Merge branch 'jgfouca/replace_xml_with_cmake_macros' into master (PR #…

…4537)

Major build system enhancement: deprecate config_compilers.xml!

This is the most significant change to the case-control system since
the cmake-ification (#3043) effort 2 years ago. This PR is a natural
follow-on to that effort that further cmake-ifies our build system and
reduces technical debt / complexity in the build system by stripping
away layers of CIME magic that were not adding much value for
us. Specifically, the config_compilers.xml file, which CIME uses to
generate the Macros.make and Macros.cmake casedir files (specifies
compilers, flags, link flags etc), will be replaced with hierarchical
CMake cache files that are persistently stored in our repo.

[BFB]

* jgfouca/replace_xml_with_cmake_macros:
  Fix handling of '\!'
  Add CIME hotfix
  Use COMP_NAME, not MODEL
  Sync with latest config_compilers.xml
  Add support for compiler_os.cmake macros
  Improve dox for compare-flags
  compare-flags: make tool more flexible and better output
  Refresh cache files after upstream merge
  Add some helper scripts for this effort
  Update CIME with latest
  Add support for universal macro
  Update CIME to bring in new macro capability
  Remove obsolete comment
  Add new cmake-based macros

cime_config/machines/cmake_macros/CNL.cmake

@@ -0,0 +1,18 @@
+if (NOT MPILIB STREQUAL impi)
+  string(APPEND CMAKE_OPTS " -DCMAKE_SYSTEM_NAME=Catamount")
+endif()
+string(APPEND CPPDEFS " -DLINUX")
+if (COMP_NAME STREQUAL gptl)
+  string(APPEND CPPDEFS " -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY")
+endif()
+set(MPICC "cc")
+set(MPICXX "CC")
+set(MPIFC "ftn")
+set(MPI_LIB_NAME "mpich")
+set(MPI_PATH "$ENV{MPICH_DIR}")
+set(NETCDF_PATH "$ENV{NETCDF_DIR}")
+set(PIO_FILESYSTEM_HINTS "lustre")
+set(PNETCDF_PATH "$ENV{PARALLEL_NETCDF_DIR}")
+set(SCC "cc")
+set(SCXX "CC")
+set(SFC "ftn")

cime_config/machines/cmake_macros/Darwin.cmake

@@ -0,0 +1,4 @@
+string(APPEND CPPDEFS " -DSYSDARWIN")
+if (COMP_CLASS STREQUAL cpl)
+  string(APPEND LDFLAGS " -all_load")
+endif()

cime_config/machines/cmake_macros/Macros.cmake

@@ -0,0 +1,39 @@
+#
+# Use this file to include the relevant macros based on
+# machine/compiler settings. This file gets copied to CASEROOT
+# and that's the one that gets included by the build system. Feel free
+# to modify this file in the CASEROOT.
+#
+cmake_policy(SET CMP0057 NEW)
+
+set(MACROS_DIR ${CASEROOT}/cmake_macros)
+
+set(UNIVERSAL_MACRO ${MACROS_DIR}/universal.cmake)
+set(COMPILER_MACRO ${MACROS_DIR}/${COMPILER}.cmake)
+set(OS_MACRO ${MACROS_DIR}/${OS}.cmake)
+set(MACHINE_MACRO ${MACROS_DIR}/${MACH}.cmake)
+set(COMPILER_OS_MACRO ${MACROS_DIR}/${COMPILER}_${OS}.cmake)
+set(COMPILER_MACHINE_MACRO ${MACROS_DIR}/${COMPILER}_${MACH}.cmake)
+
+if (CONVERT_TO_MAKE)
+  get_cmake_property(VARS_BEFORE_BUILD_INTERNAL_IGNORE VARIABLES)
+endif()
+
+# Include order defines precedence
+foreach (MACRO_FILE ${UNIVERSAL_MACRO} ${COMPILER_MACRO} ${OS_MACRO} ${MACHINE_MACRO} ${COMPILER_OS_MACRO} ${COMPILER_MACHINE_MACRO})
+  if (EXISTS ${MACRO_FILE})
+    include(${MACRO_FILE})
+  else()
+    message("No macro file found: ${MACRO_FILE}")
+  endif()
+endforeach()
+
+if (CONVERT_TO_MAKE)
+  get_cmake_property(VARS_AFTER VARIABLES)
+
+  foreach (VAR_AFTER IN LISTS VARS_AFTER)
+    if (NOT VAR_AFTER IN_LIST VARS_BEFORE_BUILD_INTERNAL_IGNORE)
+      message("E3SM_SET_MAKEFILE_VAR ${VAR_AFTER} := ${${VAR_AFTER}}")
+    endif()
+  endforeach()
+endif()

cime_config/machines/cmake_macros/cray.cmake

@@ -0,0 +1,26 @@
+if (compile_threaded)
+  string(APPEND CFLAGS " -h omp")
+endif()
+if (DEBUG)
+  string(APPEND CFLAGS " -g -O0")
+endif()
+string(APPEND CPPDEFS " -DFORTRANUNDERSCORE -DNO_R16 -DCPRCRAY")
+set(FC_AUTO_R8 "-s real64")
+set(FFLAGS "-f free -N 255 -h byteswapio -em")
+if (compile_threaded)
+  string(APPEND FFLAGS " -h omp")
+endif()
+if (NOT compile_threaded)
+  string(APPEND FFLAGS " -M1077")
+endif()
+if (DEBUG)
+  string(APPEND FFLAGS " -g -O0")
+endif()
+set(FFLAGS_NOOPT "-O0")
+set(HAS_F2008_CONTIGUOUS "TRUE")
+set(LDFLAGS "-Wl,--allow-multiple-definition -h byteswapio")
+if (compile_threaded)
+  string(APPEND LDFLAGS " -h omp")
+endif()
+set(SUPPORTS_CXX "TRUE")
+set(CXX_LINKER "FORTRAN")

cime_config/machines/cmake_macros/cray_theta.cmake

@@ -0,0 +1,21 @@
+if (NOT DEBUG)
+  string(APPEND CFLAGS " -O1")
+endif()
+if (NOT DEBUG)
+  string(APPEND FFLAGS " -O1")
+endif()
+if (COMP_NAME STREQUAL eam)
+  string(APPEND FFLAGS " -vector0")
+endif()
+set(CXX_LINKER "CXX")
+set(KOKKOS_OPTIONS "--gcc-toolchain=/opt/gcc/9.3.0/snos --with-serial")
+set(CXXFLAGS "-std=c++14")
+if (compile_threaded)
+  string(APPEND CXXFLAGS " -fopenmp")
+endif()
+if (DEBUG)
+  string(APPEND CXXFLAGS " -g -Wall")
+endif()
+if (NOT DEBUG)
+  string(APPEND CXXFLAGS " -O1")
+endif()

cime_config/machines/cmake_macros/gnu.cmake

@@ -0,0 +1,56 @@
+set(CFLAGS "-mcmodel=medium")
+if (compile_threaded)
+  string(APPEND CFLAGS " -fopenmp")
+endif()
+if (DEBUG)
+  string(APPEND CFLAGS " -g -Wall -fbacktrace -fcheck=bounds -ffpe-trap=invalid,zero,overflow")
+endif()
+if (NOT DEBUG)
+  string(APPEND CFLAGS " -O")
+endif()
+if (COMP_NAME STREQUAL csm_share)
+  string(APPEND CFLAGS " -std=c99")
+endif()
+set(CXXFLAGS "-std=c++14")
+if (compile_threaded)
+  string(APPEND CXXFLAGS " -fopenmp")
+endif()
+if (DEBUG)
+  string(APPEND CXXFLAGS " -g -Wall -fbacktrace")
+endif()
+if (NOT DEBUG)
+  string(APPEND CXXFLAGS " -O")
+endif()
+if (COMP_NAME STREQUAL cism)
+  string(APPEND CMAKE_OPTS " -D CISM_GNU=ON")
+endif()
+string(APPEND CPPDEFS " -DFORTRANUNDERSCORE -DNO_R16 -DCPRGNU")
+if (DEBUG)
+  string(APPEND CPPDEFS " -DYAKL_DEBUG")
+endif()
+set(CXX_LINKER "FORTRAN")
+set(FC_AUTO_R8 "-fdefault-real-8")
+set(FFLAGS "-mcmodel=medium -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none")
+if (compile_threaded)
+  string(APPEND FFLAGS " -fopenmp")
+endif()
+if (DEBUG)
+  string(APPEND FFLAGS " -g -Wall -fbacktrace -fcheck=bounds -ffpe-trap=zero,overflow")
+endif()
+if (NOT DEBUG)
+  string(APPEND FFLAGS " -O")
+endif()
+set(FFLAGS_NOOPT "-O0")
+set(FIXEDFLAGS "-ffixed-form")
+set(FREEFLAGS "-ffree-form")
+set(HAS_F2008_CONTIGUOUS "FALSE")
+if (compile_threaded)
+  string(APPEND LDFLAGS " -fopenmp")
+endif()
+set(MPICC "mpicc")
+set(MPICXX "mpicxx")
+set(MPIFC "mpif90")
+set(SCC "gcc")
+set(SCXX "g++")
+set(SFC "gfortran")
+set(SUPPORTS_CXX "TRUE")

cime_config/machines/cmake_macros/gnu_anlworkstation.cmake

@@ -0,0 +1,15 @@
+set(ALBANY_PATH "/projects/install/rhel6-x86_64/ACME/AlbanyTrilinos/Albany/build/install")
+if (NOT DEBUG)
+  string(APPEND CFLAGS " -O2")
+endif()
+set(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 " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0} -lblas -llapack")
+set(NETCDF_PATH "$ENV{NETCDF_PATH}")
+set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")
+set(HDF5_PATH "$ENV{HDF5_PATH}")
+set(SZIP_PATH "$ENV{SZIP_PATH}")
+set(ZLIB_PATH "$ENV{ZLIB_PATH}")

cime_config/machines/cmake_macros/gnu_anvil.cmake

@@ -0,0 +1,12 @@
+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 " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0}")
+set(CXX_LIBS "-lstdc++")
+set(NETCDF_C_PATH "$ENV{NETCDF_C_PATH}")
+set(NETCDF_FORTRAN_PATH "$ENV{NETCDF_FORTRAN_PATH}")
+set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")

cime_config/machines/cmake_macros/gnu_ascent.cmake

@@ -0,0 +1,27 @@
+if (NOT DEBUG)
+  string(APPEND CFLAGS " -O2")
+endif()
+if (NOT DEBUG)
+  string(APPEND FFLAGS " -O2")
+endif()
+if (COMP_NAME STREQUAL gptl)
+  string(APPEND CPPDEFS " -DHAVE_SLASHPROC")
+endif()
+if (MPILIB STREQUAL mpi-serial)
+  string(APPEND SLIBS " -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}/lib -llapack")
+endif()
+if (NOT MPILIB STREQUAL mpi-serial)
+  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}/lib -llapack")
+endif()
+set(CXX_LIBS "-lstdc++")
+set(MPICC "mpicc")
+set(MPICXX "mpiCC")
+set(MPIFC "mpif90")
+set(SCC "gcc")
+set(SCXX "g++")
+set(SFC "gfortran")
+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}")
+set(SUPPORTS_CXX "TRUE")

cime_config/machines/cmake_macros/gnu_badger.cmake

@@ -0,0 +1,16 @@
+set(PIO_FILESYSTEM_HINTS "lustre")
+set(MPICC "mpicc")
+set(MPIFC "mpif90")
+set(MPICXX "mpic++")
+set(SFC "gfortran")
+set(SCC "gcc")
+set(SCXX "g++")
+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 " $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 $ENV{MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a -lpthread -lm -lz")
+set(CXX_LIBS "-lstdc++")
+set(NETCDF_C_PATH "$ENV{NETCDF_PATH}")
+set(NETCDF_FORTRAN_PATH "$ENV{NETCDF_PATH}")
+set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")

cime_config/machines/cmake_macros/gnu_bebop.cmake

@@ -0,0 +1,11 @@
+if (COMP_NAME STREQUAL gptl)
+  string(APPEND CPPDEFS " -DHAVE_SLASHPROC")
+endif()
+set(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")
+set(NETCDF_C_PATH "$ENV{NETCDF_C_PATH}")
+set(NETCDF_FORTRAN_PATH "$ENV{NETCDF_FORTRAN_PATH}")
+set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")

cime_config/machines/cmake_macros/gnu_cades.cmake

@@ -0,0 +1,33 @@
+if (compile_threaded)
+  string(APPEND CFLAGS " -fopenmp")
+endif()
+if (COMP_NAME STREQUAL cism)
+  string(APPEND CMAKE_OPTS " -D CISM_GNU=ON")
+endif()
+string(APPEND CPPDEFS " -DFORTRANUNDERSCORE -DNO_R16")
+set(CXX_LINKER "FORTRAN")
+set(FC_AUTO_R8 "-fdefault-real-8")
+set(FFLAGS "-O -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none -fno-range-check")
+if (compile_threaded)
+  string(APPEND FFLAGS " -fopenmp")
+endif()
+if (DEBUG)
+  string(APPEND FFLAGS " -g -Wall")
+endif()
+set(FIXEDFLAGS "-ffixed-form")
+set(FREEFLAGS "-ffree-form")
+set(HDF5_PATH "/software/dev_tools/swtree/cs400_centos7.2_pe2016-08/hdf5-parallel/1.8.17/centos7.2_gnu5.3.0")
+set(NETCDF_PATH "/software/dev_tools/swtree/cs400_centos7.2_pe2016-08/netcdf-hdf5parallel/4.3.3.1/centos7.2_gnu5.3.0")
+set(PNETCDF_PATH "/software/dev_tools/swtree/cs400_centos7.2_pe2016-08/pnetcdf/1.9.0/centos7.2_gnu5.3.0")
+set(LAPACK_LIBDIR "/software/tools/compilers/intel_2017/mkl/lib/intel64")
+if (compile_threaded)
+  string(APPEND LDFLAGS " -fopenmp")
+endif()
+string(APPEND SLIBS " -L${NETCDF_PATH}/lib -Wl,-rpath=${NETCDF_PATH}/lib -lnetcdff -lnetcdf")
+set(MPICC "mpicc")
+set(MPICXX "mpic++")
+set(MPIFC "mpif90")
+set(SCC "gcc")
+set(SCXX "gcpp")
+set(SFC "gfortran")
+set(SUPPORTS_CXX "TRUE")

cime_config/machines/cmake_macros/gnu_chrysalis.cmake

@@ -0,0 +1,12 @@
+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)
+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 " -Wl,--start-group $ENV{MKLROOT}/lib/intel64/libmkl_gf_lp64.a $ENV{MKLROOT}/lib/intel64/libmkl_sequential.a $ENV{MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl")
+set(CXX_LIBS "-lstdc++")
+set(NETCDF_C_PATH "$ENV{NETCDF_C_PATH}")
+set(NETCDF_FORTRAN_PATH "$ENV{NETCDF_FORTRAN_PATH}")
+set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")

cime_config/machines/cmake_macros/gnu_cori-haswell.cmake

@@ -0,0 +1,7 @@
+if (NOT DEBUG)
+  string(APPEND CFLAGS " -O2")
+endif()
+if (NOT DEBUG)
+  string(APPEND FFLAGS " -O2")
+endif()
+set(CXX_LIBS "-lstdc++")

cime_config/machines/cmake_macros/gnu_cori-knl.cmake

@@ -0,0 +1,7 @@
+if (NOT DEBUG)
+  string(APPEND CFLAGS " -O2")
+endif()
+if (NOT DEBUG)
+  string(APPEND FFLAGS " -O2")
+endif()
+set(CXX_LIBS "-lstdc++")

cime_config/machines/cmake_macros/gnu_eddi.cmake

@@ -0,0 +1,18 @@
+set(SUPPORTS_CXX "TRUE")
+if (COMP_NAME STREQUAL gptl)
+  string(APPEND CPPDEFS " -DHAVE_VPRINTF -DHAVE_GETTIMEOFDAY -DHAVE_BACKTRACE")
+endif()
+set(NETCDF_PATH "$ENV{NETCDF_HOME}")
+if (NOT DEBUG)
+  string(APPEND FFLAGS " -fno-unsafe-math-optimizations")
+endif()
+if (DEBUG)
+  string(APPEND FFLAGS " -g -fbacktrace -fbounds-check -ffpe-trap=invalid,zero,overflow")
+endif()
+string(APPEND SLIBS " -L$ENV{NETCDF_HOME}/lib/ -lnetcdff -lnetcdf -lcurl -llapack -lblas")
+if (MPILIB STREQUAL mpi-serial)
+  set(SCC "gcc")
+endif()
+if (MPILIB STREQUAL mpi-serial)
+  set(SFC "gfortran")
+endif()

cime_config/machines/cmake_macros/gnu_gcp.cmake

@@ -0,0 +1,20 @@
+set(SUPPORTS_CXX "TRUE")
+if (COMP_NAME STREQUAL gptl)
+  string(APPEND CPPDEFS " -DHAVE_VPRINTF -DHAVE_GETTIMEOFDAY -DHAVE_BACKTRACE -DHAVE_SLASHPROC")
+endif()
+set(CXX_LIBS "-lstdc++")
+if (NOT DEBUG)
+  string(APPEND FFLAGS " -fno-unsafe-math-optimizations")
+endif()
+if (DEBUG)
+  string(APPEND FFLAGS " -g -fbacktrace -fbounds-check -ffpe-trap=invalid,zero,overflow")
+endif()
+string(APPEND SLIBS " -L$ENV{HDF5_PATH}/lib -lhdf5_fortran -lhdf5 -lhdf5_hl -lhdf5hl_fortran")
+string(APPEND SLIBS " -L$ENV{NETCDF_C_PATH}/lib -lnetcdf -L$ENV{NETCDF_FORTRAN_PATH}/lib -lnetcdff")
+string(APPEND SLIBS " -L$ENV{CURL_PATH}/lib -lcurl -lblas -llapack")
+string(APPEND SLIBS " -L$ENV{LAPACK_PATH}/lib64 -lblas -llapack")
+string(APPEND SLIBS " -L$ENV{PNETCDF_PATH}/lib -lpnetcdf")
+set(HDF5_PATH "$ENV{HDF5_PATH}")
+set(NETCDF_C_PATH "$ENV{NETCDF_C_PATH}")
+set(NETCDF_FORTRAN_PATH "$ENV{NETCDF_FORTRAN_PATH}")
+set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")

cime_config/machines/cmake_macros/gnu_grizzly.cmake

@@ -0,0 +1,16 @@
+set(PIO_FILESYSTEM_HINTS "lustre")
+set(MPICC "mpicc")
+set(MPIFC "mpif90")
+set(MPICXX "mpic++")
+set(SFC "gfortran")
+set(SCC "gcc")
+set(SCXX "g++")
+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 " $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 $ENV{MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a -lpthread -lm -lz")
+set(CXX_LIBS "-lstdc++")
+set(NETCDF_C_PATH "$ENV{NETCDF_PATH}")
+set(NETCDF_FORTRAN_PATH "$ENV{NETCDF_PATH}")
+set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")

cime_config/machines/cmake_macros/gnu_jlse.cmake

@@ -0,0 +1,14 @@
+string(APPEND CPPDEFS " -DHAVE_SLASHPROC")
+if (NOT DEBUG)
+  string(APPEND CFLAGS " -O2")
+endif()
+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 " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0} -Wl,-rpath -Wl,$ENV{NETCDF_PATH}/lib")
+execute_process(COMMAND $ENV{NETCDF_PATH}/bin/nc-config --libs OUTPUT_VARIABLE SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0 OUTPUT_STRIP_TRAILING_WHITESPACE)
+string(APPEND SLIBS " ${SHELL_CMD_OUTPUT_BUILD_INTERNAL_IGNORE0}")
+string(APPEND SLIBS " -L/home/azamat/soft/libs -llapack -lblas")
+set(NETCDF_PATH "$ENV{NETCDF_PATH}")
+set(PNETCDF_PATH "$ENV{PNETCDF_PATH}")