Merge pull request #523 from FESOM/bugfixes_wdeconinck

Bugfixes to parms,  widely compatable FindNETCDF, and new envs for atos and lumi

cmake/FindNETCDF.cmake

@@ -13,9 +13,13 @@ if(CMAKE_Fortran_COMPILER_LOADED)
 	if(HAVE_Fortran_NETCDF)
 		set(NETCDF_Fortran_INCLUDE_DIRECTORIES "")
 		set(NETCDF_Fortran_LIBRARIES "")
+		set(NETCDF_Fortran_FOUND 1)
 	else()
-		find_path(NETCDF_Fortran_INCLUDE_DIRECTORIES netcdf.inc HINTS $ENV{NETCDF_DIR}/include ENV NETCDF_Fortran_INCLUDE_DIRECTORIES)
+		find_path(NETCDF_Fortran_INCLUDE_DIRECTORIES netcdf.inc HINTS $ENV{NETCDF_ROOT}/include $ENV{NETCDF_DIR}/include $ENV{NETCDF4_DIR}/include ENV NETCDF_Fortran_INCLUDE_DIRECTORIES)
 		find_library(NETCDF_Fortran_LIBRARIES netcdff HINTS ${NETCDF_Fortran_INCLUDE_DIRECTORIES}/../lib)
+		if( NETCDF_Fortran_INCLUDE_DIRECTORIES AND NETCDF_Fortran_LIBRARIES )
+			set(NETCDF_Fortran_FOUND 1)
+		endif()
 	endif()	
 endif()
 
@@ -27,14 +31,18 @@ if(CMAKE_C_COMPILER_LOADED OR CMAKE_CXX_COMPILER_LOADED)
 	if(HAVE_C_NETCDF)
 		set(NETCDF_C_INCLUDE_DIRECTORIES "")
 		set(NETCDF_C_LIBRARIES "")
+		set(NETCDF_C_FOUND 1)
 	else()
-		find_path(NETCDF_C_INCLUDE_DIRECTORIES netcdf.h HINTS $ENV{NETCDF_DIR}/include ENV NETCDF_C_INCLUDE_DIRECTORIES)
+		find_path(NETCDF_C_INCLUDE_DIRECTORIES netcdf.h HINTS $ENV{NETCDF_ROOT}/include $ENV{NETCDF_DIR}/include $ENV{NETCDF4_DIR}/include ENV NETCDF_C_INCLUDE_DIRECTORIES)
 		find_library(NETCDF_C_LIBRARIES netcdf HINTS ${NETCDF_C_INCLUDE_DIRECTORIES}/../lib)
+		if( NETCDF_C_INCLUDE_DIRECTORIES AND NETCDF_C_LIBRARIES )
+			set(NETCDF_C_FOUND 1)
+		endif()
 	endif()
 endif()
 
 if(CMAKE_CXX_COMPILER_LOADED)
-	find_path(NETCDF_CXX_INCLUDE_DIRECTORIES netcdf HINTS $ENV{NETCDF_DIR}/include ENV NETCDF_CXX_INCLUDE_DIRECTORIES)
+	find_path(NETCDF_CXX_INCLUDE_DIRECTORIES netcdf HINTS $ENV{NETCDF_ROOT}/include $ENV{NETCDF_DIR}/include $ENV{NETCDF4_DIR} ENV NETCDF_CXX_INCLUDE_DIRECTORIES)
 	# the cray toolchain (e.g. hlrn) disables dynamic linking by default. to enable it at build time do e.g. "CRAYPE_LINK_TYPE=dynamic make".	
 	find_library(NETCDF_CXX_LIBRARIES NAMES netcdf_c++4 netcdf-cxx4 HINTS ${NETCDF_CXX_INCLUDE_DIRECTORIES}/../lib)
 	if(NETCDF_CXX_INCLUDE_DIRECTORIES AND NETCDF_C_INCLUDE_DIRECTORIES)
@@ -43,4 +51,21 @@ if(CMAKE_CXX_COMPILER_LOADED)
 	if(NETCDF_CXX_LIBRARIES AND NETCDF_C_LIBRARIES)
 		list(APPEND NETCDF_CXX_LIBRARIES ${NETCDF_C_LIBRARIES})
 	endif()
-endif()
+	if( NETCDF_CXX_INCLUDE_DIRECTORIES AND NETCDF_CXX_LIBRARIES )
+		set(NETCDF_CXX_FOUND 1)
+	endif()
+endif()
+
+if(NOT ${CMAKE_FIND_PACKAGE_NAME}_FIND_COMPONENTS)
+  set(${CMAKE_FIND_PACKAGE_NAME}_FIND_COMPONENTS C)
+endif()
+
+unset({CMAKE_FIND_PACKAGE_NAME}_REQUIRED_VARS)
+foreach(COMP C CXX Fortran)
+  if("${COMP}" IN_LIST ${CMAKE_FIND_PACKAGE_NAME}_FIND_COMPONENTS) 
+    list(APPEND ${CMAKE_FIND_PACKAGE_NAME}_REQUIRED_VARS NETCDF_${COMP}_FOUND)
+  endif()
+endforeach()
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(${CMAKE_FIND_PACKAGE_NAME} HANDLE_COMPONENTS REQUIRED_VARS ${CMAKE_FIND_PACKAGE_NAME}_REQUIRED_VARS)
+

env/atosecmwf/shell

@@ -33,7 +33,5 @@ module load cmake/3.20.2
 module load ninja/1.10.0
 module load fcm/2019.05.0
 
-export NETCDF_DIR=$NETCDF4_DIR
+export FC=ifort CC=icc CXX=icpc
 
-export FC=mpif90 CC=mpicc CXX=mpicxx	# MPI wrappers for Fortran, cc and CC similarly
-#export FC=mpif90 CC=gcc CXX=mpicxx	# MPI wrappers for Fortran, cc and CC similarly

env/lumi/shell

@@ -11,10 +11,10 @@ module load cray-netcdf/4.8.1.5
 export FC=ftn
 export CC=cc
 export CXX=cc
-export NETCDF_Fortran_INCLUDE_DIRECTORIES=$CRAY_NETCDF_DIR/include
-export NETCDF_C_INCLUDE_DIRECTORIES=$CRAY_NETCDF_DIR/include
-export NETCDF_C_LIBRARIES=$CRAY_NETCDF_DIR/lib
-export NETCDF_Fortran_LIBRARIES=$CRAY_NETCDF_DIR/lib
+#export NETCDF_Fortran_INCLUDE_DIRECTORIES=$CRAY_NETCDF_DIR/include
+#export NETCDF_C_INCLUDE_DIRECTORIES=$CRAY_NETCDF_DIR/include
+#export NETCDF_C_LIBRARIES=$CRAY_NETCDF_DIR/lib
+#export NETCDF_Fortran_LIBRARIES=$CRAY_NETCDF_DIR/lib
 $CC -v
 $FC -V
 $CXX -v

lib/parms/src/DDPQ/arms2.c

@@ -227,14 +227,15 @@ static int parms_arms_getssize_vcsr(parms_Operator self)
 }
 
 static struct parms_Operator_ops parms_arms_sol_vptr = {
-  parms_arms_sol_vcsr,
-  parms_arms_lsol_vcsr,
-  parms_arms_invs_vcsr,
-  parms_arms_ascend_vcsr,
-  parms_arms_getssize_vcsr,
-  parms_arms_nnz,
-  arms_free_vcsr,
-  arms_view_vcsr
+  parms_arms_sol_vcsr,        /* apply */
+  parms_arms_lsol_vcsr,       /* lsol */
+  parms_arms_invs_vcsr,       /* invs */
+  NULL,                       /* getu             !!! WARNING,  UNASSIGNED !!! */
+  parms_arms_ascend_vcsr,     /* ascend */
+  parms_arms_getssize_vcsr,   /* getssize */
+  parms_arms_nnz,             /* getnnz */
+  arms_free_vcsr,             /* operator_free */
+  arms_view_vcsr              /* operator_view */
 };
 
 

lib/parms/src/DDPQ/sets.c

@@ -11,15 +11,15 @@
 void parms_errexit( char *f_str, ... )
 {
   va_list argp;
-  char out1[256], out2[256];
+  char out1[256], out2[512];
 
   va_start(argp, f_str);
   vsprintf(out1, f_str, argp);
   va_end(argp);
 
   sprintf(out2, "Error! %s\n", out1);
 
-  fprintf(stdout, out2);
+  fprintf(stdout, "%s", out2);
   fflush(stdout);
 
   exit( -1 );

lib/parms/src/parms_ilu_vcsr.c

@@ -1683,14 +1683,15 @@ int parms_ilu_update(parms_Mat self, parms_FactParam param, void *mat,
       if(ABS_VALUE(t1) < DBL_EPSILON) continue;
 
       if( ii+start < schur_start ){	
-	for(jj = 1; jj < nnz; jj++) {
-	  iw = jw[rowjj[jj]];
-	  if(iw != -1) 
-	    if(iw < ii+start)	      	      
-	      rowm[iw] -= t1*rowmm[jj];	  	   
-	    else
-	      data->U->pa[ii+start][iw-ii-start] -= t1*rowmm[jj];	  
-	}
+        for(jj = 1; jj < nnz; jj++) {
+          iw = jw[rowjj[jj]];
+          if(iw != -1) {
+            if(iw < ii+start)
+              rowm[iw] -= t1*rowmm[jj];
+            else
+              data->U->pa[ii+start][iw-ii-start] -= t1*rowmm[jj];
+          }
+        }
       }
       else {	
 	for(jj = 1; jj < nnz; jj++){	  	 

lib/parms/src/parms_pc_schurras.c

@@ -10,6 +10,11 @@
 #endif 
 #endif 
 
+/* Forward declarations */
+int parms_OperatorGetU(parms_Operator self, void **mat);
+int parms_MatGetOffDiag(parms_Mat self, void **mat);
+int parms_CommGetOdvlist(parms_Comm self, int **odvlist);
+
 typedef struct schurras_data {
 
   parms_Operator op_out,op_in;

src/gen_modules_partitioning.F90

@@ -93,8 +93,10 @@ subroutine par_ex(COMM, mype, abort)       ! finalizes MPI
 #else
   !For ECHAM coupled runs we use the old OASIS nameing scheme (prism / prism_proto)
   use mod_prism 
-#endif ! oifs/echam
-#endif ! oasis
+#endif
+         ! oifs/echam
+#endif
+         ! oasis
 
   implicit none
   integer,           intent(in)   :: COMM
@@ -112,7 +114,8 @@ subroutine par_ex(COMM, mype, abort)       ! finalizes MPI
      call  MPI_Barrier(COMM, error)
      call  MPI_Finalize(error)
   endif
-#else ! standalone
+#else 
+      ! standalone
 
 ! From here on the two coupled options
 !-------------------------------------
@@ -136,8 +139,10 @@ subroutine par_ex(COMM, mype, abort)       ! finalizes MPI
 
   if (mype==0) print *, 'FESOM calls MPI_Finalize'
   call MPI_Finalize(error)
-#endif ! oifs/echam
-#endif ! oasis
+#endif
+         ! oifs/echam
+#endif
+         ! oasis
 
 ! Regardless of standalone, OpenIFS oder ECHAM coupling, if we reach to this point
 ! we should be fine shutting the whole model down