
+
+
+Additional Details:
+- The '-b' flag can be combined with '-bd' to specify the location where you 
+  want the baseline dataset to be written.  Without specifying '-bd', the
+  baseline dataset will be written to the default baseline directory found
+  in the env.<machine> file (CICE_MACHINE_BASELINE).
+- If '-b' is not passed, the '-bd' option will specify the location of the
+  baseline dataset that you want to compare to.  Without specifying '-bd',
+  the scripts will look for baseline datasets in the default baseline 
+  directory found in the env.<machine> file (CICE_MACHINE_BASELINE).
+- To generate a baseline dataset for a specific version (for regression testing),
+  use '-b' in conjunction to '-bg <version_name>'.  The scripts will then place
+  the baseline dataset in $CICE_MACHINE_BASELINE/<version_name>/

From 77160325f96b29759091f7d608a2c1f5720690bd Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 15 Jun 2017 20:52:03 +0000
Subject: [PATCH 24/29] Add logic to handle cases where -bg and -bc are both
 passed.  Bugfix for setting CICE_BASELINE, remove call to cice.restart.csh

---
 create.case | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/create.case b/create.case
index 1f88cbf4e..2840ed192 100755
--- a/create.case
+++ b/create.case
@@ -158,6 +158,11 @@ if ($test != $spval && $test != 'smoke' && $test != '10day' && $test != 'annual'
   exit -1
 endif
 
+# If both -bg and -bc were used, set baseline to 2 (regression test)
+if ($baseGen != $spval && $baseCom != $spval) then
+  set baseline = 2
+endif
+
 set chck = `echo ${pesx} | sed 's/^[0-9]\+x[0-9]\+$/OK/'`
 if (${chck} == OK) then
   set task = `echo ${pesx} | sed s/x.\*//`
@@ -180,14 +185,18 @@ else
     # Only include $testid in testname if this is not a baseline-generating run
     if ($baseline == 0) then
       set testname = "${test}_${grid}_${mach}_${pesx}_${soptions}.${testid}"
+      set testname_noid = "${test}_${grid}_${mach}_${pesx}_${soptions}"
     else
       set testname = "${test}_${grid}_${mach}_${pesx}_${soptions}"
+      set testname_noid = $testname
     endif
   else
     if ($baseline == 0) then
       set testname = "${test}_${grid}_${mach}_${pesx}.${testid}"
+      set testname_noid = "${test}_${grid}_${mach}_${pesx}"
     else
       set testname = "${test}_${grid}_${mach}_${pesx}"
+      set testname_noid = $testname
     endif
   endif
   if (-d $testname) then
@@ -288,7 +297,7 @@ kmt_file          = '${CICE_DECOMP_KMTFILE}'
 EOF1
 
 # If this is a baseline generating test, and baseGen is passed, modify CICE_RUNDIR
-if ($test != $spval && $baseline == 1) then
+if ($test != $spval && $baseline != 0) then
   if ($baseGen != $spval) then
     if ($bdir != $spval) then
       setenv rundir_tmp ${bdir}/$baseGen
@@ -307,7 +316,7 @@ else
 endif
 
 # If this is a baseline-compare test, modify CICE_RUNDIR
-if ($test != $spval && $baseline == 0) then
+if ($test != $spval) then
   if ($baseCom != $spval)then
     if ($bdir != $spval) then
       setenv basedir_tmp ${bdir}/$baseCom
@@ -321,6 +330,8 @@ if ($test != $spval && $baseline == 0) then
       setenv basedir_tmp ${CICE_MACHINE_BASELINE}
     endif
   endif
+else
+  setenv basedir_tmp ${CICE_MACHINE_BASELINE}
 endif
 
 cat >! ${fsmods} << EOF1
@@ -396,11 +407,7 @@ if ($test != $spval) then
   echo "Creating scripts for $test test"
 
   # Generate test script
-  if ($test == 'restart') then
-    ${CICE_SCRDIR}/tests/cice.restart.csh ${CICE_SCRDIR}
-  else
-    ${CICE_SCRDIR}/tests/cice.test.csh ${CICE_SCRDIR} $baseline ${CICE_BASELINE}/$casename
-  endif
+  ${CICE_SCRDIR}/tests/cice.test.csh ${CICE_SCRDIR} $baseline ${CICE_BASELINE}/$testname_noid $test
 endif
 
 echo " "

From 39b3e56d7de4b321bd32f13183f6801999db1231 Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 15 Jun 2017 20:54:02 +0000
Subject: [PATCH 25/29] Add test name as an argument.  Add logic to handle
 regression runs.  Combine the cice.restart.csh and cice.test.csh scripts into
 a single cice.test.csh script.

---
 configuration/scripts/tests/cice.restart.csh | 101 ---------------
 configuration/scripts/tests/cice.test.csh    | 126 ++++++++++++++++---
 2 files changed, 112 insertions(+), 115 deletions(-)
 delete mode 100755 configuration/scripts/tests/cice.restart.csh

diff --git a/configuration/scripts/tests/cice.restart.csh b/configuration/scripts/tests/cice.restart.csh
deleted file mode 100755
index d1338db9c..000000000
--- a/configuration/scripts/tests/cice.restart.csh
+++ /dev/null
@@ -1,101 +0,0 @@
-#! /bin/csh -f
-
-echo ${0}
-
-# Define this as a test case in the cice.settings file
-cat >> ./cice.settings << EOF
-
-# Add variable defining this case_dir as a test
-setenv CICE_TEST true
-EOF
-
-source ./cice.settings
-source ${CICE_CASEDIR}/env.${CICE_MACHINE} || exit 2
-
-set jobfile = cice.test
-set subfile = cice.submit
-
-set nthrds = ${CICE_NTHRDS}
-
-#==========================================
-
-# Create test script that runs cice.run, and validates
-#==========================================
-
-# Write the batch code into the job file
-$1/cice.batch.csh ${jobfile}
-
-cat >> ${jobfile} << EOF2
-cd ${CICE_CASEDIR}
-source ./cice.settings || exit 2
-source ./env.\${CICE_MACHINE} || exit 2
-
-# Check to see if executable exists in CICE_RUNDIR
-if ( ! -f \${CICE_RUNDIR}/cice ) then
-  echo "cice executable does not exist in \${CICE_RUNDIR}.  "
-  echo "Please run cice.build before this test."
-  exit 99
-endif
-
-# Run the CICE model for the 2-day simulation
-./cice.run
-if ( \$? != 0 ) then
-  echo "FAIL \${CICE_CASENAME} 2-day-run" >> \${CICE_CASEDIR}/test_output
-  exit 99
-else
-  echo "PASS \${CICE_CASENAME} 2-day-run" >> \${CICE_CASEDIR}/test_output
-endif
-
-# Prepend 'baseline_' to the final restart file to save for comparison
-foreach file (\${CICE_RUNDIR}/restart/*)
-  set test_data = \$file
-end
-set baseline_data = \${CICE_RUNDIR}/restart/baseline_\$test_data:t
-mv \$test_data \$baseline_data
-
-# Modify the contents of the pointer file for restart
-perl -i -pe's/(\d{4})-(\d{2})-(\d{2})/sprintf("%04d-%02d-%02d",\$1,\$2,\$3-1)/e' \${CICE_RUNDIR}/ice.restart_file
-
-# Modify the namelist for the restart simulation
-cp ice_in ice_in.2-day
-\${CICE_CASEDIR}/casescripts/parse_namelist.sh ice_in \${CICE_CASEDIR}/casescripts/test_nml.restart2
-
-# Run the CICE model for the restart simulation
-./cice.run
-cp ice_in ice_in.restart
-cp ice_in.2-day ice_in
-if ( \$? != 0 ) then
-  echo "FAIL \${CICE_CASENAME} restart-run" >> \${CICE_CASEDIR}/test_output
-  exit 99
-else
-  echo "PASS \${CICE_CASENAME} restart-run" >> \${CICE_CASEDIR}/test_output
-endif
-
-EOF2
-
-cat >> ${jobfile} << EOF3
-echo "Performing binary comparison between files:"
-echo "baseline: \$baseline_data"
-echo "test:     \$test_data"
-if ( { cmp -s \$test_data \$baseline_data } ) then
-  echo "PASS \${CICE_CASENAME} compare" >> ${CICE_CASEDIR}/test_output
-else
-  echo "FAIL \${CICE_CASENAME} compare" >> ${CICE_CASEDIR}/test_output
-endif
-EOF3
-
-#==========================================
-
-chmod +x ${jobfile}
-
-#==========================================
-
-cat >! ${subfile} << EOFS
-#!/bin/csh -f 
-
-${CICE_MACHINE_SUBMIT} ${jobfile}
-echo "\`date\` \${0}: ${CICE_CASENAME} job submitted"  >> ${CICE_CASEDIR}/README.case
-
-EOFS
-
-chmod +x ${subfile}
diff --git a/configuration/scripts/tests/cice.test.csh b/configuration/scripts/tests/cice.test.csh
index 1de419768..ce1c4462f 100755
--- a/configuration/scripts/tests/cice.test.csh
+++ b/configuration/scripts/tests/cice.test.csh
@@ -5,6 +5,7 @@ echo ${0}
 # $1 = ${CICE_SCRDIR}
 # $2 = $baseline
 # $3 = baseline (compare) directory
+# $4 = $test
 
 source ./cice.settings
 source ${CICE_CASEDIR}/env.${CICE_MACHINE} || exit 2
@@ -18,15 +19,22 @@ set nthrds = ${CICE_NTHRDS}
 
 # Print information about this test to stdout
 echo ""
+echo "Test name: $4"
 echo "Test case directory: ${CICE_CASEDIR}"
-if ($2 == 1) then
-  # This is a baseline generating run
-  echo "This is a baseline-generating test."
-  echo "Baseline datasets will be stored in: ${CICE_RUNDIR}"
-else
-  # This is not a baseline-generating run
-  echo "This is not a baseline-generating run."
-  echo "Test data will be compared to data in $3"
+if ($4 != 'restart') then
+  if ($2 == 2) then
+    echo "This is a regression run"
+    echo "Baseline datasets will be stored in: ${CICE_RUNDIR}"
+    echo "Data will be compared to data in $3"
+  else if ($2 == 1) then
+    # This is a baseline generating run
+    echo "This is a baseline-generating test."
+    echo "Baseline datasets will be stored in: ${CICE_RUNDIR}"
+  else
+    # This is not a baseline-generating run
+    echo "This is not a baseline-generating run."
+    echo "Test data will be compared to data in $3"
+  endif
 endif
 
 # Create test script that runs cice.run, and validates
@@ -38,6 +46,10 @@ if ($? == -1) then
   exit -1
 endif
 
+if ($4 == 'restart') then
+  goto restart
+endif
+
 cat >> ${jobfile} << EOF2
 cd ${CICE_CASEDIR}
 source ./cice.settings || exit 2
@@ -71,18 +83,18 @@ cat >> ${jobfile} << EOF3
     set test_data = \$file
   end
   
-  set baseline_data = $2/\$test_data:t
+  set baseline_data = $3/restart/\$test_data:t
 
   echo "Performing binary comparison between files:"
   echo "baseline: \$baseline_data"
   echo "test:     \$test_data"
   if ( { cmp -s \$test_data \$baseline_data } ) then
-    echo "PASS \${CICE_CASENAME} test" >> ${CICE_CASEDIR}/test_output
+    echo "PASS \${CICE_CASENAME} compare" >> ${CICE_CASEDIR}/test_output
   else
-    echo "FAIL \${CICE_CASENAME} test" >> ${CICE_CASEDIR}/test_output
+    echo "FAIL \${CICE_CASENAME} compare" >> ${CICE_CASEDIR}/test_output
   endif
 EOF3
-else
+else if ($2 == 1) then
   # Baseline generating run
 cat >> ${jobfile} << EOF3
   # Get the final output filename
@@ -96,12 +108,98 @@ cat >> ${jobfile} << EOF3
     echo "FAIL \${CICE_CASENAME} generate" >> ${CICE_CASEDIR}/test_output
   endif
 EOF3
+else
+  # Regression run
+cat >> ${jobfile} << EOF3
+  # Get the final output filename
+  foreach file (\${CICE_RUNDIR}/restart/*)
+    set test_data = \$file
+  end
+  
+  if ( \$test_data != "" ) then
+    echo "PASS \${CICE_CASENAME} generate" >> ${CICE_CASEDIR}/test_output
+  else
+    echo "FAIL \${CICE_CASENAME} generate" >> ${CICE_CASEDIR}/test_output
+  endif
 
+  set baseline_data = $3/restart/\$test_data:t
+
+  echo "Performing binary comparison between files:"
+  echo "baseline: \$baseline_data"
+  echo "test:     \$test_data"
+  if ( { cmp -s \$test_data \$baseline_data } ) then
+    echo "PASS \${CICE_CASENAME} compare" >> ${CICE_CASEDIR}/test_output
+  else
+    echo "FAIL \${CICE_CASENAME} compare" >> ${CICE_CASEDIR}/test_output
+  endif
+EOF3
 endif
 
-#==========================================
+goto chmod
+
+restart:
+cat >> ${jobfile} << EOF2
+cd ${CICE_CASEDIR}
+source ./cice.settings || exit 2
+source ./env.\${CICE_MACHINE} || exit 2
+
+# Check to see if executable exists in CICE_RUNDIR
+if ( ! -f \${CICE_RUNDIR}/cice ) then
+  echo "cice executable does not exist in \${CICE_RUNDIR}.  "
+  echo "Please run cice.build before this test."
+  exit 99
+endif
+
+# Run the CICE model for the 2-day simulation
+./cice.run
+if ( \$? != 0 ) then
+  echo "FAIL \${CICE_CASENAME} 2-day-run" >> \${CICE_CASEDIR}/test_output
+  exit 99
+else
+  echo "PASS \${CICE_CASENAME} 2-day-run" >> \${CICE_CASEDIR}/test_output
+endif
+
+# Prepend 'baseline_' to the final restart file to save for comparison
+foreach file (\${CICE_RUNDIR}/restart/*)
+  set test_data = \$file
+end
+set baseline_data = \${CICE_RUNDIR}/restart/baseline_\$test_data:t
+mv \$test_data \$baseline_data
+
+# Modify the contents of the pointer file for restart
+perl -i -pe's/(\d{4})-(\d{2})-(\d{2})/sprintf("%04d-%02d-%02d",\$1,\$2,\$3-1)/e' \${CICE_RUNDIR}/ice.restart_file
 
-chmod +x ${jobfile}
+# Modify the namelist for the restart simulation
+cp ice_in ice_in.2-day
+\${CICE_CASEDIR}/casescripts/parse_namelist.sh ice_in \${CICE_CASEDIR}/casescripts/test_nml.restart2
+
+# Run the CICE model for the restart simulation
+./cice.run
+cp ice_in ice_in.restart
+cp ice_in.2-day ice_in
+if ( \$? != 0 ) then
+  echo "FAIL \${CICE_CASENAME} restart-run" >> \${CICE_CASEDIR}/test_output
+  exit 99
+else
+  echo "PASS \${CICE_CASENAME} restart-run" >> \${CICE_CASEDIR}/test_output
+endif
+
+EOF2
+
+cat >> ${jobfile} << EOF3
+echo "Performing binary comparison between files:"
+echo "baseline: \$baseline_data"
+echo "test:     \$test_data"
+if ( { cmp -s \$test_data \$baseline_data } ) then
+  echo "PASS \${CICE_CASENAME} compare" >> ${CICE_CASEDIR}/test_output
+else
+  echo "FAIL \${CICE_CASENAME} compare" >> ${CICE_CASEDIR}/test_output
+endif
+EOF3
+
+#==========================================
+chmod:
+  chmod +x ${jobfile}
 
 #==========================================
 

From 204fd6ccbeeefb1c0e078002d0548f306c58533f Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 22 Jun 2017 14:17:23 +0000
Subject: [PATCH 26/29] A few corrections in README.test.  Also added a few
 clarifying statements to the README.test file.

---
 README.test | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/README.test b/README.test
index f76619a59..4b8aef28e 100644
--- a/README.test
+++ b/README.test
@@ -13,18 +13,22 @@ CICE Consortium sea ice model.  The tests currently supported are:
                      files to a baseline dataset.
   3. Exact restart - Ensures that the output from a cold-start simulation
                      and a restart simulation provide bit-for-bit identical
-                     results.
+                     results.  No baseline dataset needs to be created for 
+                     this test, as the baseline and test datasets are computed
+                     at the same time.
   4. Annual test   - Ensures that the model compiles successfully and runs
                      to completion for an annual simulation.  Validation is
                      determined by performing a binary comparison on restart
                      files to a baseline dataset.
 
+Please run './create.case -h' for additional details.
+
 --- To generate a baseline dataset for a test case ---
 
 Quickstart (example):
 
 ./create.case -t smoke -m conrad -b
-cd smoke_baseline_gx3_conrad_4x1
+cd smoke_gx3_conrad_4x1
 ./cice.build
 ./cice.submit
 # After job finishes, check output
@@ -36,7 +40,7 @@ cat test_output
 Quickstart (example):
 
 ./create.case -t smoke -m conrad
-cd smoke_gx3_conrad_4x1
+cd smoke_gx3_conrad_4x1.t00
 ./cice.build
 ./cice.submit
 # After job finishes, check output
@@ -56,14 +60,16 @@ cat test_output
 
 
 Additional Details:
+- The available options for '-t' are 'smoke', '10day', 'annual', and 'restart'.
+- For a 'restart' test, no baseline dataset needs to be generated or compared against.
 - The '-b' flag can be combined with '-bd' to specify the location where you 
   want the baseline dataset to be written.  Without specifying '-bd', the
   baseline dataset will be written to the default baseline directory found
   in the env.<machine> file (CICE_MACHINE_BASELINE).
-- If '-b' is not passed, the '-bd' option will specify the location of the
-  baseline dataset that you want to compare to.  Without specifying '-bd',
-  the scripts will look for baseline datasets in the default baseline 
-  directory found in the env.<machine> file (CICE_MACHINE_BASELINE).
+- If neither '-b' or '-bd' are passed, the scripts will look for baseline datasets
+  in the default baseline directory found in the env.<machine> file (CICE_MACHINE_BASELINE).
+  If the '-bd' option is passed, the scripts will look for baseline datasets in the
+  location passed to the -bd argument.
 - To generate a baseline dataset for a specific version (for regression testing),
   use '-b' in conjunction to '-bg <version_name>'.  The scripts will then place
   the baseline dataset in $CICE_MACHINE_BASELINE/<version_name>/

From cb845efe77ededa6790524bac7e7c642925fb52d Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 22 Jun 2017 14:22:46 +0000
Subject: [PATCH 27/29] Change diagfreq from once per year to daily for annual
 test case

---
 configuration/scripts/options/test_nml.annual | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/configuration/scripts/options/test_nml.annual b/configuration/scripts/options/test_nml.annual
index 43006c3cc..3b5850fa8 100644
--- a/configuration/scripts/options/test_nml.annual
+++ b/configuration/scripts/options/test_nml.annual
@@ -1,7 +1,7 @@
 npt            = 8760
 dumpfreq       = 'm'
 dumpfreq_n     = 12
-diagfreq       = 8760
+diagfreq       = 24
 bfbflag        = .true.
 diag_type      = 'stdout'
 print_global   = .true.

From 544567135b2b3d2b1d866402dc6c41cb75861f83 Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Thu, 22 Jun 2017 14:27:51 +0000
Subject: [PATCH 28/29] Update the list of available tests in README.test to
 also specify the argument passed to '-t' in order to create the test case

---
 README.test | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/README.test b/README.test
index 4b8aef28e..c73f6eb20 100644
--- a/README.test
+++ b/README.test
@@ -6,20 +6,24 @@ CICE Consortium sea ice model.  The tests currently supported are:
   1. "Smoke" test  - Ensures that the model compiles successfully and runs
                      to completion for a 1 day simulation.  Validation is
                      determined by performing a binary comparison on restart
-                     files to a baseline dataset.
+                     files to a baseline dataset.  This test is created by
+                     passing 'smoke' to the '-t' argument.
   2. 10-day test   - Ensures that the model compiles successfully and runs
                      to completion for a 10 day simulation.  Validation is
                      determined by performing a binary comparison on restart
-                     files to a baseline dataset.
+                     files to a baseline dataset.  This test is created by 
+                     passing '10day' to the '-t' argument.
   3. Exact restart - Ensures that the output from a cold-start simulation
                      and a restart simulation provide bit-for-bit identical
                      results.  No baseline dataset needs to be created for 
                      this test, as the baseline and test datasets are computed
-                     at the same time.
+                     at the same time.  This test is created by passing 'restart'
+                     to the '-t' argument.
   4. Annual test   - Ensures that the model compiles successfully and runs
                      to completion for an annual simulation.  Validation is
                      determined by performing a binary comparison on restart
-                     files to a baseline dataset.
+                     files to a baseline dataset.  This test is created by 
+                     passing 'annual' to the '-t' argument.
 
 Please run './create.case -h' for additional details.
 

From 3984d9970d6f7227c262321c0b25ff29c207a054 Mon Sep 17 00:00:00 2001
From: mattdturner <matt.turner.ctr@engilitycorp.com>
Date: Tue, 27 Jun 2017 15:54:33 +0000
Subject: [PATCH 29/29] Add information about the -testid flag to README.test

---
 README.test | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/README.test b/README.test
index c73f6eb20..248b23c38 100644
--- a/README.test
+++ b/README.test
@@ -67,13 +67,16 @@ Additional Details:
 - The available options for '-t' are 'smoke', '10day', 'annual', and 'restart'.
 - For a 'restart' test, no baseline dataset needs to be generated or compared against.
 - The '-b' flag can be combined with '-bd' to specify the location where you 
-  want the baseline dataset to be written.  Without specifying '-bd', the
-  baseline dataset will be written to the default baseline directory found
-  in the env.<machine> file (CICE_MACHINE_BASELINE).
+    want the baseline dataset to be written.  Without specifying '-bd', the
+    baseline dataset will be written to the default baseline directory found
+    in the env.<machine> file (CICE_MACHINE_BASELINE).
 - If neither '-b' or '-bd' are passed, the scripts will look for baseline datasets
-  in the default baseline directory found in the env.<machine> file (CICE_MACHINE_BASELINE).
-  If the '-bd' option is passed, the scripts will look for baseline datasets in the
-  location passed to the -bd argument.
+    in the default baseline directory found in the env.<machine> file (CICE_MACHINE_BASELINE).
+    If the '-bd' option is passed, the scripts will look for baseline datasets in the
+    location passed to the -bd argument.
 - To generate a baseline dataset for a specific version (for regression testing),
-  use '-b' in conjunction to '-bg <version_name>'.  The scripts will then place
-  the baseline dataset in $CICE_MACHINE_BASELINE/<version_name>/
+    use '-b' in conjunction to '-bg <version_name>'.  The scripts will then place
+    the baseline dataset in $CICE_MACHINE_BASELINE/<version_name>/
+- The '-testid' flag allows users to specify a testing id that will be added to the
+    end of the case directory.  For example, "./create.case -m conrad -t smoke -testid t12"
+    creates the directory smoke_gx3_conrad_4x1.t12.  The default test id is "t00".