Fix HOMME builds on NERSC machines

Need to set PNETCDF in homme machine cmake files. Need to refer to MKLROOT correctly in config_compilers.xml. [BFB]
E3SM-Project · Apr 2, 2017 · e8fe4f8 · e8fe4f8
1 parent 7d39622
commit e8fe4f8
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Showing 4 changed files with 6 additions and 5 deletions.
diff --git a/cime/cime_config/acme/machines/config_compilers.xml b/cime/cime_config/acme/machines/config_compilers.xml
@@ -552,7 +552,7 @@ for mct, etc.
   <ADD_CFLAGS DEBUG="FALSE"> -O2  </ADD_CFLAGS>
   <CONFIG_ARGS> --host=Linux </CONFIG_ARGS>
   <ADD_SLIBS> -L$(NETCDF_DIR) -lnetcdff -Wl,--as-needed,-L$(NETCDF_DIR)/lib -lnetcdff -lnetcdf </ADD_SLIBS>
-  <ADD_SLIBS> ${MKLROOT}/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_sequential.a -Wl,--end-group ${MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a -lpthread -lm -z muldefs</ADD_SLIBS>
+  <ADD_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 $ENV{MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a -lpthread -lm -z muldefs</ADD_SLIBS>
   <ADD_GPTL_CPPDEFS> -DHAVE_PAPI </ADD_GPTL_CPPDEFS>
   <MPIFC> ftn </MPIFC>
   <MPICC> cc </MPICC>
@@ -572,7 +572,7 @@ for mct, etc.
   <ADD_LDFLAGS compile_threaded="true"> -qopenmp </ADD_LDFLAGS>
   <CONFIG_ARGS> --host=Linux </CONFIG_ARGS>
   <ADD_SLIBS> -L$(NETCDF_DIR) -lnetcdff -Wl,--as-needed,-L$(NETCDF_DIR)/lib -lnetcdff -lnetcdf </ADD_SLIBS>
-  <ADD_SLIBS> ${MKLROOT}/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_sequential.a -Wl,--end-group ${MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a -lpthread -lm </ADD_SLIBS>
+  <ADD_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 $ENV{MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a -lpthread -lm </ADD_SLIBS>
   <!--ADD_SLIBS> -mkl -lpthread -lm </ADD_SLIBS-->
   <ADD_GPTL_CPPDEFS> -DHAVE_PAPI </ADD_GPTL_CPPDEFS>
   <ADD_CPPDEFS> -DHAVE_SLASHPROC </ADD_CPPDEFS>
@@ -614,7 +614,7 @@ for mct, etc.
   <ADD_CFLAGS DEBUG="FALSE"> -O2  </ADD_CFLAGS>
   <CONFIG_ARGS> --host=Linux </CONFIG_ARGS>
   <ADD_SLIBS> -L$(NETCDF_DIR) -lnetcdff -Wl,--as-needed,-L$(NETCDF_DIR)/lib -lnetcdff -lnetcdf </ADD_SLIBS>
-  <ADD_SLIBS> ${MKLROOT}/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_sequential.a -Wl,--end-group ${MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a -lpthread -lm </ADD_SLIBS>
+  <ADD_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 </ADD_SLIBS>
   <ADD_GPTL_CPPDEFS> -DHAVE_PAPI </ADD_GPTL_CPPDEFS>
   <MPIFC> ftn </MPIFC>
   <MPICC> cc </MPICC>

diff --git a/components/homme/cmake/machineFiles/cori-haswell.cmake b/components/homme/cmake/machineFiles/cori-haswell.cmake
@@ -8,6 +8,7 @@ SET (CMAKE_C_COMPILER cc CACHE FILEPATH "")
 SET (CMAKE_CXX_COMPILER CC CACHE FILEPATH "")
 
 SET (NETCDF_DIR $ENV{NETCDF_DIR} CACHE FILEPATH "")
+SET (PNETCDF_DIR $ENV{PARALLEL_NETCDF_DIR} CACHE FILEPATH "")
 SET (HDF5_DIR $ENV{HDF5_DIR} CACHE FILEPATH "")
 
 #ZLIB_DIR=/global/common/cori/software/zlib/1.2.8/hsw/intel

diff --git a/components/homme/cmake/machineFiles/cori-knl.cmake b/components/homme/cmake/machineFiles/cori-knl.cmake
@@ -8,6 +8,7 @@ SET (CMAKE_C_COMPILER cc CACHE FILEPATH "")
 SET (CMAKE_CXX_COMPILER CC CACHE FILEPATH "")
 
 SET (NETCDF_DIR $ENV{NETCDF_DIR} CACHE FILEPATH "")
+SET (PNETCDF_DIR $ENV{PARALLEL_NETCDF_DIR} CACHE FILEPATH "")
 SET (HDF5_DIR $ENV{HDF5_DIR} CACHE FILEPATH "")
 
 #ZLIB_DIR=/global/common/cori/software/zlib/1.2.8/hsw/intel

diff --git a/components/homme/cmake/machineFiles/edison.cmake b/components/homme/cmake/machineFiles/edison.cmake
@@ -8,8 +8,7 @@ SET (CMAKE_C_COMPILER cc CACHE FILEPATH "")
 SET (CMAKE_CXX_COMPILER CC CACHE FILEPATH "")
 SET (NETCDF_DIR $ENV{NETCDF_DIR} CACHE FILEPATH "")
 SET (HDF5_DIR $ENV{HDF5_DIR} CACHE FILEPATH "")
-#ndk SET (PNETCDF_DIR $ENV{PARALLEL_NETCDF_DIR} CACHE FILEPATH "")
-# this env var is not set with module cray-netcdf-hdf5parallel/4.3.3.1
+SET (PNETCDF_DIR $ENV{PARALLEL_NETCDF_DIR} CACHE FILEPATH "")
 
 SET (HDF5_DIR $ENV{HDF5_DIR} CACHE FILEPATH "")