Merge remote-tracking branch 'gfdl/dev/gfdl' into iOM4_is_dev2

.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

@@ -554,8 +554,8 @@ $(WORKSPACE)/work/%/$(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." \
 	  )
@@ -630,8 +630,8 @@ $(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
@@ -641,8 +641,8 @@ $(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." \
 	  )
 
@@ -652,26 +652,7 @@ $(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
 
 
 #---

.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/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])]

ac/makedep

@@ -16,6 +16,13 @@ re_use = re.compile(r"^ *use +([a-z_0-9]+)")
 re_cpp_include = re.compile(r"^ *# *include *[<\"']([a-zA-Z_0-9\.]+)[>\"']")
 re_f90_include = re.compile(r"^ *include +[\"']([a-zA-Z_0-9\.]+)[\"']")
 re_program = re.compile(r"^ *[pP][rR][oO][gG][rR][aA][mM] +([a-zA-Z_0-9]+)")
+re_end = re.compile(r"^ *end *(module|procedure) ", re.IGNORECASE)
+# NOTE: This excludes comments and tokens with substrings containing `function`
+# or `subroutine`, but will fail if the keywords appear in other contexts.
+re_procedure = re.compile(
+    r"^[^!]*(?<![a-z_])(function|subroutine)(?![a-z_])",
+    re.IGNORECASE
+)
 
 
 def create_deps(src_dirs, makefile, debug, exec_target, fc_rule,
@@ -30,6 +37,7 @@ def create_deps(src_dirs, makefile, debug, exec_target, fc_rule,
     F90_files = [
         f for f in all_files
         if f.endswith('.f90') or f.endswith('.F90')
+        or f.endswith('.f') or f.endswith('.F')
     ]
     #  ... all C source
     c_files = [f for f in all_files if f.endswith('.c')]
@@ -58,7 +66,7 @@ def create_deps(src_dirs, makefile, debug, exec_target, fc_rule,
     o2mods, o2uses, o2h, o2inc, o2prg, prg2o, mod2o = {}, {}, {}, {}, {}, {}, {}
     externals, all_modules = [], []
     for f in F90_files:
-        mods, used, cpp, inc, prg = scan_fortran_file(f)
+        mods, used, cpp, inc, prg, has_externals = scan_fortran_file(f)
         # maps object file to modules produced
         o2mods[object_file(f)] = mods
         # maps module produced to object file
@@ -85,12 +93,12 @@ def create_deps(src_dirs, makefile, debug, exec_target, fc_rule,
                     o2prg[o] = ['[ignored %s]' % (p)]
                 else:
                     prg2o[p] = object_file(f)
-        if not mods and not prg:
+        if has_externals:
             externals.append(object_file(f))
         all_modules += mods
 
     for f in c_files:
-        _, _, cpp, inc, _ = scan_fortran_file(f)
+        _, _, cpp, inc, _, _ = scan_fortran_file(f)
         # maps object file to .h files included
         o2h[object_file(f)] = cpp
         externals.append(object_file(f))
@@ -238,7 +246,7 @@ def nested_inc(inc_files, f2F):
     def recur(hfile):
         if hfile not in f2F.keys():
             return
-        _, _, cpp, inc, _ = scan_fortran_file(f2F[hfile])
+        _, _, cpp, inc, _, _ = scan_fortran_file(f2F[hfile])
         if len(cpp) + len(inc) > 0:
             for h in cpp+inc:
                 if h not in hlst and h in f2F.keys():
@@ -258,25 +266,49 @@ def scan_fortran_file(src_file):
     module_decl, used_modules, cpp_includes, f90_includes, programs = [], [], [], [], []
     with io.open(src_file, 'r', errors='replace') as file:
         lines = file.readlines()
+
+        external_namespace = True
+
+        file_has_externals = False
+
         for line in lines:
             match = re_module.match(line.lower())
             if match:
                 if match.group(1) not in 'procedure':   # avoid "module procedure" statements
                     module_decl.append(match.group(1))
+                    external_namespace = False
+
             match = re_use.match(line.lower())
             if match:
                 used_modules.append(match.group(1))
+
             match = re_cpp_include.match(line)
             if match:
                 cpp_includes.append(match.group(1))
+
             match = re_f90_include.match(line)
             if match:
                 f90_includes.append(match.group(1))
+
             match = re_program.match(line)
             if match:
                 programs.append(match.group(1))
+                external_namespace = False
+
+            match = re_end.match(line)
+            if match:
+                external_namespace = True
+
+            # Check for any external procedures; if present, flag the file
+            # as a potential source of
+            # NOTE: This a very weak test that needs further modification
+            if external_namespace and not file_has_externals:
+                match = re_procedure.match(line)
+                if match:
+                    file_has_externals = True
+
     used_modules = [m for m in sorted(set(used_modules)) if m not in module_decl]
-    return add_suff(module_decl, '.mod'), add_suff(used_modules, '.mod'), cpp_includes, f90_includes, programs
+    return add_suff(module_decl, '.mod'), add_suff(used_modules, '.mod'), cpp_includes, f90_includes, programs, file_has_externals
     # return add_suff(module_decl, '.mod'), add_suff(sorted(set(used_modules)), '.mod'), cpp_includes, f90_includes, programs
 
 
@@ -297,8 +329,9 @@ def find_files(src_dirs):
             for file in f:
                 # TODO: use any()
                 if (file.endswith('.F90') or file.endswith('.f90')
+                        or file.endswith('.f') or file.endswith('.F')
                         or file.endswith('.h') or file.endswith('.inc')
-                        or file.endswith('.c')):
+                        or file.endswith('.c') or file.endswith('.H')):
                     files.append(p+'/'+file)
     return sorted(set(files))