use shared_lib

.gitignore

@@ -11,3 +11,4 @@ src/externals/mct/config.status
 *.py[cod]
 build
 bld
+*.egg-info

README.md

@@ -13,6 +13,8 @@ This section shows you how to install eCLM on your local machine. If you are a u
 
 ### Minimum system requirements
 
+#### CentOS-8
+
 * MPI 3.1
 * netCDF-C 4.7.4
 * netCDF-Fortran 4.5.2
@@ -23,6 +25,17 @@ This section shows you how to install eCLM on your local machine. If you are a u
   - GCC 9.3.0
   - Intel 19.1.2
 
+#### Ubuntu-22.04
+
+- `OpenMPI`: 4.1.2
+- `netCDF-C`: 4.8.1
+- `netCDF-Fortran`: 4.6.0
+- `PnetCDF`: 1.12.1
+- `CMake`: 3.22.1
+- `gcc`: 11.4.0
+- `mpicc`: 11.4.0
+
+
 ### Building eCLM
 
 1. Configure CMake build options.

run.sh

@@ -6,7 +6,7 @@ INSTALL_DIR="eclm"
 cmake -S src -B "$BUILD_DIR" \
       -DCMAKE_INSTALL_PREFIX="$INSTALL_DIR" \
       -DCMAKE_C_COMPILER=mpicc \
-      -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch -fallow-invalid-boz" \
+      -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch -fallow-invalid-boz -fPIC" \
       -DCMAKE_Fortran_COMPILER=mpifort
 
 cd bld

src/CMakeLists.txt

@@ -1,6 +1,9 @@
 cmake_minimum_required (VERSION 3.16.3)
 project (eCLM LANGUAGES C Fortran)
 
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fPIC -shared")
+set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC -shared")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -shared")
 
 if(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
   if(CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER_EQUAL 10)

src/clm5/CMakeLists.txt

@@ -1,6 +1,7 @@
 project (clm LANGUAGES Fortran)
 
-add_library(${PROJECT_NAME} STATIC)
+# add_library(${PROJECT_NAME} STATIC)
+add_library(${PROJECT_NAME} SHARED)
 
 target_compile_definitions(${PROJECT_NAME} PRIVATE NDEBUG)
 target_include_directories(${PROJECT_NAME} PUBLIC ${CMAKE_CURRENT_BINARY_DIR})
@@ -324,4 +325,4 @@ if(LAPACK_FOUND)
     target_link_libraries(${PROJECT_NAME} PRIVATE LAPACK::LAPACK)
 endif()
 target_link_libraries(${PROJECT_NAME} PRIVATE csm_share)
-install (TARGETS ${PROJECT_NAME} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+install (TARGETS ${PROJECT_NAME} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})

src/csm_share/CMakeLists.txt

@@ -1,6 +1,7 @@
 project (csm_share LANGUAGES C Fortran)
 
-add_library(${PROJECT_NAME} STATIC)
+# add_library(${PROJECT_NAME} STATIC)
+add_library(${PROJECT_NAME} SHARED)
 
 # TODO: NUM_COMP_INST_<COMP> should be adjusted for ensemble runs. See the ff. for more info:
 # https://esmci.github.io/cime/versions/cesm2.2/html/users_guide/multi-instance.html

src/datm/CMakeLists.txt

@@ -1,6 +1,6 @@
 project (datm LANGUAGES Fortran)
 
-add_library(${PROJECT_NAME} STATIC)
+add_library(${PROJECT_NAME} SHARED)
 
 target_include_directories(${PROJECT_NAME} PUBLIC ${CMAKE_CURRENT_BINARY_DIR})
 target_link_directories(${PROJECT_NAME} PUBLIC ${CMAKE_CURRENT_BINARY_DIR})
@@ -12,4 +12,4 @@ target_sources(${PROJECT_NAME}
         atm_comp_mct.F90
 )
 target_link_libraries(${PROJECT_NAME} PRIVATE csm_share)
-install (TARGETS ${PROJECT_NAME} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+install (TARGETS ${PROJECT_NAME} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})

src/externals/CMakeLists.txt

@@ -11,8 +11,8 @@ file(MAKE_DIRECTORY ${GPTL_BLD_DIR}/include ${GPTL_BLD_DIR}/lib)
 set(GPTL_MACROS_FILE ${GPTL_BLD_DIR}/Macros.make)
 file(WRITE  ${GPTL_MACROS_FILE} "  MPICC := ${CMAKE_C_COMPILER}\n")
 file(APPEND ${GPTL_MACROS_FILE} "  MPIFC := ${CMAKE_Fortran_COMPILER}\n")
-file(APPEND ${GPTL_MACROS_FILE} "  CLAGS := ${CMAKE_C_FLAGS}\n")
-file(APPEND ${GPTL_MACROS_FILE} " FFLAGS := ${CMAKE_Fortran_FLAGS}\n")
+file(APPEND ${GPTL_MACROS_FILE} "  CLAGS := ${CMAKE_C_FLAGS} -fPIC -shared\n")
+file(APPEND ${GPTL_MACROS_FILE} " FFLAGS := ${CMAKE_Fortran_FLAGS} -fPIC -shared\n")
 file(APPEND ${GPTL_MACROS_FILE} "CPPDEFS := -DFORTRANUNDERSCORE\n")
 
 ExternalProject_Add(gptl_external
@@ -26,15 +26,15 @@ ExternalProject_Add(gptl_external
                       SHAREDPATH=${GPTL_BLD_DIR}
     INSTALL_COMMAND   ""
     BUILD_ALWAYS      YES
-    BUILD_BYPRODUCTS  ${GPTL_BLD_DIR}/lib/libgptl.a
+    BUILD_BYPRODUCTS  ${GPTL_BLD_DIR}/lib/libgptl.so
 )
 
 add_library(gptl INTERFACE IMPORTED GLOBAL)
 target_include_directories(gptl INTERFACE ${GPTL_BLD_DIR}/include)
 target_link_directories(gptl INTERFACE ${GPTL_BLD_DIR}/lib)
-target_link_libraries(gptl INTERFACE libgptl.a)
+target_link_libraries(gptl INTERFACE libgptl.so)
 add_dependencies(gptl gptl_external)
-install (FILES ${GPTL_BLD_DIR}/lib/libgptl.a TYPE LIB)
+install (FILES ${GPTL_BLD_DIR}/lib/libgptl.so TYPE LIB)
 
 
 # ===========
@@ -75,4 +75,4 @@ endif()
 # ===========
 #     PIO
 # ===========
-add_subdirectory(pio1)
+add_subdirectory(pio1)

src/externals/gptl/CMakeLists.txt

@@ -21,4 +21,4 @@ SET(SRCS_C  GPTLget_memusage.c
 SET(SRCS_F90  perf_mod.F90
               perf_utils.F90)
 
-ADD_LIBRARY(timing ${SRCS_F90} ${SRCS_C})
+ADD_LIBRARY(timing SHARED ${SRCS_F90} ${SRCS_C})

src/externals/gptl/Makefile

@@ -48,10 +48,12 @@ OBJS = gptl.o GPTLutil.o GPTLget_memusage.o GPTLprint_memusage.o \
 AR ?= ar
 ARFLAGS ?= ruv
 
-libgptl.a: $(OBJS)
+libgptl.so: $(OBJS)
 	$(AR) $(ARFLAGS) $@ $(OBJS)
 
 
+CFLAGS=-fPIC -shared
+FFLAGS=-fPIC -shared
 
 .c.o:
 	$(CC) -c $(INCLDIR) $(INCS) $(CFLAGS) $(CPPDEFS) $<
@@ -69,10 +71,10 @@ clean:
 	$(RM) -f *.f *.f90 *.d *.$(MOD_SUFFIX) $(OBJS)
 
 
-install: libgptl.a
+install: libgptl.so
 	cp -p $(GPTL_DIR)/gptl.h $(SHAREDPATH)/include
 	cp -p *.$(MOD_SUFFIX) $(SHAREDPATH)/include
-	cp -p libgptl.a $(SHAREDPATH)/lib
+	cp -p libgptl.so $(SHAREDPATH)/lib
 
 
 perf_mod.o: perf_utils.o

src/externals/mct/.gitignore

@@ -6,4 +6,5 @@ autom4te.cache
 *.o
 *.mod
 lib*.a
+lib*.so
 data

src/externals/mct/benchmarks/Makefile

@@ -44,7 +44,7 @@ clean:
 
 # DEPENDENCIES:
 
-$(OBJS_ALL): $(MCTPATH)/libmct.a
+$(OBJS_ALL): $(MCTPATH)/libmct.so
 
 
 

src/externals/mct/configure

@@ -5482,7 +5482,7 @@ elif echo $ac_fc_version_output | grep -i sx >/dev/null 2>&1; then
 fi
 
 # Test to see if fortran compiler supports the flag
-# -fallow-argument-mismatch flag introduced in gfortran 10.
+# -fallow-argument-mismatch -shared -fPIC  flag introduced in gfortran 10.
 #
 # Also allow support for NAG compiler using the -mismatch_all flag.
 #
@@ -5496,14 +5496,14 @@ Program test
 USE ISO_C_BINDING, ONLY: C_PTRDIFF_T
 End Program
 EOF
-doit='$FC -c ${FCFLAGS} ${FCFLAGS_f90} -fallow-argument-mismatch conftest.f90'
+doit='$FC -c ${FCFLAGS} ${FCFLAGS_f90} -fallow-argument-mismatch -shared -fPIC  conftest.f90'
 if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$doit\""; } >&5
   (eval $doit) 2>&5
   ac_status=$?
   printf "%s\n" "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
    nf_allow_mismatch=yes
-   FCFLAGS="${FCFLAGS} -fallow-argument-mismatch"
+   FCFLAGS="${FCFLAGS} -fallow-argument-mismatch -shared -fPIC "
   else
    nf_allow_mismatch=no
 fi

src/externals/mct/configure.ac

@@ -459,7 +459,7 @@ elif echo $ac_fc_version_output | grep -i sx >/dev/null 2>&1; then
 fi
 
 # Test to see if fortran compiler supports the flag
-# -fallow-argument-mismatch flag introduced in gfortran 10.
+# -fallow-argument-mismatch -shared -fPIC  flag introduced in gfortran 10.
 #
 # Also allow support for NAG compiler using the -mismatch_all flag.
 #
@@ -472,10 +472,10 @@ Program test
 USE ISO_C_BINDING, ONLY: C_PTRDIFF_T
 End Program
 EOF
-doit='$FC -c ${FCFLAGS} ${FCFLAGS_f90} -fallow-argument-mismatch conftest.f90'
+doit='$FC -c ${FCFLAGS} ${FCFLAGS_f90} -fallow-argument-mismatch -shared -fPIC  conftest.f90'
 if AC_TRY_EVAL(doit); then
    nf_allow_mismatch=yes
-   FCFLAGS="${FCFLAGS} -fallow-argument-mismatch"
+   FCFLAGS="${FCFLAGS} -fallow-argument-mismatch -shared -fPIC "
   else
    nf_allow_mismatch=no
 fi

src/externals/mct/mct/Makefile

@@ -41,10 +41,9 @@ OBJS_ALL	= $(SRCS_F90:.F90=.o)
 include ../Makefile.conf
 
 # TARGETS
+all: 	lib$(MODULE).so
 
-all: 	lib$(MODULE).a
-
-lib$(MODULE).a:	$(OBJS_ALL)
+lib$(MODULE).so:	$(OBJS_ALL)
 	$(RM) $@
 	$(AR) $@ $(OBJS_ALL)
 	$(RANLIB) $@
@@ -63,19 +62,19 @@ MCTFLAGS = $(INCFLAG)$(MPEUPATH)
 
 
 clean:
-	${RM} *.o *.mod lib$(MODULE).a
+	${RM} *.o *.mod lib$(MODULE).so
 
 install: all
 	$(MKINSTALLDIRS) $(libdir) $(includedir)
-	$(INSTALL) lib$(MODULE).a -m 644 $(libdir)
+	$(INSTALL) lib$(MODULE).so -m 644 $(libdir)
 	@for modfile in *.mod; do                         \
 	  echo $(INSTALL) $$modfile -m 644 $(includedir); \
 	  $(INSTALL) $$modfile -m 644 $(includedir);      \
 	done
 
 # DEPENDENCIES
 
-$(OBJS_ALL): $(MPEUPATH)/libmpeu.a
+$(OBJS_ALL): $(MPEUPATH)/libmpeu.so
 
 m_AttrVect.o:
 m_Accumulator.o: m_AttrVect.o

src/externals/mct/mpeu/Makefile

@@ -48,9 +48,9 @@ OBJS_ALL	= $(SRCS_C:.c=.o)  \
 
 # TARGETS
 
-all:	lib$(MODULE).a
+all:	lib$(MODULE).so
 
-lib$(MODULE).a:	$(OBJS_ALL)
+lib$(MODULE).so:	$(OBJS_ALL)
 	$(RM) $@
 	$(AR) $@ $(OBJS_ALL)
 	$(RANLIB) $@
@@ -71,11 +71,11 @@ MPEUFLAGS =
 	$(FC) -c $(INCPATH) $(FPPDEFS) $(FCFLAGS) $(MPEUFLAGS) $<
 
 clean:
-	${RM} *.o *.mod lib$(MODULE).a
+	${RM} *.o *.mod lib$(MODULE).so
 
 install: all
 	$(MKINSTALLDIRS) $(libdir) $(includedir)
-	$(INSTALL) lib$(MODULE).a -m 644 $(libdir)
+	$(INSTALL) lib$(MODULE).so -m 644 $(libdir)
 	@for modfile in *.mod; do                         \
 	  echo $(INSTALL) $$modfile -m 644 $(includedir); \
 	  $(INSTALL) $$modfile -m 644 $(includedir);      \

src/externals/mct/mpi-serial/configure

@@ -5018,7 +5018,7 @@ elif echo $ac_fc_version_output | grep -i nag >/dev/null 2>&1; then
 fi
 
 # Test to see if fortran compiler supports the flag
-# -fallow-argument-mismatch flag introduced in gfortran 10.
+# -fallow-argument-mismatch -shared -fPIC  flag introduced in gfortran 10.
 #
 # Also allow support for NAG compiler using the -mismatch_all flag.
 #
@@ -5032,14 +5032,14 @@ Program test
 USE ISO_C_BINDING, ONLY: C_PTRDIFF_T
 End Program
 EOF
-doit='$FC -c ${FCFLAGS} ${FCFLAGS_f90} -fallow-argument-mismatch conftest.f90'
+doit='$FC -c ${FCFLAGS} ${FCFLAGS_f90} -fallow-argument-mismatch -shared -fPIC  conftest.f90'
 if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$doit\""; } >&5
   (eval $doit) 2>&5
   ac_status=$?
   printf "%s\n" "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }; then
    nf_allow_mismatch=yes
-   FCFLAGS="${FCFLAGS} -fallow-argument-mismatch"
+   FCFLAGS="${FCFLAGS} -fallow-argument-mismatch -shared -fPIC "
   else
    nf_allow_mismatch=no
 fi

src/externals/mct/mpi-serial/configure.ac

@@ -85,7 +85,7 @@ elif echo $ac_fc_version_output | grep -i nag >/dev/null 2>&1; then
 fi
 
 # Test to see if fortran compiler supports the flag
-# -fallow-argument-mismatch flag introduced in gfortran 10.
+# -fallow-argument-mismatch -shared -fPIC  flag introduced in gfortran 10.
 #
 # Also allow support for NAG compiler using the -mismatch_all flag.
 #
@@ -98,10 +98,10 @@ Program test
 USE ISO_C_BINDING, ONLY: C_PTRDIFF_T
 End Program
 EOF
-doit='$FC -c ${FCFLAGS} ${FCFLAGS_f90} -fallow-argument-mismatch conftest.f90'
+doit='$FC -c ${FCFLAGS} ${FCFLAGS_f90} -fallow-argument-mismatch -shared -fPIC  conftest.f90'
 if AC_TRY_EVAL(doit); then
    nf_allow_mismatch=yes
-   FCFLAGS="${FCFLAGS} -fallow-argument-mismatch"
+   FCFLAGS="${FCFLAGS} -fallow-argument-mismatch -shared -fPIC "
   else
    nf_allow_mismatch=no
 fi

src/externals/pio1/CMakeLists.txt

@@ -1,5 +1,5 @@
 project(pio C Fortran)
-add_library(${PROJECT_NAME} STATIC)
+add_library(${PROJECT_NAME} SHARED)
 
 find_file(TESTFILE NAMES TryCSizeOf.f90 PATHS ${CMAKE_MODULE_PATH} NO_DEFAULT_PATH)
 get_filename_component(TESTFILEPATH ${TESTFILE} PATH)
@@ -153,4 +153,4 @@ endforeach()
 
 target_sources(${PROJECT_NAME} PRIVATE ${SRCS_F90} ${SRCS_C} ${TEMPSRCF90})
 
-install (TARGETS ${PROJECT_NAME} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+install (TARGETS ${PROJECT_NAME} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})

src/mosart/CMakeLists.txt

@@ -1,6 +1,6 @@
 project (mosart LANGUAGES Fortran)
 
-add_library(${PROJECT_NAME} STATIC)
+add_library(${PROJECT_NAME} SHARED)
 
 target_include_directories(${PROJECT_NAME} PUBLIC ${CMAKE_CURRENT_BINARY_DIR})
 target_link_directories(${PROJECT_NAME} PUBLIC ${CMAKE_CURRENT_BINARY_DIR})
@@ -23,4 +23,4 @@ target_sources(${PROJECT_NAME} PRIVATE
 )
 
 target_link_libraries(${PROJECT_NAME} PRIVATE csm_share)
-install (TARGETS ${PROJECT_NAME} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+install (TARGETS ${PROJECT_NAME} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})