From 3ed236c859e83b13f8d9b1d8eac47218a318d8cf Mon Sep 17 00:00:00 2001
From: laurenchilutti <60401591+laurenchilutti@users.noreply.github.com>
Date: Wed, 7 Jun 2023 14:58:12 -0400
Subject: [PATCH] Bug Fixes (#23)

* -DHAVE_GETTID should only be added the FMS build cppdefs when on Gaea.

* fixing intel.mk

* loading python causes problems in gnu.mk and intel.mk because nc-config --libs is no longer blank.  And fixing error in intel.mk and gnu.mk

* update use yaml functionality in COMPILE and MAKE_libFMS so that building FMS without the -Duse_yaml flag is the defualt
---
 Build/COMPILE                |  1 +
 Build/mk_scripts/MAKE_libFMS |  4 ++--
 site/environment.gnu.sh      | 12 ++++++++++--
 site/environment.intel.sh    | 12 ++++++++++--
 site/gnu.mk                  |  4 ++--
 site/intel.mk                |  4 ++--
 6 files changed, 27 insertions(+), 10 deletions(-)

diff --git a/Build/COMPILE b/Build/COMPILE
index 4b61c0b..06061c1 100755
--- a/Build/COMPILE
+++ b/Build/COMPILE
@@ -156,6 +156,7 @@ echo -e "\tbit      = $bit"
 echo -e "\tavx      = $avx"
 echo -e "\tcompiler = $compiler"
 echo -e "\tclean    = $clean"
+echo -e "\tyaml     = $yaml"
 echo -e "\n"
 sleep 5
 
diff --git a/Build/mk_scripts/MAKE_libFMS b/Build/mk_scripts/MAKE_libFMS
index fb4f10e..6bd8cba 100755
--- a/Build/mk_scripts/MAKE_libFMS
+++ b/Build/mk_scripts/MAKE_libFMS
@@ -42,7 +42,7 @@ do
         ;;
         noyaml|yaml)
         YAML="${arg#*=}"
-	if [ $YAML='yaml' ] ; then
+	if [ ${YAML} = 'yaml' ] ; then
           USE_YAML=-Duse_yaml
         fi
 	shift # Remove yaml from processing
@@ -56,7 +56,7 @@ done
 
 #
 # CPPDEFS needed to build libFMS
-cppDefs="-Duse_libMPI -Duse_netCDF -Duse_LARGEFILE -DHAVE_SCHED_GETAFFINITY -DINTERNAL_FILE_NML -DGFS_PHYS -DGFS_CONSTANTS ${USE_YAML} -DHAVE_GETTID"
+cppDefs="-Duse_libMPI -Duse_netCDF -Duse_LARGEFILE -DHAVE_SCHED_GETAFFINITY -DINTERNAL_FILE_NML -DGFS_PHYS -DGFS_CONSTANTS ${USE_YAML} ${FMS_CPPDEFS}"
 
 #
 # clean up and create the FMS library directory
diff --git a/site/environment.gnu.sh b/site/environment.gnu.sh
index ecdcb52..f91e287 100755
--- a/site/environment.gnu.sh
+++ b/site/environment.gnu.sh
@@ -40,9 +40,11 @@ case $hostname in
        module load cray-netcdf/4.9.0.3
        module load craype-hugepages4M
        module load cmake/3.23.1
-       module load python/3.9
        module load libyaml/0.2.5
 
+       # Add -DHAVE_GETTID to the FMS cppDefs
+       export FMS_CPPDEFS=-DHAVE_GETTID
+
        # make your compiler selections here
        export FC=ftn
        export CC=cc
@@ -72,9 +74,11 @@ case $hostname in
        module load cray-netcdf/4.8.1.3
        module load craype-hugepages4M
        module load cmake/3.20.1
-       module load python/3.9
        module load libyaml/0.2.5
 
+       # Add -DHAVE_GETTID to the FMS cppDefs
+       export FMS_CPPDEFS=-DHAVE_GETTID
+
        # make your compiler selections here
        export FC=ftn
        export CC=cc
@@ -103,6 +107,7 @@ case $hostname in
        export HDF5=${HDF5_ROOT}
        export LIBRARY_PATH="${LIBRARY_PATH}:${NETCDF}/lib:${HDF5}/lib"
        export NETCDF_DIR=${NETCDF}
+       export FMS_CPPDEFS=""
 
        # make your compiler selections here
        export FC=mpif90
@@ -131,6 +136,7 @@ case $hostname in
 
        export LIBRARY_PATH="${LIBRARY_PATH}:${NETCDF4}/lib:${HDF5}/lib"
        export NETCDF_DIR=${NETCDF4}
+       export FMS_CPPDEFS=""
 
        # make your compiler selections here
        export FC=mpif90
@@ -158,6 +164,7 @@ case $hostname in
 
        export LIBRARY_PATH="${LIBRARY_PATH}:${NETCDF}/lib:${HDF5}/lib"
        export NETCDF_DIR=${NETCDF}
+       export FMS_CPPDEFS=""
 
        # make your compiler selections here
        export FC=mpif90
@@ -185,6 +192,7 @@ case $hostname in
 
        export CPATH="${NETCDF_ROOT}/include:${CPATH}"
        export NETCDF_DIR=${NETCDF_ROOT}
+       export FMS_CPPDEFS=""
 
        # make your compiler selections here
        export FC=mpif90
diff --git a/site/environment.intel.sh b/site/environment.intel.sh
index 196dd85..b3eced6 100755
--- a/site/environment.intel.sh
+++ b/site/environment.intel.sh
@@ -43,9 +43,11 @@ case $hostname in
       module load cray-netcdf
       module load craype-hugepages4M
       module load cmake/3.23.1
-      module load python/3.9
       module load libyaml/0.2.5
 
+      # Add -DHAVE_GETTID to the FMS cppDefs
+      export FMS_CPPDEFS=-DHAVE_GETTID
+
       # make your compiler selections here
       export FC=ftn
       export CC=cc
@@ -74,9 +76,11 @@ case $hostname in
       module load cray-netcdf/4.8.1.3
       module load craype-hugepages4M
       module load cmake/3.20.1
-      module load python/3.9
       module load libyaml/0.2.5
 
+      # Add -DHAVE_GETTID to the FMS cppDefs
+      export FMS_CPPDEFS=-DHAVE_GETTID
+
       # make your compiler selections here
       export FC=ftn
       export CC=cc
@@ -104,6 +108,7 @@ case $hostname in
       export HDF5=${HDF5_ROOT}
       export LIBRARY_PATH="${LIBRARY_PATH}:${NETCDF}/lib:${HDF5}/lib"
       export NETCDF_DIR=${NETCDF}
+      export FMS_CPPDEFS=""
 
       # make your compiler selections here
       export FC=mpiifort
@@ -133,6 +138,7 @@ case $hostname in
 
       export LIBRARY_PATH="${LIBRARY_PATH}:${NETCDF4}/lib:${HDF5}/lib"
       export NETCDF_DIR=${NETCDF4}
+      export FMS_CPPDEFS=""
 
       # make your compiler selections here
       export FC=mpiifort
@@ -155,6 +161,7 @@ case $hostname in
 
       export LIBRARY_PATH="${LIBRARY_PATH}:${NETCDF}/lib:${HDF5}/lib"
       export NETCDF_DIR=${NETCDF}
+      export FMS_CPPDEFS=""
 
       # make your compiler selections here
       export FC=mpiifort
@@ -182,6 +189,7 @@ case $hostname in
 
       export CPATH="${NETCDF_ROOT}/include:${CPATH}"
       export NETCDF_DIR=${NETCDF_ROOT}
+      export FMS_CPPDEFS=""
 
       # make your compiler selections here
       export FC=mpiifort
diff --git a/site/gnu.mk b/site/gnu.mk
index b6bbc36..e14ac7d 100644
--- a/site/gnu.mk
+++ b/site/gnu.mk
@@ -39,7 +39,7 @@ else
   INCLUDE = -I$(NETCDF_ROOT)/include
   LIBS += -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
 endif
-INCLUDE := $(shell pkg-config --cflags yaml-0.1)
+INCLUDE += $(shell pkg-config --cflags yaml-0.1)
 FPPFLAGS := -cpp -Wp,-w $(INCLUDE)
 CPPFLAGS := $(shell pkg-config --cflags yaml-0.1)
 
@@ -120,7 +120,7 @@ ifeq ($(NETCDF),3)
     CPPDEFS += -Duse_LARGEFILE
   endif
 endif
-LIBS := $(shell pkg-config --libs yaml-0.1)
+LIBS += $(shell pkg-config --libs yaml-0.1)
 LDFLAGS += $(LIBS) -L$(NETCDF_ROOT)/lib -L$(HDF5_DIR)/lib
 
 #---------------------------------------------------------------------------
diff --git a/site/intel.mk b/site/intel.mk
index db01c74..26dace6 100644
--- a/site/intel.mk
+++ b/site/intel.mk
@@ -39,7 +39,7 @@ else
   INCLUDE = -I$(NETCDF_ROOT)/include
   LIBS += -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
 endif
-INCLUDE := $(shell pkg-config --cflags yaml-0.1)
+INCLUDE += $(shell pkg-config --cflags yaml-0.1)
 FPPFLAGS := -fpp -Wp,-w $(INCLUDE)
 CPPFLAGS := $(shell pkg-config --cflags yaml-0.1)
 
@@ -123,7 +123,7 @@ ifeq ($(NETCDF),3)
   endif
 endif
 
-LIBS := $(shell pkg-config --libs yaml-0.1)
+LIBS += $(shell pkg-config --libs yaml-0.1)
 LDFLAGS += $(LIBS)
 
 #---------------------------------------------------------------------------