streamline run_jedi_exe ctests (#223)

NOAA-EMC · Feb 6, 2023 · 9dbc973 · 9dbc973
1 parent 9029966
commit 9dbc973
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Showing 5 changed files with 104 additions and 106 deletions.
diff --git a/test/atm/CMakeLists.txt b/test/atm/CMakeLists.txt
@@ -25,6 +25,21 @@ if (BUILD_GDASBUNDLE)
           ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/ush:$ENV{PYTHONPATH}"
   )
 
+  # test for ush/run_jedi_exe.py 3dhofx
+  add_test(NAME test_gdasapp_run_jedi_exe_3dhofx
+           COMMAND ${PROJECT_SOURCE_DIR}/test/atm/run_jedi_exe_3dhofx.sh ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
+           WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/)
+
+  # test for ush/run_jedi_exe.py 3dvar
+  add_test(NAME test_gdasapp_run_jedi_exe_3dvar
+           COMMAND ${PROJECT_SOURCE_DIR}/test/atm/run_jedi_exe_3dvar.sh ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
+           WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/)
+
+  # test for ush/run_jedi_exe.py letkf
+  add_test(NAME test_gdasapp_run_jedi_exe_letkf
+           COMMAND ${PROJECT_SOURCE_DIR}/test/atm/run_jedi_exe_letkf.sh ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
+           WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/)
+
 # Test exgdas scripts from the global-worflow
   if (WORKFLOW_TESTS)
     add_subdirectory(global-workflow)

diff --git a/test/atm/global-workflow/CMakeLists.txt b/test/atm/global-workflow/CMakeLists.txt
@@ -35,22 +35,3 @@ add_test(NAME test_gdasapp_atm_jjob_ens_post
   COMMAND ${PROJECT_SOURCE_DIR}/test/atm/global-workflow/jjob_ens_post.sh
           ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
   WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/atm/global-workflow/testrun)
-
-# run_jedi_exe ctests do not require g-w.  place here due to longer run time
-# test for ush/run_jedi_exe.py 3dhofx
-add_test(NAME test_gdasapp_run_jedi_exe_3dhofx
-  COMMAND ${PROJECT_SOURCE_DIR}/test/atm/global-workflow/run_jedi_exe_3dhofx.sh
-          ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
-  WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/atm/global-workflow/testrun)
-
-# test for ush/run_jedi_exe.py 3dvar
-add_test(NAME test_gdasapp_run_jedi_exe_3dvar
-  COMMAND ${PROJECT_SOURCE_DIR}/test/atm/global-workflow/run_jedi_exe_3dvar.sh
-          ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
-  WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/atm/global-workflow/testrun)
-
-# test for ush/run_jedi_exe.py letkf
-add_test(NAME test_gdasapp_run_jedi_exe_letkf
-  COMMAND ${PROJECT_SOURCE_DIR}/test/atm/global-workflow/run_jedi_exe_letkf.sh
-          ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
-  WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/atm/global-workflow/testrun)
diff --git a/...tm/global-workflow/run_jedi_exe_3dhofx.sh → test/atm/run_jedi_exe_3dhofx.sh b/...tm/global-workflow/run_jedi_exe_3dhofx.sh → test/atm/run_jedi_exe_3dhofx.sh
@@ -4,6 +4,7 @@ set -x
 bindir=$1
 srcdir=$2
 
+# Identify machine
 if [[ -d /scratch1 ]] ; then
     machine="hera"
 elif [[ -d /work ]] ; then
@@ -13,12 +14,14 @@ else
     exit 99
 fi
 
+# Load modules
 set +x
 module use ${srcdir}/modulefiles
 module load GDAS/${machine}
 set -x
 module list
 
+# Set machine dependent variables
 if [ "$machine" = "hera" ] ; then
     partition="hera"
     gdasfix="/scratch1/NCEPDEV/da/Cory.R.Martin/GDASApp/fix"
@@ -27,9 +30,11 @@ elif [ "$machine" = "orion" ]; then
     gdasfix="/work2/noaa/da/cmartin/GDASApp/fix"
 fi
 
+# Create test run directory
 mkdir -p ${bindir}/test/atm/global-workflow/testrun/gdas_single_test_hofx3d
 cd ${bindir}/test/atm/global-workflow/testrun/gdas_single_test_hofx3d
 
+# Create input yaml
 cat > ./3dhofx_example.yaml << EOF
 working directory: ./
 GDASApp home: ${srcdir}
@@ -44,9 +49,9 @@ config:
   layout_x: 3
   layout_y: 2
   atm_window_length: PT6H
-  valid_time: 2021-08-01T00:00:00Z
+  valid_time: 2021-12-21T06:00:00Z
   dump: gdas
-  case: C768
+  case: C96
   levs: 128
   interp_method: barycentric
 job options:
@@ -60,42 +65,39 @@ job options:
   modulepath: ${srcdir}/modulefiles
 EOF
 
-rm stdout.txt
-${srcdir}/ush/run_jedi_exe.py -c ./3dhofx_example.yaml > stdout.txt
+# Execute run_jedi_exe.py
+if [ -e stdout.txt ]; then
+    rm -f stdout.txt
+fi
+${srcdir}/ush/run_jedi_exe.py -c ./3dhofx_example.yaml > stdout.txt 2>&1
 rc=$?
 if [ $rc -ne 0 ]; then
     exit $rc
 fi
 
-sleep 10
-jobid=$(grep "Submitted" stdout.txt | awk -F' ' '{print $4}')
-echo "jobid is $jobid"
+# Check for job submission error
+error=$(grep -i "error" stdout.txt | wc -l)
+if [ $error -ne 0 ]; then
+    rc=$error
+    exit $rc
+fi
 
-nloop=100
-n=1
-while [ $n -le $nloop ]; do
-    if [ -s GDASApp.o$jobid ]; then
-	break
-    fi
-    sleep 10
-    n=$((n+1))
-done
+# Cancel submitted job
+jobid=$(grep "Submitted" stdout.txt | awk -F' ' '{print $4}')
+scancel $jobid
+rc=$?
+if [ $rc -ne 0 ]; then
+    exit $rc
+fi
 
-rc=1
-n=1
-while [ $n -le $nloop ]; do
-    count=$(cat GDASApp.o$jobid | grep "OOPS_STATS Run end" | wc -l)
-    if [ $count -gt 0 ]; then
-	rc=0
-	break
-    fi
-    count=$(cat GDASApp.o$jobid | grep "srun: error" | wc -l)
-    if [ $count -gt 0 ]; then
-        rc=9
-        break
+# Check for valid yaml files
+ylist="3dhofx_example.yaml gdas_hofx.yaml"
+for yfile in $ylist; do
+    python3 -c 'import yaml, sys; yaml.safe_load(sys.stdin)' < $yfile
+    rc=$?
+    if [ $rc -ne 0 ]; then
+	exit $rc
     fi
-    sleep 10
-    n=$((n+1))
 done
 
 exit $rc
diff --git a/...atm/global-workflow/run_jedi_exe_3dvar.sh → test/atm/run_jedi_exe_3dvar.sh b/...atm/global-workflow/run_jedi_exe_3dvar.sh → test/atm/run_jedi_exe_3dvar.sh
@@ -4,6 +4,7 @@ set -x
 bindir=$1
 srcdir=$2
 
+# Identify machine
 if [[ -d /scratch1 ]] ; then
     machine="hera"
 elif [[ -d /work ]] ; then
@@ -13,12 +14,14 @@ else
     exit 99
 fi
 
+# Load modules
 set +x
 module use ${srcdir}/modulefiles
 module load GDAS/${machine}
 set -x
 module list
 
+# Set machine dependent variables
 if [ "$machine" = "hera" ] ; then
     partition="hera"
     gdasfix="/scratch1/NCEPDEV/da/Cory.R.Martin/GDASApp/fix"
@@ -27,9 +30,11 @@ elif [ "$machine" = "orion" ]; then
     gdasfix="/work2/noaa/da/cmartin/GDASApp/fix"
 fi
 
+# Create test run directory
 mkdir -p ${bindir}/test/atm/global-workflow/testrun/gdas_single_test_3dvar
 cd ${bindir}/test/atm/global-workflow/testrun/gdas_single_test_3dvar
 
+# Create input yaml
 cat > ./3dvar_example.yaml << EOF
 working directory: ./
 GDASApp home: ${srcdir}
@@ -69,45 +74,39 @@ job options:
   modulepath: ${srcdir}/modulefiles
 EOF
 
+# Execute run_jedi_exe.py
 if [ -e stdout.txt ]; then
     rm -f stdout.txt
 fi
-
-${srcdir}/ush/run_jedi_exe.py -c ./3dvar_example.yaml > stdout.txt
+${srcdir}/ush/run_jedi_exe.py -c ./3dvar_example.yaml > stdout.txt 2>&1
 rc=$?
 if [ $rc -ne 0 ]; then
     exit $rc
 fi
 
-sleep 10
-jobid=$(grep "Submitted" stdout.txt | awk -F' ' '{print $4}')
-echo "jobid is $jobid"
+# Check for job submission error
+error=$(grep -i "error" stdout.txt | wc -l)
+if [ $error -ne 0 ]; then
+    rc=$error
+    exit $rc
+fi
 
-nloop=100
-n=1
-while [ $n -le $nloop ]; do
-    if [ -s GDASApp.o$jobid ]; then
-	break
-    fi
-    sleep 10
-    n=$((n+1))
-done
+# Cancel submitted job
+jobid=$(grep "Submitted" stdout.txt | awk -F' ' '{print $4}')
+scancel $jobid
+rc=$?
+if [ $rc -ne 0 ]; then
+    exit $rc
+fi
 
-rc=1
-n=1
-while [ $n -le $nloop ]; do
-    count=$(cat GDASApp.o$jobid | grep "OOPS_STATS Run end" | wc -l)
-    if [ $count -gt 0 ]; then
-	rc=0
-	break
-    fi
-    count=$(cat GDASApp.o$jobid | grep "srun: error" | wc -l)
-    if [ $count -gt 0 ]; then
-        rc=9
-        break
+# Check for valid yaml files
+ylist="3dvar_example.yaml gdas_variational.yaml"
+for yfile in $ylist; do
+    python3 -c 'import yaml, sys; yaml.safe_load(sys.stdin)' < $yfile
+    rc=$?
+    if [ $rc -ne 0 ]; then
+	exit $rc
     fi
-    sleep 10
-    n=$((n+1))
 done
 
 exit $rc
diff --git a/...atm/global-workflow/run_jedi_exe_letkf.sh → test/atm/run_jedi_exe_letkf.sh b/...atm/global-workflow/run_jedi_exe_letkf.sh → test/atm/run_jedi_exe_letkf.sh
@@ -4,6 +4,7 @@ set -x
 bindir=$1
 srcdir=$2
 
+# Identify machine
 if [[ -d /scratch1 ]] ; then
     machine="hera"
 elif [[ -d /work ]] ; then
@@ -13,12 +14,14 @@ else
     exit 99
 fi
 
+# Load modules
 set +x
 module use ${srcdir}/modulefiles
 module load GDAS/${machine}
 set -x
 module list
 
+# Set machine dependent variables
 if [ "$machine" = "hera" ] ; then
     cominges="/scratch1/NCEPDEV/da/Russ.Treadon/GDASApp/cases"
     partition="hera"
@@ -29,9 +32,11 @@ elif [ "$machine" = "orion" ]; then
     gdasfix="/work2/noaa/da/cmartin/GDASApp/fix"
 fi
 
+# Create test run directory
 mkdir -p ${bindir}/test/atm/global-workflow/testrun/gdas_single_test_letkf
 cd ${bindir}/test/atm/global-workflow/testrun/gdas_single_test_letkf
 
+# Create input yaml
 cat > ./letkf_example.yaml << EOF
 working directory: ./
 GDASApp home: ${srcdir}
@@ -71,43 +76,39 @@ job options:
   modulepath: ${srcdir}/modulefiles
 EOF
 
-rm stdout.txt
-${srcdir}/ush/run_jedi_exe.py -c ./letkf_example.yaml > stdout.txt
+# Execute run_jedi_exe.py
+if [ -e stdout.txt ]; then
+    rm -f stdout.txt
+fi
+${srcdir}/ush/run_jedi_exe.py -c ./letkf_example.yaml > stdout.txt 2>&1
 rc=$?
 if [ $rc -ne 0 ]; then
     exit $rc
 fi
 
-sleep 10
-jobid=$(grep "Submitted" stdout.txt | awk -F' ' '{print $4}')
-echo "jobid is $jobid"
+# Check for job submission error
+error=$(grep -i "error" stdout.txt | wc -l)
+if [ $error -ne 0 ]; then
+    rc=$error
+    exit $rc
+fi
 
-nloop=100
-n=1
-while [ $n -le $nloop ]; do
-    if [ -s GDASApp.o$jobid ]; then
-	break
-    fi
-    sleep 10
-    n=$((n+1))
-done
+# Cancel submitted job
+jobid=$(grep "Submitted" stdout.txt | awk -F' ' '{print $4}')
+scancel $jobid
+rc=$?
+if [ $rc -ne 0 ]; then
+    exit $rc
+fi
 
-rc=1
-n=1
-while [ $n -le $nloop ]; do
-    count=$(cat GDASApp.o$jobid | grep "OOPS_STATS Run end" | wc -l)
-    if [ $count -gt 0 ]; then
-	rc=0
-	break
-    fi
-    count=$(cat GDASApp.o$jobid | grep "srun: error" | wc -l)
-    if [ $count -gt 0 ]; then
-        rc=9
-        break
+# Check for valid yaml files
+ylist="letkf_example.yaml gdas_letkf.yaml"
+for yfile in $ylist; do
+    python3 -c 'import yaml, sys; yaml.safe_load(sys.stdin)' < $yfile
+    rc=$?
+    if [ $rc -ne 0 ]; then
+	exit $rc
     fi
-    sleep 10
-    n=$((n+1))
 done
 
 exit $rc
-