Merge branch 'origin/oksanaguba/homme/compy-cmake-file' into next (PR #…

…3117)

Adding cmake cache files for compy intel and pgi.
Fixes for cxx building and for a linker for building with cime.

Fixes #3225 .

[bfb] for the machines we run on.

cime/config/e3sm/machines/config_compilers.xml

@@ -1086,6 +1086,10 @@ for mct, etc.
     <append DEBUG="FALSE"> -O2 </append>
     <append MODEL="gptl"> -DHAVE_SLASHPROC </append>
   </CFLAGS>
+  <CXX_LIBS>
+    <base>-lstdc++</base>
+  </CXX_LIBS>
+  <CXX_LINKER>FORTRAN</CXX_LINKER>
   <CONFIG_ARGS>
     <base> --host=Linux </base>
   </CONFIG_ARGS>

components/homme/CMakeLists.txt

@@ -198,9 +198,6 @@ ELSE()
     FIND_PACKAGE(LAPACK REQUIRED)
   ELSE()
     SET(HOMME_FIND_BLASLAPACK FALSE)
-    # Build the blas and lapack provided with homme
-    ADD_SUBDIRECTORY(libs/blas)
-    ADD_SUBDIRECTORY(libs/lapack)
   ENDIF()
 ENDIF()
 

components/homme/cmake/machineFiles/compy-intel.cmake

@@ -0,0 +1,20 @@
+
+SET(CMAKE_C_COMPILER "mpiicc" CACHE STRING "")
+SET(CMAKE_CXX_COMPILER "mpiicpc" CACHE STRING "")
+SET(CMAKE_Fortran_COMPILER "mpiifort" CACHE STRING "")
+
+SET (WITH_PNETCDF FALSE CACHE FILEPATH "")
+
+SET (NETCDF_DIR "$ENV{NETCDF_ROOT}" CACHE STRING "")
+
+#is there a better way? without this linker does not see C netcdf library
+SET (ADD_LINKER_FLAGS "-L/$ENV{NETCDF_ROOT}/lib -lnetcdff -lnetcdf" CACHE STRING "")
+SET (ADD_Fortran_FLAGS "-traceback" CACHE STRING "")
+
+SET (USE_MPIEXEC "srun" CACHE STRING "")
+SET (USE_MPI_OPTIONS " --mpi=pmi2 --kill-on-bad-exit --cpu_bind=cores" CACHE STRING "")
+SET (HOMME_USE_MKL "TRUE" CACHE FILEPATH "") # for Intel
+SET (USE_QUEUING FALSE CACHE BOOL "")
+# for standalone HOMME builds:
+#SET (CPRNC_DIR /lcrc/group/acme/tools/cprnc CACHE FILEPATH "")
+

components/homme/cmake/machineFiles/compy-pgi.cmake

@@ -0,0 +1,20 @@
+# O. Guba 08/2019 
+#module purge
+
+SET(CMAKE_C_COMPILER "mpipgcc" CACHE STRING "")
+SET(CMAKE_CXX_COMPILER "mpipgcxx" CACHE STRING "")
+SET(CMAKE_Fortran_COMPILER "mpipgf90" CACHE STRING "")
+
+SET (WITH_PNETCDF FALSE CACHE FILEPATH "")
+
+SET (NETCDF_DIR "$ENV{NETCDF_ROOT}" CACHE STRING "")
+
+#is there a better way? without this linker does not see C netcdf library
+SET (ADD_LINKER_FLAGS "-L/$ENV{MKLROOT}/lib/intel64 -L/$ENV{NETCDF_ROOT}/lib -lnetcdff -lnetcdf -lmkl_rt" CACHE STRING "")
+SET (ADD_Fortran_FLAGS "-traceback" CACHE STRING "")
+
+SET (USE_MPIEXEC "srun" CACHE STRING "")
+SET (USE_MPI_OPTIONS "--mpi=pmi2 --kill-on-bad-exit --cpu_bind=cores" CACHE STRING "")
+SET (USE_QUEUING FALSE CACHE BOOL "")
+# for standalone HOMME builds:
+#SET (CPRNC_DIR /lcrc/group/acme/tools/cprnc CACHE FILEPATH "")

components/homme/cmake/machineFiles/compy.cmake

@@ -0,0 +1,20 @@
+# O. Guba 08/2019 
+#module purge
+
+SET(CMAKE_C_COMPILER "mpipgcc" CACHE STRING "")
+SET(CMAKE_CXX_COMPILER "mpipgcxx" CACHE STRING "")
+SET(CMAKE_Fortran_COMPILER "mpipgf90" CACHE STRING "")
+
+SET (WITH_PNETCDF FALSE CACHE FILEPATH "")
+
+SET (NETCDF_DIR "$ENV{NETCDF_ROOT}" CACHE STRING "")
+
+#is there a better way? without this linker does not see C netcdf library
+SET (ADD_LINKER_FLAGS "-L/$ENV{MKLROOT}/lib/intel64 -L/$ENV{NETCDF_ROOT}/lib -lnetcdff -lnetcdf -lmkl_rt" CACHE STRING "")
+SET (ADD_Fortran_FLAGS "-traceback" CACHE STRING "")
+
+SET (USE_MPIEXEC "srun" CACHE STRING "")
+SET (USE_MPI_OPTIONS "--mpi=pmi2 --kill-on-bad-exit --cpu_bind=cores" CACHE STRING "")
+SET (USE_QUEUING FALSE CACHE BOOL "")
+# for standalone HOMME builds:
+#SET (CPRNC_DIR /lcrc/group/acme/tools/cprnc CACHE FILEPATH "")

components/homme/src/share/mesh_mod.F90

@@ -824,7 +824,6 @@ subroutine mesh_init_sfc_from_centroids(nelem, face_numbers, centroids, h, sfcid
     ! find_next_factorable for a smaller ne2.
     ne2 = 2**ceiling(log(real(ne))/log(2d0))
     ne2sq = ne2*ne2
-    print *,'ne,ne2',ne,ne2
 
     o = sfcmap_init(ne2, sfcmap)
     allocate(inds(2,nelem))