Merge branch 'ndk/machinefiles/homme-cori-cmake' (PR #1230)

Changes to allow for the HOMME test to pass for cori-haswell and cori-knl. Add "module load zlib" and use this library. Add custom srun flags temporarily Remove old corip1 config file [BFB]
ESMCI · Jan 20, 2017 · a5b870b · a5b870b
2 parents b7929bf + 93c5397
commit a5b870b
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Showing 4 changed files with 61 additions and 41 deletions.
diff --git a/cime/cime_config/acme/machines/config_machines.xml b/cime/cime_config/acme/machines/config_machines.xml
@@ -292,6 +292,7 @@
 	<command name="load">cmake/3.3.2</command>
 	<command name="load">pmi/5.0.10-1.0000.11050.0.0.ari</command>
 	<command name="load">papi/5.4.3.2</command>
+	<command name="load">zlib</command>
 	<!--command name="load">cray-petsc/3.7.0.0</command-->
       </modules>
     </module_system>
@@ -422,6 +423,7 @@
 	<command name="load">cmake/3.3.2</command>
 	<command name="load">pmi/5.0.10-1.0000.11050.0.0.ari</command>
 	<command name="load">papi/5.4.3.2</command>
+	<command name="load">zlib</command>
 	<!--command name="load">cray-petsc/3.7.0.0</command-->
       </modules>
     </module_system>

diff --git a/components/homme/cmake/machineFiles/cori-haswell.cmake b/components/homme/cmake/machineFiles/cori-haswell.cmake
@@ -8,18 +8,39 @@ SET (CMAKE_C_COMPILER cc CACHE FILEPATH "")
 SET (CMAKE_CXX_COMPILER CC CACHE FILEPATH "")
 
 SET (NETCDF_DIR $ENV{NETCDF_DIR} CACHE FILEPATH "")
-#example with module cray-netcdf-hdf5parallel/4.3.3.1:
-# NETCDF_DIR=/opt/cray/netcdf-hdf5parallel/4.3.3.1/INTEL/14.0
-
-#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 (HDF5_DIR $ENV{HDF5_DIR} CACHE FILEPATH "")
-#example with module cray-hdf5-parallel/1.8.14: 
-# HDF5_DIR=/opt/cray/hdf5-parallel/1.8.14/INTEL/14.0
+
+#ZLIB_DIR=/global/common/cori/software/zlib/1.2.8/hsw/intel
+SET (ZLIB_DIR $ENV{ZLIB_DIR} CACHE FILEPATH "")
+SET (ZLIB_LIBRARY ${ZLIB_DIR}/lib/libz.a CACHE FILEPATH "")
+#MESSAGE(STATUS " cori-haswell.cmake ENV(ZLIB_DIR)=$ENV{ZLIB_DIR}")
+#MESSAGE(STATUS " cori-haswell.cmake ZLIB_DIR=${ZLIB_DIR}")
+#MESSAGE(STATUS " cori-haswell.cmake ZLIB_LIBRARY=${ZLIB_LIBRARY}")
+
+EXECUTE_PROCESS(COMMAND which nf-config
+  RESULT_VARIABLE NFCONFIG_PATH_RESULT
+  OUTPUT_VARIABLE NFCONFIG_PATH_OUTPUT
+  ERROR_VARIABLE  NFCONFIG_PATH_ERROR
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+EXECUTE_PROCESS(COMMAND ${NFCONFIG_PATH_OUTPUT} --flibs
+  RESULT_VARIABLE NFCONFIG_RESULT
+  OUTPUT_VARIABLE NFCONFIG_OUTPUT
+  ERROR_VARIABLE  NFCONFIG_ERROR
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+IF (${NFCONFIG_ERROR})
+  MESSAGE(WARNING "${NETCDF_DIR}/bin/nf-config --flibs produced an error. Default linking will be used.")
+ELSE ()
+  SET (ADD_LINKER_FLAGS " ${NFCONFIG_OUTPUT} " CACHE STRING "")
+ENDIF ()
+#MESSAGE(STATUS " cori-haswell.cmake NFCONFIG_OUTPUT=${NFCONFIG_OUTPUT}")
 
 SET (CMAKE_SYSTEM_NAME Catamount CACHE FILEPATH "")
 
 SET (USE_QUEUING FALSE CACHE BOOL "")
 
 SET (USE_MPIEXEC "srun" CACHE STRING "")
+
+# temporary fix:
+SET (USE_MPI_OPTIONS "-c 2 --cpu_bind=cores" CACHE STRING "")
diff --git a/components/homme/cmake/machineFiles/cori-knl.cmake b/components/homme/cmake/machineFiles/cori-knl.cmake
@@ -8,18 +8,40 @@ SET (CMAKE_C_COMPILER cc CACHE FILEPATH "")
 SET (CMAKE_CXX_COMPILER CC CACHE FILEPATH "")
 
 SET (NETCDF_DIR $ENV{NETCDF_DIR} CACHE FILEPATH "")
-#example with module cray-netcdf-hdf5parallel/4.3.3.1:
-# NETCDF_DIR=/opt/cray/netcdf-hdf5parallel/4.3.3.1/INTEL/14.0
-
-#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 (HDF5_DIR $ENV{HDF5_DIR} CACHE FILEPATH "")
-#example with module cray-hdf5-parallel/1.8.14: 
-# HDF5_DIR=/opt/cray/hdf5-parallel/1.8.14/INTEL/14.0
+
+#ZLIB_DIR=/global/common/cori/software/zlib/1.2.8/hsw/intel
+SET (ZLIB_DIR $ENV{ZLIB_DIR} CACHE FILEPATH "")
+SET (ZLIB_LIBRARY ${ZLIB_DIR}/lib/libz.a CACHE FILEPATH "")
+#MESSAGE(STATUS " cori-knl.cmake ENV(ZLIB_DIR)=$ENV{ZLIB_DIR}")
+#MESSAGE(STATUS " cori-knl.cmake ZLIB_DIR=${ZLIB_DIR}")
+#MESSAGE(STATUS " cori-knl.cmake ZLIB_LIBRARY=${ZLIB_LIBRARY}")
+
+EXECUTE_PROCESS(COMMAND which nf-config
+  RESULT_VARIABLE NFCONFIG_PATH_RESULT
+  OUTPUT_VARIABLE NFCONFIG_PATH_OUTPUT
+  ERROR_VARIABLE  NFCONFIG_PATH_ERROR
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+EXECUTE_PROCESS(COMMAND ${NFCONFIG_PATH_OUTPUT} --flibs
+  RESULT_VARIABLE NFCONFIG_RESULT
+  OUTPUT_VARIABLE NFCONFIG_OUTPUT
+  ERROR_VARIABLE  NFCONFIG_ERROR
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+IF (${NFCONFIG_ERROR})
+  MESSAGE(WARNING "${NETCDF_DIR}/bin/nf-config --flibs produced an error. Default linking will be used.")
+ELSE ()
+  SET (ADD_LINKER_FLAGS " ${NFCONFIG_OUTPUT} " CACHE STRING "")
+ENDIF ()
+#MESSAGE(STATUS " cori-knl.cmake NFCONFIG_OUTPUT=${NFCONFIG_OUTPUT}")
 
 SET (CMAKE_SYSTEM_NAME Catamount CACHE FILEPATH "")
 
 SET (USE_QUEUING FALSE CACHE BOOL "")
 
 SET (USE_MPIEXEC "srun" CACHE STRING "")
+
+# temporary fix:
+SET (USE_MPI_OPTIONS "-c 4 --cpu_bind=cores" CACHE STRING "")
+
diff --git a/components/homme/cmake/machineFiles/corip1.cmake b/components/homme/cmake/machineFiles/corip1.cmake