Fixes #111 and other mixed clang/gfortran issues

cmake/SCHISM.homebrew.gfortran-clang

@@ -0,0 +1,35 @@
+# CMake presets for compiling on a Homebrew (Linux/macOS) system
+#
+# SPDX-FileCopyrightText: 2024-2025 Helmholtz-Zentrum hereon GmbH
+# SPDX-License-Identifier: CC0-1.0
+# SPDX-FileContributor: Carsten Lemmen <[email protected]>
+#
+# Prerequisites:
+#   brew install llvm gfortran cmake make
+#
+
+# Detect Homebrew prefix for macOS and Linux
+if(EXISTS /opt/homebrew)
+  set(HOMEBREW_PREFIX /opt/homebrew)
+elseif(EXISTS $ENV{HOME}/.linuxbrew)
+  set(HOMEBREW_PREFIX $ENV{HOME}/.linuxbrew)
+elseif(EXISTS /home/linuxbrew/.linuxbrew)
+  set(HOMEBREW_PREFIX /home/linuxbrew/.linuxbrew)
+elseif(EXISTS /usr/local)
+  set(HOMEBREW_PREFIX /usr/local)
+else()
+  message(FATAL_ERROR "Homebrew prefix not found.")
+endif()
+
+# Set parallel compilers from Homebrew MPI wrappers
+set(CMAKE_Fortran_COMPILER ${HOMEBREW_PREFIX}/bin/mpifort CACHE PATH "Path to parallel Fortran compiler")
+set(CMAKE_C_COMPILER ${HOMEBREW_PREFIX}/bin/mpicc CACHE PATH "Path to parallel C compiler")
+set(CMAKE_CXX_COMPILER ${HOMEBREW_PREFIX}/bin/mpicxx CACHE PATH "Path to parallel C++ compiler")
+
+# Fortran compiler flags
+set(CMAKE_Fortran_FLAGS "-ffree-line-length-none -fallow-argument-mismatch" CACHE STRING "Fortran flags" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -ffree-line-length-none -static-libgfortran -finit-local-zero" CACHE STRING "Fortran release flags" FORCE)
+
+# NetCDF library paths (Homebrew default prefix)
+set(NetCDF_FORTRAN_DIR ${HOMEBREW_PREFIX} CACHE PATH "Path to NetCDF Fortran library")
+set(NetCDF_C_DIR ${HOMEBREW_PREFIX} CACHE PATH "Path to NetCDF C library")

cmake/SCHISM.local.conda

@@ -5,21 +5,19 @@
 # SPDX-License-Identifier: CC0-1.0
 # SPDX-FileContributor Carsten Lemmen <[email protected]
 
-message(WARNING "If you get an error 'Error copying Fortran module' with uppercase/lowercase mismatch, then try setting the CMAKE_C_PREPROCESS_FLAG to an empty string in cmake/SCHISMCompile.cmake")
+if(NOT DEFINED ENV{CONDA_PREFIX})
+  message(FATAL_ERROR "CONDA_PREFIX is not set. Please activate your conda environment before configuring.")
+endif()
 
 set(CMAKE_Fortran_COMPILER $ENV{CONDA_PREFIX}/bin/mpifort CACHE PATH "Path to parallel Fortran compiler")
 set(CMAKE_C_COMPILER $ENV{CONDA_PREFIX}/bin/mpicc CACHE PATH "Path to parallel C compiler")
 set(CMAKE_CXX_COMPILER $ENV{CONDA_PREFIX}/bin/mpicxx CACHE PATH "Path to parallel C++ compiler")
-set(PARMETIS_ROOT $ENV{CONDA_PREFIX} CACHE PATH "Root path for external (par)metis")
-
-set_source_files_properties(
-  *.F90
-  PROPERTIES Fortran_PREPROCESS ON
-)
 
-# Fix gfortran/clang for conda environments
-if("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "GNU")
-    if("${CMAKE_C_COMPILER_ID}" STREQUAL "Clang")
-      set( C_PREPROCESS_FLAG "" CACHE STRING "C Preprocessor Flag")
-    endif()
+# Prefer conda parmetis by defining PARMETIS_ROOT if it is installed in conda.  
+# Validation is leveraged to the FindParMETIS cmake module
+if(EXISTS "$ENV{CONDA_PREFIX}/include/parmetis.h")
+  message(STATUS "Found ParMETIS header in conda environment; setting PARMETIS_ROOT to $ENV{CONDA_PREFIX}")
+  set(PARMETIS_ROOT "$ENV{CONDA_PREFIX}" CACHE PATH "Root path for external (par)metis")
+else()
+  message(STATUS "ParMETIS header not found in conda environment; PARMETIS_ROOT not set")
 endif()

cmake/SCHISMCompile.cmake

@@ -32,17 +32,20 @@ if("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "PGI")
     set( C_PREPROCESS_FLAG "-Mpreprocess" CACHE STRING "C Preprocessor Flag")
 endif()
 
+# Both Clang and GNU compilers need an empty C_PREPROCESS_FLAG
 if("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "GNU")
     set (SCHISM_GFORTRAN_OPTIONS " -ffree-line-length-none")
     set( CMAKE_Fortran_FLAGS_RELEASE_INIT "-O2 ${SCHISM_GFORTRAN_OPTIONS}")
     set( CMAKE_Fortran_FLAGS_DEBUG_INIT "-g ${SCHISM_GFORTRAN_OPTIONS}")
     set( CMAKE_Fortran_FLAGS_RELWITHDEBINFO_INIT "-O2 -g ${SCHISM_GFORTRAN_OPTIONS}")
-    unset( C_PREPROCESS_FLAG CACHE)
-    if("${CMAKE_C_COMPILER_ID}" STREQUAL "Clang")
-      set( C_PREPROCESS_FLAG "--preprocess" CACHE STRING "C Preprocessor Flag")
-    elseif("${CMAKE_C_COMPILER_ID}" STREQUAL "AppleClang")
-      set( C_PREPROCESS_FLAG "--preprocess" CACHE STRING "C Preprocessor Flag")
-    else()
-      set( C_PREPROCESS_FLAG "-cpp" CACHE STRING "C Preprocessor Flag")
-    endif()
+    set( C_PREPROCESS_FLAG "" CACHE STRING "C Preprocessor Flag")
 endif()
+
+if("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "FLANG")
+    set (SCHISM_FLANG_OPTIONS " -Mfreeform -Mstandard")
+    set( CMAKE_Fortran_FLAGS_RELEASE_INIT "-O2 ${SCHISM_FLANG_OPTIONS}")
+    set( CMAKE_Fortran_FLAGS_DEBUG_INIT "-g ${SCHISM_FLANG_OPTIONS}")
+    set( CMAKE_Fortran_FLAGS_RELWITHDEBINFO_INIT "-O2 -g ${SCHISM_FLANG_OPTIONS}")
+    set( C_PREPROCESS_FLAG "" CACHE STRING "C Preprocessor Flag")
+endif()
+

src/Fabm/fabm_schism.F90

@@ -11,7 +11,7 @@
 !> @author Jan Kossack <[email protected]>
 !> @author Wang Zhenggui
 
-!> @copyright Copyright 2021-2024 Helmholtz-Zentrum hereon GmbH
+!> @copyright Copyright 2021-2025 Helmholtz-Zentrum hereon GmbH
 !> @copyright Copyright 2021-2022 Virginia Institute of Marine Science
 !> @copyright Copyright 2017-2021 Helmholtz-Zentrum Geesthacht GmbH
 !
@@ -400,7 +400,7 @@ subroutine fabm_schism_init_stage2
   call fs%model%set_mask(fs%mask_hz)
 #endif
 #endif
-#endif
+!#endif
 
   allocate(bottom_idx(1:ne))
   do i=1,ne