Merge branch 'jgfouca/cmake_mct_csm_share' into master (PR #5964)

CMake: Improve dependency management for mct and csm_share Neither of these packages are cmake packages, so we have to roll our own Find$package.cmake modules. These can be pretty simple for e3sm since we build them ourselves (no worries about version or not found etc). Also, remove a lot of unused for special handling of clm and stuff for pio building. [BFB]
E3SM-Project · Oct 5, 2023 · 2ff3742 · 2ff3742
2 parents 573137b + 653b97b
commit 2ff3742
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diff --git a/cime_config/machines/cmake_macros/amdclang_alvarez.cmake b/cime_config/machines/cmake_macros/amdclang_alvarez.cmake
@@ -1,13 +1,7 @@
 if (COMP_NAME STREQUAL gptl)
   string(APPEND CPPDEFS " -DHAVE_NANOTIME -DBIT64 -DHAVE_SLASHPROC -DHAVE_GETTIMEOFDAY")
 endif()
-string(APPEND SLIBS " -L$ENV{CRAY_HDF5_PARALLEL_PREFIX}/lib -lhdf5_hl -lhdf5 -L$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX} -L$ENV{CRAY_PARALLEL_NETCDF_PREFIX}/lib -lpnetcdf -lnetcdf -lnetcdff")
 string(APPEND SLIBS " -lblas -llapack -lamdlibm")
-set(NETCDF_PATH "$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}")
-set(NETCDF_C_PATH "$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}")
-set(NETCDF_FORTRAN_PATH "$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}")
-set(HDF5_PATH "$ENV{CRAY_HDF5_PARALLEL_PREFIX}")
-set(PNETCDF_PATH "$ENV{CRAY_PARALLEL_NETCDF_PREFIX}")
 if (NOT DEBUG)
   string(APPEND CFLAGS " -O2 -g")
   string(APPEND CXXFLAGS " -O2 -g")

diff --git a/cime_config/machines/cmake_macros/amdclang_chicoma-cpu.cmake b/cime_config/machines/cmake_macros/amdclang_chicoma-cpu.cmake
@@ -1,13 +1,7 @@
 if (COMP_NAME STREQUAL gptl)
   string(APPEND CPPDEFS " -DHAVE_NANOTIME -DBIT64 -DHAVE_SLASHPROC -DHAVE_GETTIMEOFDAY")
 endif()
-string(APPEND SLIBS " -L$ENV{CRAY_HDF5_PARALLEL_PREFIX}/lib -lhdf5_hl -lhdf5 -L$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX} -L$ENV{CRAY_PARALLEL_NETCDF_PREFIX}/lib -lpnetcdf -lnetcdf -lnetcdff")
 string(APPEND SLIBS " -lblas -llapack -lamdlibm")
-set(NETCDF_PATH "$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}")
-set(NETCDF_C_PATH "$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}")
-set(NETCDF_FORTRAN_PATH "$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}")
-set(HDF5_PATH "$ENV{CRAY_HDF5_PARALLEL_PREFIX}")
-set(PNETCDF_PATH "$ENV{CRAY_PARALLEL_NETCDF_PREFIX}")
 set(PIO_FILESYSTEM_HINTS "lustre")
 if (NOT DEBUG)
   string(APPEND CFLAGS " -O2 -g")

diff --git a/cime_config/machines/cmake_macros/amdclang_crusher.cmake b/cime_config/machines/cmake_macros/amdclang_crusher.cmake
@@ -5,15 +5,9 @@ set(SCC "cc")
 set(SCXX "CC")
 set(SFC "ftn")
 
-set(NETCDF_PATH "$ENV{NETCDF_DIR}")
-set(PNETCDF_PATH "$ENV{PNETCDF_DIR}")
 string(APPEND CPPDEFS " -DLINUX")
 if (COMP_NAME STREQUAL gptl)
     string(APPEND CPPDEFS " -DHAVE_NANOTIME -DBIT64 -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY")
 endif()
-string(APPEND SLIBS " -L$ENV{PNETCDF_PATH}/lib -lpnetcdf -L$ENV{CRAY_LIBSCI_PREFIX_DIR}/lib -lsci_amd")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib64 -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl -ladios2_enet")
-endif()
-set(PNETCDF_PATH "$ENV{PNETCDF_DIR}")
+string(APPEND SLIBS " -L$ENV{CRAY_LIBSCI_PREFIX_DIR}/lib -lsci_amd")
 set(CRAY_LIBSCI_PREFIX_DIR "$ENV{CRAY_LIBSCI_PREFIX_DIR}")
diff --git a/cime_config/machines/cmake_macros/amdclang_frontier.cmake b/cime_config/machines/cmake_macros/amdclang_frontier.cmake
@@ -5,15 +5,9 @@ set(SCC "cc")
 set(SCXX "CC")
 set(SFC "ftn")
 
-set(NETCDF_PATH "$ENV{NETCDF_DIR}")
-set(PNETCDF_PATH "$ENV{PNETCDF_DIR}")
 string(APPEND CPPDEFS " -DLINUX")
 if (COMP_NAME STREQUAL gptl)
     string(APPEND CPPDEFS " -DHAVE_NANOTIME -DBIT64 -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY")
 endif()
-string(APPEND SLIBS " -L$ENV{PNETCDF_PATH}/lib -lpnetcdf -L$ENV{CRAY_LIBSCI_PREFIX_DIR}/lib -lsci_amd")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib64 -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl -ladios2_enet")
-endif()
-set(PNETCDF_PATH "$ENV{PNETCDF_DIR}")
+string(APPEND SLIBS " -L$ENV{CRAY_LIBSCI_PREFIX_DIR}/lib -lsci_amd")
 set(CRAY_LIBSCI_PREFIX_DIR "$ENV{CRAY_LIBSCI_PREFIX_DIR}")
diff --git a/cime_config/machines/cmake_macros/amdclang_pm-cpu.cmake b/cime_config/machines/cmake_macros/amdclang_pm-cpu.cmake
@@ -1,16 +1,7 @@
 if (COMP_NAME STREQUAL gptl)
   string(APPEND CPPDEFS " -DHAVE_NANOTIME -DBIT64 -DHAVE_SLASHPROC -DHAVE_GETTIMEOFDAY")
 endif()
-string(APPEND SLIBS " -L$ENV{CRAY_HDF5_PARALLEL_PREFIX}/lib -lhdf5_hl -lhdf5 -L$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX} -L$ENV{CRAY_PARALLEL_NETCDF_PREFIX}/lib -lpnetcdf -lnetcdf -lnetcdff")
 string(APPEND SLIBS " -lblas -llapack -lamdlibm")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib64 -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl -ladios2_enet")
-endif()
-set(NETCDF_PATH "$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}")
-set(NETCDF_C_PATH "$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}")
-set(NETCDF_FORTRAN_PATH "$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}")
-set(HDF5_PATH "$ENV{CRAY_HDF5_PARALLEL_PREFIX}")
-set(PNETCDF_PATH "$ENV{CRAY_PARALLEL_NETCDF_PREFIX}")
 if (NOT DEBUG)
   string(APPEND CFLAGS " -O2 -g")
   string(APPEND CXXFLAGS " -O2 -g")

diff --git a/cime_config/machines/cmake_macros/amdclanggpu_crusher.cmake b/cime_config/machines/cmake_macros/amdclanggpu_crusher.cmake
@@ -5,8 +5,6 @@ set(SCC "cc")
 set(SCXX "CC")
 set(SFC "ftn")
 
-set(NETCDF_PATH "$ENV{NETCDF_DIR}")
-set(PNETCDF_PATH "$ENV{PNETCDF_DIR}")
 string(APPEND CPPDEFS " -DLINUX")
 if (COMP_NAME STREQUAL gptl)
     string(APPEND CPPDEFS " -DHAVE_NANOTIME -DBIT64 -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY")
@@ -17,18 +15,13 @@ if (NOT DEBUG)
   string(APPEND FFLAGS   " -O2")
 endif()
 
-set(NETCDF_PATH "$ENV{NETCDF_DIR}")
-set(PNETCDF_PATH "$ENV{PNETCDF_DIR}")
 string(APPEND CMAKE_OPTS " -DPIO_ENABLE_TOOLS:BOOL=OFF")
 string(APPEND SLIBS " -L$ENV{CRAY_LIBSCI_PREFIX_DIR}/lib -lsci_amd")
 
 set(MPICXX "hipcc")
 set(SCXX "hipcc")
 string(APPEND CXXFLAGS " -I$ENV{MPICH_DIR}/include --offload-arch=gfx90a")
 string(APPEND SLIBS    " -L$ENV{MPICH_DIR}/lib -lmpi -L$ENV{CRAY_MPICH_ROOTDIR}/gtl/lib -lmpi_gtl_hsa")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib64 -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl -ladios2_enet")
-endif()
 string(APPEND KOKKOS_OPTIONS " -DKokkos_ENABLE_HIP=On -DKokkos_ARCH_ZEN3=On -DKokkos_ARCH_VEGA90A=On")
 
 set(USE_HIP "TRUE")

diff --git a/cime_config/machines/cmake_macros/amdclanggpu_frontier.cmake b/cime_config/machines/cmake_macros/amdclanggpu_frontier.cmake
@@ -5,8 +5,6 @@ set(SCC "cc")
 set(SCXX "CC")
 set(SFC "ftn")
 
-set(NETCDF_PATH "$ENV{NETCDF_DIR}")
-set(PNETCDF_PATH "$ENV{PNETCDF_DIR}")
 string(APPEND CPPDEFS " -DLINUX")
 if (COMP_NAME STREQUAL gptl)
     string(APPEND CPPDEFS " -DHAVE_NANOTIME -DBIT64 -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY")
@@ -17,18 +15,13 @@ if (NOT DEBUG)
   string(APPEND FFLAGS   " -O2")
 endif()
 
-set(NETCDF_PATH "$ENV{NETCDF_DIR}")
-set(PNETCDF_PATH "$ENV{PNETCDF_DIR}")
 string(APPEND CMAKE_OPTS " -DPIO_ENABLE_TOOLS:BOOL=OFF")
 string(APPEND SLIBS " -L$ENV{CRAY_LIBSCI_PREFIX_DIR}/lib -lsci_amd")
 
 set(MPICXX "hipcc")
 set(SCXX "hipcc")
 string(APPEND CXXFLAGS " -I$ENV{MPICH_DIR}/include --offload-arch=gfx90a")
 string(APPEND SLIBS    " -L$ENV{MPICH_DIR}/lib -lmpi -L$ENV{CRAY_MPICH_ROOTDIR}/gtl/lib -lmpi_gtl_hsa")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib64 -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl -ladios2_enet")
-endif()
 string(APPEND KOKKOS_OPTIONS " -DKokkos_ENABLE_HIP=On -DKokkos_ARCH_ZEN3=On -DKokkos_ARCH_VEGA90A=On")
 
 set(USE_HIP "TRUE")

diff --git a/cime_config/machines/cmake_macros/crayclang-scream_crusher-scream-cpu.cmake b/cime_config/machines/cmake_macros/crayclang-scream_crusher-scream-cpu.cmake
@@ -5,12 +5,6 @@ if (compile_threaded)
   string(APPEND LDFLAGS " -fopenmp")
 endif()
 
-string(APPEND SLIBS " -L$ENV{PNETCDF_PATH}/lib -lpnetcdf")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib64 -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl -ladios2_enet")
-endif()
-set(NETCDF_PATH "$ENV{NETCDF_DIR}")
-set(PNETCDF_PATH "$ENV{PNETCDF_DIR}")
 set(PIO_FILESYSTEM_HINTS "gpfs")
 string(APPEND CXX_LIBS " -lstdc++")
 

diff --git a/cime_config/machines/cmake_macros/crayclang-scream_crusher-scream-gpu.cmake b/cime_config/machines/cmake_macros/crayclang-scream_crusher-scream-gpu.cmake
@@ -5,12 +5,6 @@ if (compile_threaded)
   string(APPEND LDFLAGS " -fopenmp")
 endif()
 
-string(APPEND SLIBS " -L$ENV{PNETCDF_PATH}/lib -lpnetcdf")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib64 -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl -ladios2_enet")
-endif()
-set(NETCDF_PATH "$ENV{NETCDF_DIR}")
-set(PNETCDF_PATH "$ENV{PNETCDF_DIR}")
 set(PIO_FILESYSTEM_HINTS "gpfs")
 string(APPEND CXX_LIBS " -lstdc++")
 

diff --git a/cime_config/machines/cmake_macros/crayclang-scream_crusher-scream.cmake b/cime_config/machines/cmake_macros/crayclang-scream_crusher-scream.cmake
@@ -10,8 +10,5 @@ endif()
 string(APPEND FFLAGS " -hipa0 -hzero")
 string(APPEND FFLAGS " -em -ef")
 
-string(APPEND SLIBS " -L$ENV{PNETCDF_PATH}/lib -lpnetcdf")
-set(NETCDF_PATH "$ENV{NETCDF_DIR}")
-set(PNETCDF_PATH "$ENV{PNETCDF_DIR}")
 set(PIO_FILESYSTEM_HINTS "gpfs")
 string(APPEND CXX_LIBS " -lstdc++")
diff --git a/cime_config/machines/cmake_macros/crayclang_crusher.cmake b/cime_config/machines/cmake_macros/crayclang_crusher.cmake
@@ -9,10 +9,4 @@ string(APPEND FFLAGS " -hipa0 -hzero")
 # Scorpio installs
 string(APPEND FFLAGS " -em -ef")
 
-string(APPEND SLIBS " -L$ENV{PNETCDF_PATH}/lib -lpnetcdf")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib64 -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl -ladios2_enet")
-endif()
-set(NETCDF_PATH "$ENV{NETCDF_DIR}")
-set(PNETCDF_PATH "$ENV{PNETCDF_DIR}")
 string(APPEND CXX_LIBS " -lstdc++")
diff --git a/cime_config/machines/cmake_macros/crayclang_frontier.cmake b/cime_config/machines/cmake_macros/crayclang_frontier.cmake
@@ -9,10 +9,4 @@ string(APPEND FFLAGS " -hipa0 -hzero")
 # Scorpio installs
 string(APPEND FFLAGS " -em -ef")
 
-string(APPEND SLIBS " -L$ENV{PNETCDF_PATH}/lib -lpnetcdf")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib64 -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl -ladios2_enet")
-endif()
-set(NETCDF_PATH "$ENV{NETCDF_DIR}")
-set(PNETCDF_PATH "$ENV{PNETCDF_DIR}")
 string(APPEND CXX_LIBS " -lstdc++")
diff --git a/cime_config/machines/cmake_macros/crayclanggpu_crusher.cmake b/cime_config/machines/cmake_macros/crayclanggpu_crusher.cmake
@@ -60,17 +60,12 @@ endif()
 # https://github.com/E3SM-Project/E3SM/pull/5208
 string(APPEND FFLAGS " -hipa0 -hzero -em -ef -hnoacc")
 
-set(NETCDF_PATH "$ENV{NETCDF_DIR}")
-set(PNETCDF_PATH "$ENV{PNETCDF_DIR}")
 string(APPEND CMAKE_OPTS " -DPIO_ENABLE_TOOLS:BOOL=OFF")
 string(APPEND CXX_LIBS " -lstdc++")
 
 string(APPEND CXXFLAGS " -I$ENV{MPICH_DIR}/include --offload-arch=gfx90a")
 string(APPEND SLIBS    " -L$ENV{MPICH_DIR}/lib -lmpi -L$ENV{CRAY_MPICH_ROOTDIR}/gtl/lib -lmpi_gtl_hsa")
 string(APPEND SLIBS " -L$ENV{ROCM_PATH}/lib -lamdhip64")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib64 -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl -ladios2_enet")
-endif()
 
 string(APPEND KOKKOS_OPTIONS " -DKokkos_ENABLE_HIP=On -DKokkos_ARCH_ZEN3=On -DKokkos_ARCH_VEGA90A=On")
 

diff --git a/cime_config/machines/cmake_macros/crayclanggpu_frontier.cmake b/cime_config/machines/cmake_macros/crayclanggpu_frontier.cmake
@@ -60,18 +60,12 @@ endif()
 # https://github.com/E3SM-Project/E3SM/pull/5208
 string(APPEND FFLAGS " -hipa0 -hzero -em -ef -hnoacc")
 
-set(NETCDF_PATH "$ENV{NETCDF_DIR}")
-set(PNETCDF_PATH "$ENV{PNETCDF_DIR}")
 string(APPEND CMAKE_OPTS " -DPIO_ENABLE_TOOLS:BOOL=OFF")
 string(APPEND CXX_LIBS " -lstdc++")
 
 string(APPEND CXXFLAGS " -I$ENV{MPICH_DIR}/include --offload-arch=gfx90a")
 string(APPEND SLIBS    " -L$ENV{MPICH_DIR}/lib -lmpi -L$ENV{CRAY_MPICH_ROOTDIR}/gtl/lib -lmpi_gtl_hsa")
 string(APPEND SLIBS " -L$ENV{ROCM_PATH}/lib -lamdhip64")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib64 -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl -ladios2_enet")
-endif()
-
 
 string(APPEND KOKKOS_OPTIONS " -DKokkos_ENABLE_HIP=On -DKokkos_ARCH_ZEN3=On -DKokkos_ARCH_VEGA90A=On")
 

diff --git a/cime_config/machines/cmake_macros/fj.cmake b/cime_config/machines/cmake_macros/fj.cmake
@@ -32,12 +32,7 @@ set(MPIFC "mpifrt")
 set(SCC "fcc")
 set(SCXX "FCC")
 set(SFC "frt")
-set(NETCDF_C_PATH "$ENV{NETCDF_C_PATH}")
-set(NETCDF_FORTRAN_PATH "$ENV{NETCDF_FORTRAN_PATH}")
-set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")
-execute_process(COMMAND $ENV{NETCDF_FORTRAN_PATH}/bin/nf-config --flibs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0 OUTPUT_STRIP_TRAILING_WHITESPACE)
-execute_process(COMMAND $ENV{NETCDF_C_PATH}/bin/nc-config --libs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE1 OUTPUT_STRIP_TRAILING_WHITESPACE)
-string(APPEND SLIBS " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0} ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE1} -lblas -llapack")
+string(APPEND SLIBS " -lblas -llapack")
 if (COMP_NAME MATCHES "^pio")
   string(APPEND CMAKE_OPTS " -DPIO_ENABLE_TOOLS:BOOL=OFF")
 endif()
diff --git a/cime_config/machines/cmake_macros/gnu9_mappy.cmake b/cime_config/machines/cmake_macros/gnu9_mappy.cmake
@@ -8,10 +8,7 @@ string(APPEND CXX_LIBS " -lstdc++")
 if (NOT DEBUG)
   string(APPEND FFLAGS " -O2")
 endif()
-string(APPEND FFLAGS " -I$ENV{NETCDFROOT}/include")
-set(NETCDF_PATH "$ENV{NETCDFROOT}")
 if (MPILIB STREQUAL mpi-serial AND NOT compile_threaded)
   set(PFUNIT_PATH "$ENV{SEMS_PFUNIT_ROOT}")
 endif()
-execute_process(COMMAND ${NETCDF_PATH}/bin/nf-config --flibs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0 OUTPUT_STRIP_TRAILING_WHITESPACE)
-string(APPEND SLIBS " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0} -lblas -llapack")
+string(APPEND SLIBS " -lblas -llapack")
diff --git a/cime_config/machines/cmake_macros/gnu_WSL2.cmake b/cime_config/machines/cmake_macros/gnu_WSL2.cmake
@@ -1,11 +1,4 @@
 set(HDF5_PATH "$ENV{HDF5_PATH}")
-set(NETCDF_PATH "$ENV{NETCDF_PATH}")
-set(NETCDF_C_PATH "$ENV{NETCDF_C_PATH}")
-set(NETCDF_FORTRAN_PATH "$ENV{NETCDF_FORTRAN_PATH}")
 set(LAPACK_LIBDIR "$ENV{BLASLAPACK_LIBDIR}")
 set(CXX_LINKER "CXX")
-execute_process(COMMAND ${NETCDF_PATH}/bin/nf-config --flibs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0 OUTPUT_STRIP_TRAILING_WHITESPACE)
-string(APPEND SLIBS " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0}")
-execute_process(COMMAND ${NETCDF_PATH}/bin/nc-config --libs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0 OUTPUT_STRIP_TRAILING_WHITESPACE)
-string(APPEND SLIBS " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0}")
 string(APPEND SLIBS " -L${LAPACK_LIBDIR} -lblas -llapack")
diff --git a/cime_config/machines/cmake_macros/gnu_alvarez.cmake b/cime_config/machines/cmake_macros/gnu_alvarez.cmake
@@ -2,14 +2,8 @@ string(APPEND CONFIG_ARGS " --host=cray")
 if (COMP_NAME STREQUAL gptl)
   string(APPEND CPPDEFS " -DHAVE_NANOTIME -DBIT64 -DHAVE_SLASHPROC -DHAVE_GETTIMEOFDAY")
 endif()
-string(APPEND SLIBS " -L$ENV{CRAY_HDF5_PARALLEL_PREFIX}/lib -lhdf5_hl -lhdf5 -L$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}/lib -L$ENV{CRAY_PARALLEL_NETCDF_PREFIX}/lib -lpnetcdf -lnetcdf -lnetcdff")
 string(APPEND SLIBS " -lblas -llapack")
 set(CXX_LINKER "FORTRAN")
-set(NETCDF_PATH "$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}")
-set(NETCDF_C_PATH "$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}")
-set(NETCDF_FORTRAN_PATH "$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}")
-set(HDF5_PATH "$ENV{CRAY_HDF5_PARALLEL_PREFIX}")
-set(PNETCDF_PATH "$ENV{CRAY_PARALLEL_NETCDF_PREFIX}")
 if (NOT DEBUG)
   string(APPEND CFLAGS " -O2 -g")
 endif()

diff --git a/cime_config/machines/cmake_macros/gnu_anlgce-ub18.cmake b/cime_config/machines/cmake_macros/gnu_anlgce-ub18.cmake
@@ -5,13 +5,5 @@ string(APPEND CXX_LIBS " -lstdc++")
 if (NOT DEBUG)
   string(APPEND FFLAGS " -O2")
 endif()
-execute_process(COMMAND $ENV{NETCDF_PATH}/bin/nf-config --flibs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0 OUTPUT_STRIP_TRAILING_WHITESPACE)
-execute_process(COMMAND $ENV{NETCDF_PATH}/bin/nc-config --libs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE1 OUTPUT_STRIP_TRAILING_WHITESPACE)
-string(APPEND SLIBS " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0} ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE1} -lblas -llapack")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl -ladios2_enet")
-endif()
-set(NETCDF_PATH "$ENV{NETCDF_PATH}")
-set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")
-set(HDF5_PATH "$ENV{HDF5_PATH}")
+string(APPEND SLIBS " -lblas -llapack")
 set(ZLIB_PATH "$ENV{ZLIB_PATH}")
diff --git a/cime_config/machines/cmake_macros/gnu_anlgce.cmake b/cime_config/machines/cmake_macros/gnu_anlgce.cmake
@@ -5,13 +5,5 @@ string(APPEND CXX_LIBS " -lstdc++")
 if (NOT DEBUG)
   string(APPEND FFLAGS " -O2")
 endif()
-execute_process(COMMAND $ENV{NETCDF_PATH}/bin/nf-config --flibs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0 OUTPUT_STRIP_TRAILING_WHITESPACE)
-execute_process(COMMAND $ENV{NETCDF_PATH}/bin/nc-config --libs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE1 OUTPUT_STRIP_TRAILING_WHITESPACE)
-string(APPEND SLIBS " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0} ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE1} -lblas -llapack")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl -ladios2_enet")
-endif()
-set(NETCDF_PATH "$ENV{NETCDF_PATH}")
-set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")
-set(HDF5_PATH "$ENV{HDF5_PATH}")
+string(APPEND SLIBS " -lblas -llapack")
 set(ZLIB_PATH "$ENV{ZLIB_PATH}")
diff --git a/cime_config/machines/cmake_macros/gnu_anlworkstation.cmake b/cime_config/machines/cmake_macros/gnu_anlworkstation.cmake
@@ -5,13 +5,6 @@ string(APPEND CXX_LIBS " -lstdc++")
 if (NOT DEBUG)
   string(APPEND FFLAGS " -O2")
 endif()
-execute_process(COMMAND $ENV{NETCDF_PATH}/bin/nf-config --flibs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0 OUTPUT_STRIP_TRAILING_WHITESPACE)
-string(APPEND SLIBS " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0} -lblas -llapack")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -lpthread")
-endif()
-set(NETCDF_PATH "$ENV{NETCDF_PATH}")
-set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")
-set(HDF5_PATH "$ENV{HDF5_PATH}")
+string(APPEND SLIBS " -lblas -llapack")
 set(SZIP_PATH "$ENV{SZIP_PATH}")
 set(ZLIB_PATH "$ENV{ZLIB_PATH}")
diff --git a/cime_config/machines/cmake_macros/gnu_anvil.cmake b/cime_config/machines/cmake_macros/gnu_anvil.cmake
@@ -2,14 +2,5 @@ if (COMP_NAME STREQUAL gptl)
   string(APPEND CPPDEFS " -DHAVE_NANOTIME -DBIT64 -DHAVE_SLASHPROC -DHAVE_GETTIMEOFDAY")
 endif()
 set(PIO_FILESYSTEM_HINTS "gpfs")
-execute_process(COMMAND $ENV{NETCDF_FORTRAN_PATH}/bin/nf-config --flibs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0 OUTPUT_STRIP_TRAILING_WHITESPACE)
-string(APPEND SLIBS " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0}  -L$ENV{MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl")
-execute_process(COMMAND $ENV{NETCDF_C_PATH}/bin/nc-config --libs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0 OUTPUT_STRIP_TRAILING_WHITESPACE)
-string(APPEND SLIBS " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0}")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib64 -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl -ladios2_enet")
-endif()
+string(APPEND SLIBS " -L$ENV{MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl")
 string(APPEND CXX_LIBS " -lstdc++")
-set(NETCDF_C_PATH "$ENV{NETCDF_C_PATH}")
-set(NETCDF_FORTRAN_PATH "$ENV{NETCDF_FORTRAN_PATH}")
-set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")
diff --git a/cime_config/machines/cmake_macros/gnu_ascent.cmake b/cime_config/machines/cmake_macros/gnu_ascent.cmake
@@ -8,10 +8,7 @@ endif()
 if (COMP_NAME STREQUAL gptl)
   string(APPEND CPPDEFS " -DHAVE_SLASHPROC")
 endif()
-string(APPEND SLIBS " -L$ENV{PNETCDF_PATH}/lib -lpnetcdf -L$ENV{HDF5_PATH}/lib -lhdf5_hl -lhdf5 -L$ENV{NETCDF_C_PATH}/lib -lnetcdf -L$ENV{NETCDF_FORTRAN_PATH}/lib -lnetcdff -L$ENV{ESSL_PATH}/lib64 -lessl -L$ENV{OLCF_NETLIB_LAPACK_ROOT}/lib64 -llapack")
+string(APPEND SLIBS " -L$ENV{ESSL_PATH}/lib64 -lessl -L$ENV{OLCF_NETLIB_LAPACK_ROOT}/lib64 -llapack")
 string(APPEND CXX_LIBS " -lstdc++")
 set(MPICXX "mpiCC")
 set(PIO_FILESYSTEM_HINTS "gpfs")
-set(NETCDF_C_PATH "$ENV{NETCDF_C_PATH}")
-set(NETCDF_FORTRAN_PATH "$ENV{NETCDF_FORTRAN_PATH}")
-set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")
diff --git a/cime_config/machines/cmake_macros/gnu_badger.cmake b/cime_config/machines/cmake_macros/gnu_badger.cmake
@@ -1,11 +1,5 @@
 set(PIO_FILESYSTEM_HINTS "lustre")
 set(MPICXX "mpic++")
-execute_process(COMMAND nc-config --libs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0 OUTPUT_STRIP_TRAILING_WHITESPACE)
-string(APPEND SLIBS " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0}")
-execute_process(COMMAND nf-config --flibs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0 OUTPUT_STRIP_TRAILING_WHITESPACE)
-string(APPEND SLIBS " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0} -lnetcdff -llapack -lblas")
+string(APPEND SLIBS " -llapack -lblas")
 string(APPEND SLIBS " $ENV{MKLROOT}/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group $ENV{MKLROOT}/lib/intel64/libmkl_intel_lp64.a $ENV{MKLROOT}/lib/intel64/libmkl_core.a $ENV{MKLROOT}/lib/intel64/libmkl_sequential.a -Wl,--end-group $ENV{MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a -lpthread -lm -lz")
 string(APPEND CXX_LIBS " -lstdc++")
-set(NETCDF_C_PATH "$ENV{NETCDF_PATH}")
-set(NETCDF_FORTRAN_PATH "$ENV{NETCDF_PATH}")
-set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")
diff --git a/cime_config/machines/cmake_macros/gnu_bebop.cmake b/cime_config/machines/cmake_macros/gnu_bebop.cmake
@@ -2,14 +2,4 @@ if (COMP_NAME STREQUAL gptl)
   string(APPEND CPPDEFS " -DHAVE_SLASHPROC")
 endif()
 string(APPEND CXX_LIBS " -lstdc++")
-execute_process(COMMAND $ENV{NETCDF_FORTRAN_PATH}/bin/nf-config --flibs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0 OUTPUT_STRIP_TRAILING_WHITESPACE)
-execute_process(COMMAND $ENV{NETCDF_C_PATH}/bin/nc-config --libs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE1 OUTPUT_STRIP_TRAILING_WHITESPACE)
-string(APPEND SLIBS " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0} ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE1}")
 string(APPEND SLIBS " -L$ENV{MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl")
-if (NOT MPILIB STREQUAL mpi-serial)
-  string(APPEND SLIBS " -L$ENV{ADIOS2_DIR}/lib64 -ladios2_c_mpi -ladios2_c -ladios2_core_mpi -ladios2_core -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl -ladios2_enet")
-endif()
-set(NETCDF_C_PATH "$ENV{NETCDF_C_PATH}")
-set(NETCDF_FORTRAN_PATH "$ENV{NETCDF_FORTRAN_PATH}")
-set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")
-set(HDF5_PATH "$ENV{HDF5_PATH}")