Merge pull request #5 from mnlevy1981/source_file_from_path

I cleaned up a lot of the documentation in tools/mapping; I think tools that rely on $CIME/tools/configure now have consistent INSTALL instructions, ESMF version numbers have been updated to what's currently available on yellowstone and cheyenne (7.0.0), and tools that rely on ESMF executables run as expected on cheyenne.

tools/mapping/check_maps/.gitignore

@@ -1,2 +1,4 @@
 ESMF_RegridWeightGenCheck
 src/*.o
+*.nc
+*.Log

tools/mapping/check_maps/README

@@ -1,9 +1,3 @@
-==========================================================================
-$Id: README 46983 2013-05-09 22:08:12Z tcraig $
-$URL: https://svn-ccsm-models.cgd.ucar.edu/tools/mapping/trunk_tags/mapping_141106/check_maps/README $
-==========================================================================
-
-
 ===============
 ABOUT THIS TOOL
 ===============
@@ -42,23 +36,29 @@ BUILD
 =====
 
 To compile this tool, you need to have the ESMFMKFILE environment variable set.
-The easiest way to do that is to load the ESMF modules. To do this, you must
-already have the intel module loaded. Then load the version of ESMF you want
-to use (as of April 2013, the most recent version available is 6.1.1):
+The easiest way to do that is to load the ESMF modules. On yellowstone and
+cheyenne, you must already have the intel module loaded. Then load the version
+of ESMF you want to use (as of April 2017, the most recent version available is
+7.0.0):
 
+Yellowstone:
 $ module load esmf
-$ module load esmf-6.3.0r-ncdfio-uni-O
+$ module load esmf-7.0.0-ncdfio-uni-O
+
+Cheyenne:
+$ module load esmf_libs/7.0.0
+$ module load esmf-7.0.0-ncdfio-uni-O
 
-This will set ESMFMKFILE. With this variable set, enter the mapping/check_maps/src/
-directory and run gmake
+This will set ESMFMKFILE. With this variable set, enter the src/ directory and
+run gmake
 
-$ cd mapping/check_maps/src
+$ cd src
 $ gmake [VERBOSE=TRUE]
 
 VERBOSE=TRUE turns on some extra diagnostic output and is optional.
 
-Back in the mapping/check_maps/ directory, you should now have an executable
-file named ESMF_RegridWeightGenCheck.
+Back in this directory, you should now have an executable file named
+ESMF_RegridWeightGenCheck.
 
 Note that at this time, the tool only works in serial mode (building with the
 mpi-enabled version of the ESMF makefile leads to a segmentation fault when
@@ -78,6 +78,6 @@ listed in FILELIST
   --help, -h        Output this usage information
 
 Notes:
-  1) For use on yellowstone, geyser, or caldera only!
+  1) For use on cheyenne, yellowstone, geyser, or caldera only!
   2) Need to set ESMFMKFILE (see comments in Makefile) or compilation will fail
   3) If -rc option is not enabled, -v flag is ignored and verbose / concise will depend on previous compilation

tools/mapping/check_maps/src/ESMF_RegridWeightGenCheck.F90

@@ -716,6 +716,8 @@ program OfflineTester
               failCnt = failCnt + 1
               if (Verbose) then
                 print *, "FAILED: conservation error = ", totArea
+                print *, "        area1 = ", sum(grid1area)
+                print *, "        area2 = ", sum(grid2area)
               else
                 print *, "FAILED: conservation error = ", totArea, &
                          " in test ", j

tools/mapping/check_maps/src/Makefile

@@ -15,11 +15,18 @@
 ###       The executable should run on the yellowstone login node         ######
 ################################################################################
 
-ifneq ($(origin ESMFMKFILE), environment)
-$(error Environment variable ESMFMKFILE was not set.)
+# Don't require ESMF to be loaded to run "make clean":
+USE_ESMF=TRUE
+ifeq ($(MAKECMDGOALS),clean)
+  USE_ESMF=FALSE
 endif
 
-include $(ESMFMKFILE)
+ifeq ($(USE_ESMF),TRUE)
+  ifneq ($(origin ESMFMKFILE), environment)
+    $(error Environment variable ESMFMKFILE was not set.)
+  endif
+  include $(ESMFMKFILE)
+endif
 TARGET = ESMF_RegridWeightGenCheck
 
 # To compile with verbose output, run

tools/mapping/gen_domain_files/INSTALL

@@ -2,17 +2,16 @@
 HOW TO BUILD
 ============
 
-Prior to building, you must make sure environment variables CIMEROOT and CIME_MODEL are set.
-
 (1) $ cd src
-(2) $ $CIMEROOT/tools/configure --machine [machine name] --macros-format Makefile
-(3) Bash users:
-    $ . ./.env_mach_specific.sh
-    csh users:
-    $ source ./.env_mach_specific.csh
-(4) $ gmake
+(2) $ ../../../configure --macros-format Makefile --mpilib mpi-serial
+Bash users:
+(3) $ (. ./.env_mach_specific.sh ; gmake)
+csh users:
+(3) $ (source ./.env_mach_specific.csh ; gmake)
 
-Note: in the second step, replace [machine name] with the machine you are
-building on. Also, some machines have dedicated build nodes, so you might need
-to SSH to another node before the 'gmake' step.
+Note: in the second step, you may need to include "--machine [machine name]",
+where [machine name] is the name of the machine you are building on. In most
+cases configure can figure that out on its own, but if you get an error that is
+the first fix to try. Also, some machines have dedicated build nodes, so you
+might need to SSH to another node before the 'gmake' step.
 

tools/mapping/gen_domain_files/src/Makefile

@@ -36,7 +36,19 @@ default: $(EXENAME)
 $(MACROS):
 	@echo "use the configure script located in the Machines directory to create the Makefile $(MACROS) file"
 
--include $(MACROS)
+# Do not include Macros for clean or distclean targets
+USE_MACROS=TRUE
+ifeq ($(MAKECMDGOALS),clean)
+  USE_MACROS=FALSE
+endif
+ifeq ($(MAKECMDGOALS),distcleanclean)
+  USE_MACROS=FALSE
+endif
+
+ifeq ($(USE_MACROS),TRUE)
+  -include $(MACROS)
+endif
+
 # Check for the netcdf library and include directories
 ifdef NETCDF_PATH
   LIB_NETCDF:=$(NETCDF_PATH)/lib
@@ -133,7 +145,7 @@ $(EXENAME): $(OBJS)
 clean:
 	$(RM) -f $(OBJS) $(EXENAME) *.mod
 
-veryclean:
-	$(RM) -f $(OBJS) $(EXENAME) *.mod $(MACROS) env_mach* Depends* .env_mach*
+distclean: clean
+	../../../configure --clean
 
 gen_domain.o : gen_domain.F90

tools/mapping/gen_mapping_files/README

@@ -120,8 +120,8 @@ Note: if rtm is specified and lnd is not, then this tool will
 
 You can also set the following env variables:
   ESMFBIN_PATH - Path to ESMF binaries
-                 (Leave unset on yellowstone and caldera and the tool
-                 will be loaded from modules)
+                 (Leave unset on cheyenne, yellowstone, and caldera and the
+                 tool will be loaded from modules)
   MPIEXEC ------ Name of mpirun executable
                  (default is mpirun.lsf on yellowstone and caldera; if
                  you run interactively on yellowstone, mpi is not used)

tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/.gitignore

@@ -0,0 +1,2 @@
+*.Log
+*.nc

tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/README

@@ -82,8 +82,8 @@ where
 
 You can also set the following env variables:
   ESMFBIN_PATH - Path to ESMF binaries
-                 (Leave unset on yellowstone and caldera and the tool
-                 will be loaded from modules)
+                 (Leave unset on cheyenne, yellowstone, and caldera and the
+                 tool will be loaded from modules)
   MPIEXEC ------ Name of mpirun executable
                  (default is mpirun.lsf on yellowstone and caldera; if
                  you run interactively on yellowstone, mpi is not used)

tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/create_ESMF_map.sh

@@ -80,8 +80,8 @@ usage() {
   echo ''
   echo 'You can also set the following env variables:'
   echo '  ESMFBIN_PATH - Path to ESMF binaries '
-  echo '                 (Leave unset on yellowstone/caldera/pronghorn and the tool'
-  echo '                 will be loaded from modules)'
+  echo '                 (Leave unset on cheyenne/yellowstone/caldera/pronghorn'
+  echo '                 and the tool will be loaded from modules)'
   echo '  MPIEXEC ------ Name of mpirun executable'
   echo '                 (default is mpirun.lsf on yellowstone/caldera/pronghorn; if'
   echo '                 you run interactively on yellowstone, mpi is not used)'
@@ -225,6 +225,9 @@ if [ $MACH == "UNSET" ]; then
     ys* )
       MACH="yellowstone"
     ;;
+    cheyenne* )
+      MACH="cheyenne"
+    ;;
     geyser* )
       MACH="geyser"
     ;;
@@ -244,10 +247,13 @@ if [ $MACH == "UNSET" ]; then
 fi
 
 # Machine specific settings:
-# 1) can not run in parallel interactively on yellowstone
+# 1) can not run in parallel interactively on yellowstone or cheyenne
 if [ $MACH == "yellowstone" ] && [ $interactive == "YES" ]; then
   serial="TRUE"
 fi
+if [ $MACH == "cheyenne" ] && [ $interactive == "YES" ]; then
+  serial="TRUE"
+fi
 # 2) jaguar requires additional environment var
 if [ $MACH == "jaguar" ] && [ -z "$REGRID_PROC" ]; then
   REGRID_PROC=8
@@ -310,22 +316,26 @@ fi
 
 case $MACH in
   ## yellowstone, geyser, caldera, or pronghorn
-  "yellowstone" | "geyser" | "caldera" | "pronghorn" )
+  "cheyenne" | "yellowstone" | "geyser" | "caldera" | "pronghorn" )
     # From tcsh, script will not find module command
     # So check to see if module works, otherwise source an init file
     module list > /dev/null 2>&1 || source /etc/profile.d/modules.sh
     module purge
     module load intel
     module load nco
-    module load esmf
+    if [  $MACH == "cheyenne" ]; then
+      module load esmf_libs/7.0.0
+    else
+      module load esmf
+    fi
 
     if [ $serial == "TRUE" ]; then
-      module load esmf-6.3.0rp1-ncdfio-uni-O
+      module load esmf-7.0.0-ncdfio-uni-O
       if [ -z "$MPIEXEC" ]; then
         MPIEXEC=""
       fi
     else
-      module load esmf-6.3.0rp1-ncdfio-mpi-O
+      module load esmf-7.0.0-ncdfio-mpi-O
       if [ -z "$MPIEXEC" ]; then
         MPIEXEC="mpirun.lsf"
       fi

tools/mapping/map_field/INSTALL

@@ -2,17 +2,16 @@
 HOW TO BUILD
 ============
 
-Prior to building, you must make sure $CIMEROOT is set.
-
 (1) $ cd src
-(2) $ $CIMEROOT/tools/configure macros-format Makefile
-(3) Bash users:
-    $ . ./.env_mach_specific.sh
-    csh users:
-    $ source ./.env_mach_specific.csh
-(4) $ gmake
+(2) $ ../../../configure --macros-format Makefile --mpilib mpi-serial
+Bash users:
+(3) $ (. ./.env_mach_specific.sh ; gmake)
+csh users:
+(3) $ (source ./.env_mach_specific.csh ; gmake)
 
-Note: in the second step, replace [machine name] with the machine you are
-building on. Also, some machines have dedicated build nodes, so you might need
-to SSH to another node before the 'gmake' step.
+Note: in the second step, you may need to include "--machine [machine name]",
+where [machine name] is the name of the machine you are building on. In most
+cases configure can figure that out on its own, but if you get an error that is
+the first fix to try. Also, some machines have dedicated build nodes, so you
+might need to SSH to another node before the 'gmake' step.
 

tools/mapping/map_field/src/Makefile

@@ -29,14 +29,26 @@ null :=
 CURDIR = .
 EXENAME = ../map_field
 RM = rm
-MACFILE = Macros.make
+MACROS = Macros.make
 
 default: $(EXENAME)
 
-$(MACFILE):
-	@echo "use the configure script located in the Machines directory to create the Makefile $(MACFILE) file"
+$(MACROS):
+	@echo "use the configure script located in the Machines directory to create the Makefile $(MACROS) file"
+
+# Do not include Macros for clean or distclean targets
+USE_MACROS=TRUE
+ifeq ($(MAKECMDGOALS),clean)
+  USE_MACROS=FALSE
+endif
+ifeq ($(MAKECMDGOALS),distcleanclean)
+  USE_MACROS=FALSE
+endif
+
+ifeq ($(USE_MACROS),TRUE)
+  -include $(MACROS)
+endif
 
--include $(MACFILE)
 # Check for the netcdf library and include directories
 ifdef NETCDF_PATH
   LIB_NETCDF:=$(NETCDF_PATH)/lib
@@ -97,7 +109,7 @@ else
   FPPDEFS := $(CPPDEFS)
 endif
 #Primary Target: build the tool
-all: $(EXENAME) $(MACFILE)
+all: $(EXENAME) $(MACROS)
 
 OBJS := map_field.o
 
@@ -133,7 +145,7 @@ $(EXENAME): $(OBJS)
 clean:
 	$(RM) -f $(OBJS) $(EXENAME) *.mod
 
-veryclean:
-	$(RM) -f $(OBJS) $(EXENAME) *.mod $(MACFILE) .env_mach* env_mach*
+distclean: clean
+	../../../configure --clean
 
 map_field.o : map_field.F90