Merge main to dev/gfdl (2013-10-25)

.github/workflows/coverage.yml

@@ -28,10 +28,14 @@ jobs:
     - name: Report unit test coverage to CI (PR)
       if: github.event_name == 'pull_request'
       run: make report.cov.unit REQUIRE_COVERAGE_UPLOAD=true
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     - name: Report unit test coverage to CI (Push)
       if: github.event_name != 'pull_request'
       run: make report.cov.unit
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     - name: Compile ocean-only MOM6 with code coverage
       run: make -j build/cov/MOM6
@@ -42,7 +46,11 @@ jobs:
     - name: Report coverage to CI (PR)
       if: github.event_name == 'pull_request'
       run: make report.cov REQUIRE_COVERAGE_UPLOAD=true
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     - name: Report coverage to CI (Push)
       if: github.event_name != 'pull_request'
       run: make report.cov
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitlab-ci.yml

@@ -10,7 +10,6 @@ stages:
 # We use the "fetch" strategy to speed up the startup of stages
 variables:
   JOB_DIR: "/lustre/f2/scratch/oar.gfdl.ogrp-account/runner/builds/$CI_PIPELINE_ID"
-  WORKSPACE: "/lustre/f2/scratch/oar.gfdl.ogrp-account/runner/$CI_RUNNER_ID"
   GIT_STRATEGY: fetch
 
 # Always eport value of $JOB_DIR
@@ -185,9 +184,9 @@ actions:gnu:
     - make -s -j
     - MPIRUN= make preproc -s -j
     - echo -e "\e[0Ksection_end:`date +%s`:compile\r\e[0K"
-    - (echo '#!/bin/bash';echo 'make MPIRUN="srun -mblock --exclusive" WORKSPACE=$WORKSPACE test -s -j') > job.sh
-    - sbatch --clusters=c5 --nodes=2 --time=0:10:00 --account=gfdl_o --qos=debug --job-name=MOM6.gnu.testing --output=log.$CI_JOB_ID --wait job.sh || ( cat log.$CI_JOB_ID ; exit 911 ) && make WORKSPACE=$WORKSPACE test -s
-    - make WORKSPACE=$WORKSPACE test.summary
+    - (echo '#!/bin/bash';echo 'make MPIRUN="srun -mblock --exclusive" test -s -j') > job.sh
+    - sbatch --clusters=c5 --nodes=2 --time=0:10:00 --account=gfdl_o --qos=debug --job-name=MOM6.gnu.testing --output=log.$CI_JOB_ID --wait job.sh || ( cat log.$CI_JOB_ID ; exit 911 ) && make test -s
+    - make test.summary
 
 actions:intel:
   stage: tests
@@ -205,9 +204,9 @@ actions:intel:
     - make -s -j
     - MPIRUN= make preproc -s -j
     - echo -e "\e[0Ksection_end:`date +%s`:compile\r\e[0K"
-    - (echo '#!/bin/bash';echo 'make MPIRUN="srun -mblock --exclusive" WORKSPACE=$WORKSPACE test -s -j') > job.sh
-    - sbatch --clusters=c5 --nodes=2 --time=0:10:00 --account=gfdl_o --qos=debug --job-name=MOM6.intel.testing --output=log.$CI_JOB_ID --wait job.sh || ( cat log.$CI_JOB_ID ; exit 911 ) && make WORKSPACE=$WORKSPACE test -s
-    - make WORKSPACE=$WORKSPACE test.summary
+    - (echo '#!/bin/bash';echo 'make MPIRUN="srun -mblock --exclusive" test -s -j') > job.sh
+    - sbatch --clusters=c5 --nodes=2 --time=0:10:00 --account=gfdl_o --qos=debug --job-name=MOM6.intel.testing --output=log.$CI_JOB_ID --wait job.sh || ( cat log.$CI_JOB_ID ; exit 911 ) && make test -s
+    - make test.summary
 
 # Tests
 #

.testing/Makefile

@@ -547,8 +547,8 @@ $(WORKSPACE)/work/%/$(1)/ocean.stats $(WORKSPACE)/work/%/$(1)/chksum_diag: build
 	  && $(TIME) $(5) $(MPIRUN) -n $(6) $(abspath $$<) 2> std.err > std.out \
 	  || !( \
 	    mkdir -p ../../../results/$$*/ ; \
-	    cat std.out | tee ../../../results/$$*/std.$(1).out | tail -n 20 ; \
-	    cat std.err | tee ../../../results/$$*/std.$(1).err | tail -n 20 ; \
+	    cat std.out | tee ../../../results/$$*/std.$(1).out | tail -n 40 ; \
+	    cat std.err | tee ../../../results/$$*/std.$(1).err | tail -n 40 ; \
 	    rm ocean.stats chksum_diag ; \
 	    echo -e "$(FAIL): $$*.$(1) failed at runtime." \
 	  )
@@ -564,13 +564,21 @@ endef
 
 # Upload coverage reports
 CODECOV_UPLOADER_URL ?= https://uploader.codecov.io/latest/linux/codecov
+CODECOV_TOKEN ?=
+
+ifdef CODECOV_TOKEN
+  CODECOV_TOKEN_ARG = -t $(CODECOV_TOKEN)
+else
+  CODECOV_TOKEN_ARG =
+endif
+
 codecov:
 	curl -s $(CODECOV_UPLOADER_URL) -o $@
 	chmod +x codecov
 
 .PHONY: report.cov
 report.cov: run.cov codecov
-	./codecov -R build/cov -Z -f "*.gcov" \
+	./codecov $(CODECOV_TOKEN_ARG) -R build/cov -Z -f "*.gcov" \
 	  > build/cov/codecov.out \
 	  2> build/cov/codecov.err \
 	  && echo -e "${MAGENTA}Report uploaded to codecov.${RESET}" \
@@ -623,8 +631,8 @@ $(WORKSPACE)/work/%/restart/ocean.stats: build/symmetric/MOM6 | preproc
 	# Run the first half-period
 	cd $(@D) && $(TIME) $(MPIRUN) -n 1 $(abspath $<) 2> std1.err > std1.out \
 	  || !( \
-	    cat std1.out | tee ../../../results/$*/std.restart1.out | tail -n 20 ; \
-	    cat std1.err | tee ../../../results/$*/std.restart1.err | tail -n 20 ; \
+	    cat std1.out | tee ../../../results/$*/std.restart1.out | tail -n 40 ; \
+	    cat std1.err | tee ../../../results/$*/std.restart1.err | tail -n 40 ; \
 	    echo -e "$(FAIL): $*.restart failed at runtime." \
 	  )
 	# Setup the next inputs
@@ -634,8 +642,8 @@ $(WORKSPACE)/work/%/restart/ocean.stats: build/symmetric/MOM6 | preproc
 	# Run the second half-period
 	cd $(@D) && $(TIME) $(MPIRUN) -n 1 $(abspath $<) 2> std2.err > std2.out \
 	  || !( \
-	    cat std2.out | tee ../../../results/$*/std.restart2.out | tail -n 20 ; \
-	    cat std2.err | tee ../../../results/$*/std.restart2.err | tail -n 20 ; \
+	    cat std2.out | tee ../../../results/$*/std.restart2.out | tail -n 40 ; \
+	    cat std2.err | tee ../../../results/$*/std.restart2.err | tail -n 40 ; \
 	    echo -e "$(FAIL): $*.restart failed at runtime." \
 	  )
 
@@ -645,26 +653,7 @@ $(WORKSPACE)/work/%/restart/ocean.stats: build/symmetric/MOM6 | preproc
 # Not a true rule; only call this after `make test` to summarize test results.
 .PHONY: test.summary
 test.summary:
-	@if ls $(WORKSPACE)/results/*/* &> /dev/null; then \
-	  if ls $(WORKSPACE)/results/*/std.*.err &> /dev/null; then \
-	    echo "The following tests failed to complete:" ; \
-	    ls $(WORKSPACE)/results/*/std.*.out \
-	      | awk '{split($$0,a,"/"); split(a[3],t,"."); v=t[2]; if(length(t)>3) v=v"."t[3]; print a[2],":",v}'; \
-	  fi; \
-	  if ls $(WORKSPACE)/results/*/ocean.stats.*.diff &> /dev/null; then \
-	    echo "The following tests report solution regressions:" ; \
-	    ls $(WORKSPACE)/results/*/ocean.stats.*.diff \
-	      | awk '{split($$0,a,"/"); split(a[3],t,"."); v=t[3]; if(length(t)>4) v=v"."t[4]; print a[2],":",v}'; \
-	  fi; \
-	  if ls $(WORKSPACE)/results/*/chksum_diag.*.diff &> /dev/null; then \
-	    echo "The following tests report diagnostic regressions:" ; \
-	    ls $(WORKSPACE)/results/*/chksum_diag.*.diff \
-	      | awk '{split($$0,a,"/"); split(a[3],t,"."); v=t[2]; if(length(t)>3) v=v"."t[3]; print a[2],":",v}'; \
-	  fi; \
-	  false ; \
-	else \
-	  echo -e "$(PASS): All tests passed!"; \
-	fi
+	@./tools/report_test_results.sh $(WORKSPACE)/results
 
 
 #---
@@ -702,7 +691,7 @@ build/unit/MOM_file_parser_tests.F90.gcov: $(WORKSPACE)/work/unit/std.out
 
 .PHONY: report.cov.unit
 report.cov.unit: build/unit/MOM_file_parser_tests.F90.gcov codecov
-	./codecov -R build/unit -f "*.gcov" -Z -n "Unit tests" \
+	./codecov $(CODECOV_TOKEN_ARG) -R build/unit -f "*.gcov" -Z -n "Unit tests" \
 	    > build/unit/codecov.out \
 	    2> build/unit/codecov.err \
 	  && echo -e "${MAGENTA}Report uploaded to codecov.${RESET}" \

.testing/tc3/MOM_input

@@ -283,10 +283,10 @@ HMIX_FIXED = 20.0               !   [m]
 KV = 1.0E-04                    !   [m2 s-1]
                                 ! The background kinematic viscosity in the interior.
                                 ! The molecular value, ~1e-6 m2 s-1, may be used.
-KVML = 0.01                     !   [m2 s-1] default = 1.0E-04
-                                ! The kinematic viscosity in the mixed layer.  A typical
-                                ! value is ~1e-2 m2 s-1. KVML is not used if
-                                ! BULKMIXEDLAYER is true.  The default is set by KV.
+KV_ML_INVZ2 = 0.01              !   [m2 s-1] default = 0.0
+                                ! An extra kinematic viscosity in a mixed layer of thickness HMIX_FIXED, with
+                                ! the actual viscosity scaling as 1/(z*HMIX_FIXED)^2, where z is the distance
+                                ! from the surface, to allow for finite wind stresses to be transmitted through.
 HBBL = 10.0                     !   [m]
                                 ! The thickness of a bottom boundary layer with a
                                 ! viscosity of KVBBL if BOTTOMDRAGLAW is not defined, or

.testing/tools/report_test_results.sh

@@ -0,0 +1,42 @@
+#!/bin/sh
+RESULTS=${1:-${PWD}/results}
+
+GREEN="\033[0;32m"
+RESET="\033[0m"
+PASS="${GREEN}PASS${RESET}"
+
+if [ -d ${RESULTS} ]; then
+  if ls ${RESULTS}/*/std.*.err &> /dev/null; then
+    echo "The following tests failed to complete:"
+	ls ${RESULTS}/*/std.*.out \
+      | awk '{ \
+        split($$0,a,"/"); \
+        split(a[length(a)],t,"."); \
+        v=t[2]; \
+        if(length(t)>4) v=v"."t[4]; print a[length(a)-1],":",v}'
+  fi
+
+  if ls ${RESULTS}/*/ocean.stats.*.diff &> /dev/null; then
+    echo "The following tests report solution regressions:"
+    ls ${RESULTS}/*/ocean.stats.*.diff \
+      | awk '{ \
+        split($$0,a,"/"); \
+        split(a[length(a)],t,"."); \
+        v=t[3]; \
+        if(length(t)>4) v=v"."t[4]; print a[length(a)-1],":",v}'
+  fi
+
+  if ls ${RESULTS}/*/chksum_diag.*.diff &> /dev/null; then
+    echo "The following tests report diagnostic regressions:"
+    ls ${RESULTS}/*/chksum_diag.*.diff \
+      | awk '{ \
+        split($$0,a,"/"); \
+        split(a[length(a)],t,"."); \
+        v=t[2]; \
+        if(length(t)>4) v=v"."t[4]; print a[length(a)-1],":",v}'
+  fi
+
+  exit 1
+else
+  printf "${PASS}: All tests passed!\n"
+fi

ac/Makefile.in

@@ -56,3 +56,4 @@ ac-clean: distclean
 	rm -f @srcdir@/ac/aclocal.m4
 	rm -rf @srcdir@/ac/autom4te.cache
 	rm -f @srcdir@/ac/configure
+	rm -f @srcdir@/ac/configure~

ac/configure.ac

@@ -238,8 +238,13 @@ AC_COMPILE_IFELSE(
 
 # Python interpreter test
 
+# Declare the Python interpreter variable
 AC_ARG_VAR([PYTHON], [Python interpreter command])
 
+# If PYTHON is set to an empty string, then unset it
+AS_VAR_IF([PYTHON], [], [AS_UNSET([PYTHON])], [])
+
+# Now attempt to find a Python interpreter if PYTHON is unset
 AS_VAR_SET_IF([PYTHON], [
   AC_PATH_PROGS([PYTHON], ["$PYTHON"], [none])
 ], [

ac/deps/m4/ax_fc_check_c_lib.m4

@@ -0,0 +1,45 @@
+dnl AX_FC_CHECK_C_LIB(LIBRARY, FUNCTION,
+dnl                   [ACTION-IF-FOUND], [ACTION-IF-NOT-FOUND],
+dnl                   [OTHER-LDFLAGS], [OTHER-LIBS])
+dnl
+dnl This macro checks if a C library can be referenced by a Fortran compiler.
+dnl
+dnl Results are cached in `ax_fc_cv_c_lib_LIBRARY_FUNCTION`.
+dnl
+dnl NOTE: Might be possible to rewrite this to use `AX_FC_CHECK_BIND_C`.
+dnl
+AC_DEFUN([AX_FC_CHECK_C_LIB], [
+  AS_VAR_PUSHDEF([ax_fc_C_Lib], [ax_fc_cv_c_lib_$1_$2])
+  m4_ifval([$5],
+    [ax_fc_c_lib_msg_LDFLAGS=" with $5"],
+    [ax_fc_c_lib_msg_LDFLAGS=""]
+  )
+  AC_CACHE_CHECK(
+    [for $2 in -l$1$ax_fc_c_lib_msg_LDFLAGS], [ax_fc_cv_c_lib_$1_$2], [
+      ax_fc_check_c_lib_save_LDFLAGS=$LDFLAGS
+      LDFLAGS="$6 $LDFLAGS"
+      ax_fc_check_c_lib_save_LIBS=$LIBS
+      LIBS="-l$1 $7 $LIBS"
+      AC_LINK_IFELSE(
+        [AC_LANG_PROGRAM([],[dnl
+dnl begin code block
+        interface
+        subroutine test() bind(c, name="$2")
+        end subroutine test
+        end interface
+        call test])
+dnl end code block
+        ],
+        [AS_VAR_SET([ax_fc_C_Lib], [yes])],
+        [AS_VAR_SET([ax_fc_C_Lib], [no])]
+      )
+      LDFLAGS=$ax_fc_check_c_lib_save_LDFLAGS
+      LIBS=$ax_fc_check_c_lib_save_LIBS
+    ]
+  )
+  AS_VAR_IF([ax_fc_C_Lib], [yes],
+    [m4_default([$3], [LIBS="-l$1 $LIBS"])],
+    [$4]
+  )
+  AS_VAR_POPDEF([ax_fc_C_Lib])
+])

ac/deps/m4/ax_fc_check_lib.m4

@@ -18,7 +18,7 @@ dnl    library with different -L flags, or perhaps other ld configurations.
 dnl
 dnl Results are cached in the ax_fc_cv_lib_LIBRARY_FUNCTION variable.
 dnl
-AC_DEFUN([AX_FC_CHECK_LIB],[dnl
+AC_DEFUN([AX_FC_CHECK_LIB],[
   AS_VAR_PUSHDEF([ax_fc_Lib], [ax_fc_cv_lib_$1_$2])
   m4_ifval([$6],
     [ax_fc_lib_msg_LDFLAGS=" with $6"],
@@ -29,14 +29,15 @@ AC_DEFUN([AX_FC_CHECK_LIB],[dnl
     LDFLAGS="$6 $LDFLAGS"
     ax_fc_check_lib_save_LIBS=$LIBS
     LIBS="-l$1 $7 $LIBS"
-    AS_IF([test -n $3],
+    AS_IF([test -n "$3"],
       [ax_fc_use_mod="use $3"],
       [ax_fc_use_mod=""])
-    AC_LINK_IFELSE([
-        AC_LANG_PROGRAM([], [dnl
+    AC_LINK_IFELSE([dnl
+dnl Begin 7-column code block
+AC_LANG_PROGRAM([], [dnl
         $ax_fc_use_mod
-        call $2]dnl
-        )
+        call $2])dnl
+dnl End code block
       ],
       [AS_VAR_SET([ax_fc_Lib], [yes])],
       [AS_VAR_SET([ax_fc_Lib], [no])]