NOAA machine pass of base_suite #155

.github/PULL_REQUEST_TEMPLATE

@@ -1,19 +1,29 @@
-[Remove this and add a short summary line]:
 
-- Developer(s):
-
-- Please suggest code Pull Request reviewers in the column at right.
-
-- Are the code changes bit for bit, different at roundoff level, or more substantial?
-
-- Please include the link to test results or paste the summary block from the bottom of the testing output below.
-
-- Does this PR create or have dependencies on Icepack or any other models? 
-
-- Is the documentation being updated with this PR? (Y/N)
-If not, does the documentation need to be updated separately at a later time? (Y/N)
-
-Note: "Documentation" includes information on the wiki and .rst files in doc/source/, 
-which are used to create the online technical docs at https://readthedocs.org/projects/cice-consortium-cice/.
-
-- Other Relevant Details:
+For detailed information about submitting Pull Requests (PRs) to the CICE-Consortium,
+please refer to: <https://github.com/CICE-Consortium/About-Us/wiki/Resource-Index#information-for-developers>
+
+
+## PR checklist
+- [ ] Short (1 sentence) summary of your PR: 
+    ENTER INFORMATION HERE
+- [ ] Developer(s): 
+    ENTER INFORMATION HERE
+- [ ] Suggest PR reviewers from list in the column to the right.
+- [ ] Please copy the PR test results link or provide a summary of testing completed below.
+    ENTER INFORMATION HERE 
+- How much do the PR code changes differ from the unmodified code? 
+    - [ ] bit for bit
+    - [ ] different at roundoff level
+    - [ ] more substantial 
+- Does this PR create or have dependencies on Icepack or any other models?
+    - [ ] Yes
+    - [ ] No
+- Does this PR add any new test cases?
+    - [ ] Yes
+    - [ ] No
+- Is the documentation being updated? ("Documentation" includes information on the wiki or in the .rst files from doc/source/, which are used to create the online technical docs at https://readthedocs.org/projects/cice-consortium-cice/. A test build of the technical docs will be performed as part of the PR testing.)
+    - [ ] Yes
+    - [ ] No, does the documentation need to be updated at a later time?
+        - [ ] Yes
+        - [ ] No 
+- [ ] Please provide any additional information or relevant details below:

.zenodo.json

@@ -0,0 +1,104 @@
+{
+    "license": "other-open", 
+    "description": "No description provided", 
+    "language": "English", 
+    "title": "CICE-Consortium/CICE: CICE Version m.n.p", 
+    "keywords": [
+        "sea ice model, CICE, Icepack"
+    ], 
+    "version": "m.n.p", 
+    "upload_type": "software", 
+    "communities": [
+        {
+            "identifier": "cice-consortium"
+        }
+    ], 
+    "publication_date": "2019-07-25", 
+    "creators": [
+        {
+            "affiliation": "Los Alamos National Laboratory", 
+            "name": "Elizabeth Hunke"
+        }, 
+        {
+            "affiliation": "Naval Research Laboratory Stennis Space Center", 
+            "name": "Richard Allard"
+        }, 
+        {
+            "affiliation": "National Center for Atmospheric Research", 
+            "name": "David A. Bailey"
+        }, 
+        {
+            "affiliation": "Environment and Climate Change Canada", 
+            "name": "Philippe Blain"
+        }, 
+        {
+            "affiliation": "Environment and Climate Change Canada", 
+            "name": "Amelie Bouchat"
+        }, 
+        {
+            "affiliation": "National Oceanographic and Atmospheric Administration (CTR)", 
+            "name": "Tony Craig"
+        }, 
+        {
+            "affiliation": "Environment and Climate Change Canada", 
+            "name": "Frederic Dupont"
+        }, 
+        {
+            "affiliation": "National Center for Atmospheric Research", 
+            "name": "Alice DuVivier"
+        }, 
+        {
+            "affiliation": "National Oceanographic and Atmospheric Administration", 
+            "name": "Robert Grumbine"
+        }, 
+        {
+            "affiliation": "Naval Research Laboratory Stennis Space Center", 
+            "name": "David Hebert"
+        }, 
+        {
+            "affiliation": "National Center for Atmospheric Research", 
+            "name": "Marika Holland"
+        }, 
+        {
+            "affiliation": "Los Alamos National Laboratory", 
+            "name": "Nicole Jeffery"
+        }, 
+        {
+            "affiliation": "Environment and Climate Change Canada", 
+            "name": "Jean-Francois Lemieux"
+        }, 
+        {
+            "affiliation": "Danish Meteorological Institute", 
+            "name": "Till Rasmussen"
+        }, 
+        {
+            "affiliation": "Danish Meteorological Institute", 
+            "name": "Mads Ribergaard"
+        }, 
+        {
+            "affiliation": "Los Alamos National Laboratory", 
+            "name": "Andrew Roberts"
+        }, 
+        {
+            "affiliation": "Naval Research Laboratory Stennis Space Center (CTR)", 
+            "name": "Matthew Turner"
+        }, 
+        {
+            "affiliation": "Geophysical Fluid Dynamics Laboratory", 
+            "name": "Michael Winton"
+        }
+    ], 
+    "access_right": "open", 
+    "related_identifiers": [
+        {
+            "scheme": "url", 
+            "identifier": "https://github.com/CICE-Consortium/CICE/tree/CICE6.0.1", 
+            "relation": "isSupplementTo"
+        }, 
+        {
+            "scheme": "doi", 
+            "identifier": "10.5281/zenodo.1205674", 
+            "relation": "isVersionOf"
+        }
+    ]
+}

configuration/scripts/Makefile

@@ -8,7 +8,6 @@
 #   SRCS=<files>   ~ list of src files, default is all .c .F .F90 files in VPATH
 #   VPFILE=<file>  ~ file with list of dirs, used to create VPATH
 #   SRCFILE=<file> ~ file with list of src files, used to create SRCS
-#   DEPGEN=<exec>  ~ dependency generator utility, default is makdep
 #
 #   <macro defns>  ~ any macro definitions found in this file or the included 
 #                    MACFILE will be over-riden by cmd-line macro definitions
@@ -31,7 +30,9 @@ VPFILE   := NONE
 VPATH    := .
 SRCFILE  := NONE
 SRCS     := NONE
-DEPGEN   := ./makdep  # an externally provided dependency generator
+
+# dependency generator
+DEPGEN   := ./makdep
 
 ifneq ($(VPATH),.)
   # this variable was specified on cmd line or in an env var
@@ -58,26 +59,33 @@ endif
 OBJS  := $(addsuffix .o, $(sort $(basename $(notdir $(SRCS)))))
 DEPS  := $(addsuffix .d, $(sort $(basename $(notdir $(SRCS)))))
 INCS  := $(patsubst %,-I%, $(VPATH) )
+OBJS_DEPGEN := $(addprefix $(ICE_CASEDIR)/,$(addsuffix .c, $(notdir $(DEPGEN))))
+MODDIR:= -I.
 RM    := rm
 
 .SUFFIXES:
 .SUFFIXES: .F90 .F .c .o
 
+.PHONY: all cice targets target db_files db_flags clean realclean
 all: $(EXEC)
 
+cice: $(EXEC)
+
 #-------------------------------------------------------------------------------
 # include the file that provides macro definitions required by build rules
-# note: the MACFILE may not be needed for certain goals
 #-------------------------------------------------------------------------------
 
-ifneq ($(MAKECMDGOALS), db_files)
-  -include $(MACFILE)
-endif
+-include $(MACFILE)
 
 #-------------------------------------------------------------------------------
-# echo file names, paths, compile flags, etc. used during build
+# echo supported targets, file names, paths, compile flags, etc. used during build
 #-------------------------------------------------------------------------------
 
+targets:
+	@echo " "
+	@echo "Supported Makefile Targets are: cice, makdep, depends, clean, realclean, targets, db_files, db_flags"
+target: targets
+
 db_files:
 	@echo " "
 	@echo "* EXEC    := $(EXEC)"
@@ -89,12 +97,22 @@ db_files:
 	@echo "* SRCS    := $(SRCS)"
 	@echo "* OBJS    := $(OBJS)"
 	@echo "* DEPS    := $(DEPS)"
+	@echo "* ULIBS   := $(ULIBS)"
+	@echo "* SLIBS   := $(SLIBS)"
+	@echo "* INCLDIR := $(INCLDIR)"
+	@echo "* OBJS_DEPGEN := $(OBJS_DEPGEN)"
 db_flags:
 	@echo " "
-	@echo "* cpp     := $(CPP) $(CPPFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR)"
-	@echo "* cc      := $(CC) -c $(CFLAGS) $(INCS) $(INCLDIR)"
-	@echo "* .F.o    := $(FC) -c $(FFLAGS) $(FIXEDFLAGS) $(INCS) $(INCLDIR)"
-	@echo "* .F90.o  := $(FC) -c $(FFLAGS) $(FREEFLAGS) $(INCS) $(INCLDIR)"
+	@echo "* $(DEPGEN) := $(SCC) $(CFLAGS_HOST)"
+	@echo "* %.d : %.c   := $(DEPGEN) $(INCS)"
+	@echo "* %.d : %.F   := $(DEPGEN) $(INCS)"
+	@echo "* %.d : %.F90 := $(DEPGEN) $(INCS)"
+	@echo "* %.d : %.H   := $(DEPGEN) $(INCS)"
+	@echo "* cpp     := $(CPP) $(CPPFLAGS) $(CPPDEFS) $(INCLDIR)"
+	@echo "* .c.o    := $(CC) $(CFLAGS) $(CPPDEFS) $(INCLDIR)"
+	@echo "* .F.o    := $(FC) -c $(FFLAGS) $(FIXEDFLAGS) $(CPPDEFS) $(INCLDIR)"
+	@echo "* .F90.o  := $(FC) -c $(FFLAGS) $(FREEFLAGS) $(CPPDEFS) $(MODDIR) $(INCLDIR)"
+	@echo "* $(notdir $(EXEC)) := $(LD) $(LDFLAGS) $(ULIBS) $(SLIBS)"
 
 #-------------------------------------------------------------------------------
 # build rule for makdep: MACFILE, cmd-line, or env vars must provide
@@ -105,7 +123,8 @@ ifndef $(CFLAGS_HOST)
   CFLAGS_HOST :=
 endif
 
-$(DEPGEN): $(ICE_CASEDIR)/makdep.c
+$(DEPGEN): $(OBJS_DEPGEN)
+	@ echo "Building makdep"
 	$(SCC) -o $@ $(CFLAGS_HOST) $<
 
 #-------------------------------------------------------------------------------
@@ -116,58 +135,62 @@ $(EXEC): $(OBJS)
 	$(LD) -o $(EXEC) $(LDFLAGS) $(OBJS) $(ULIBS) $(SLIBS)
 
 .c.o:
-	$(CC) $(CFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $<
+	$(CC) $(CFLAGS) $(CPPDEFS) $(INCLDIR) $<
 
 .F.o:
-	$(FC) -c $(FFLAGS) $(FIXEDFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $<
+	$(FC) -c $(FFLAGS) $(FIXEDFLAGS) $(CPPDEFS) $(INCLDIR) $<
 
 .F90.o:
-	$(FC) -c $(FFLAGS) $(FREEFLAGS) $(CPPDEFS) $(INCS) $(INCLDIR) $<
-
-mostlyclean:
-	$(RM) -f *.f *.f90 
+	$(FC) -c $(FFLAGS) $(FREEFLAGS) $(CPPDEFS) $(MODDIR) $(INCLDIR) $<
 
 clean:
-	$(RM) -f *.f *.f90 *.d *.mod *.o $(EXEC)
-#	$(RM) -f *.f *.f90 *.d *.$(MOD_SUFFIX) $(OBJS)
+	$(RM) -f *.o *.d *.mod $(EXEC)
 
-realclean:
-	$(RM) -f *.f *.f90 *.d *.$(MOD_SUFFIX) $(OBJS) $(EXEC)
+realclean: clean
+	$(RM) -f $(DEPGEN)
 
 #-------------------------------------------------------------------------------
 # Build & include dependency files
 #-------------------------------------------------------------------------------
 # ASSUMPTIONS:
-# o an externally provided dependency generator, $(DEPGEN), is available, 
+# o the dependency generator, $(DEPGEN), can be built, 
 #   its cmd line syntax is compatible with the build rules below.   Eg, for 
 #   each .o file, there is a corresponding .d (dependency) file, and both
 #   will be dependent on the same src file, eg.    foo.o foo.d : foo.F90
 #   Also, the dependancy genorator's capabilities, limitations, and assumptions
 #   are understood & accepted.
 #-------------------------------------------------------------------------------
 
-%.d : %.c
+depends: $(DEPS)
+
+%.d : %.c $(DEPGEN)
 	@ echo "Building dependency for $@"
 	@ $(DEPGEN) -f $(INCS) $< | head -3  > $@
-%.d : %.F
+%.d : %.F $(DEPGEN)
 	@ echo "Building dependency for $@"
 	@ $(DEPGEN) -f $(INCS) $<  > $@
-%.d : %.F90
+%.d : %.F90 $(DEPGEN)
 	@ echo "Building dependency for $@"
 	@ $(DEPGEN) -f $(INCS) $<  > $@
-%.d : %.H
+%.d : %.H $(DEPGEN)
 	@ echo "Building dependency for $@"
 	@ $(DEPGEN) -f $(INCS) $<  > $@
 
 # the if-tests prevent DEPS files from being created when they're not needed
 ifneq ($(MAKECMDGOALS), db_files)
 ifneq ($(MAKECMDGOALS), db_flags)
-ifneq ($(MAKECMDGOALS), mostlyclean)
 ifneq ($(MAKECMDGOALS), clean)
 ifneq ($(MAKECMDGOALS), realclean)
+ifneq ($(MAKECMDGOALS), targets)
+ifneq ($(MAKECMDGOALS), target)
+ifneq ($(MAKECMDGOALS), makdep)
+ifneq ($(MAKECMDGOALS), depends)
     -include $(DEPS)
 endif
 endif
 endif
 endif
 endif
+endif
+endif
+endif

configuration/scripts/cice.batch.csh

@@ -28,17 +28,24 @@ if (${taskpernodelimit} > ${ntasks}) set taskpernodelimit = ${ntasks}
 set ptile = $taskpernode
 if ($ptile > ${maxtpn} / 2) @ ptile = ${maxtpn} / 2
 
+set runlength = ${ICE_RUNLENGTH}
+if ($?ICE_MACHINE_MAXRUNLENGTH) then
+  if (${runlength} > ${ICE_MACHINE_MAXRUNLENGTH}) then
+    set runlength = ${ICE_MACHINE_MAXRUNLENGTH}
+  endif
+endif
+
 set queue = "${ICE_QUEUE}"
 set batchtime = "00:15:00"
-if (${ICE_RUNLENGTH} >  0) set batchtime = "00:29:00"
-if (${ICE_RUNLENGTH} == 1) set batchtime = "00:59:00"
-if (${ICE_RUNLENGTH} == 2) set batchtime = "2:00:00"
-if (${ICE_RUNLENGTH} == 3) set batchtime = "3:00:00"
-if (${ICE_RUNLENGTH} == 4) set batchtime = "4:00:00"
-if (${ICE_RUNLENGTH} == 5) set batchtime = "5:00:00"
-if (${ICE_RUNLENGTH} == 6) set batchtime = "6:00:00"
-if (${ICE_RUNLENGTH} == 7) set batchtime = "7:00:00"
-if (${ICE_RUNLENGTH} >= 8) set batchtime = "8:00:00"
+if (${runlength} == 0) set batchtime = "00:29:00"
+if (${runlength} == 1) set batchtime = "00:59:00"
+if (${runlength} == 2) set batchtime = "2:00:00"
+if (${runlength} == 3) set batchtime = "3:00:00"
+if (${runlength} == 4) set batchtime = "4:00:00"
+if (${runlength} == 5) set batchtime = "5:00:00"
+if (${runlength} == 6) set batchtime = "6:00:00"
+if (${runlength} == 7) set batchtime = "7:00:00"
+if (${runlength} >= 8) set batchtime = "8:00:00"
 
 set shortcase = `echo ${ICE_CASENAME} | cut -c1-15`
 
@@ -72,6 +79,18 @@ cat >> ${jobfile} << EOFB
 #PBS -l nodes=1:ppn=24
 EOFB
 
+else if (${ICE_MACHINE} =~ izumi*) then
+if (${runlength} > 2) set queue = "medium"
+cat >> ${jobfile} << EOFB
+#PBS -j oe 
+###PBS -m ae 
+#PBS -V
+#PBS -q ${queue}
+#PBS -N ${ICE_CASENAME}
+#PBS -l nodes=${nnodes}:ppn=${taskpernode}
+#PBS -l walltime=${batchtime}
+EOFB
+
 else if (${ICE_MACHINE} =~ thunder* || ${ICE_MACHINE} =~ gordon* || ${ICE_MACHINE} =~ conrad*  || ${ICE_MACHINE} =~ gaffney* || ${ICE_MACHINE} =~ koehr*) then
 cat >> ${jobfile} << EOFB
 #PBS -N ${shortcase}
@@ -175,6 +194,14 @@ cat >> ${jobfile} << EOFB
 #SBATCH --qos=standby
 EOFB
 
+else if (${ICE_MACHINE} =~ brooks*) then
+cat >> ${jobfile} << EOFB
+#PBS -N ${ICE_CASENAME}
+#PBS -j oe
+#PBS -l select=${nnodes}:ncpus=${corespernode}:mpiprocs=${taskpernodelimit}:ompthreads=${nthrds}
+#PBS -l walltime=${batchtime}
+EOFB
+
 else if (${ICE_MACHINE} =~ theia*) then
 cat >> ${jobfile} << EOFB
 #SBATCH -J ${ICE_CASENAME}