USE_NETCDF->USE_PNETCDF and added documentation

Docs/sphinx_doc/building.rst

@@ -8,7 +8,7 @@ REMORA can be built using either GNU Make or CMake. The following instructions a
 Minimum Requirements
 ~~~~~~~~~~~~~~~~~~~~
 
-ERF requires a C++ compiler that supports the C++17 standard and a C compiler that supports the C99 standard.
+REMORA requires a C++ compiler that supports the C++17 standard and a C compiler that supports the C99 standard.
 Building with GPU support may be done with CUDA, HIP, or SYCL.
 For CUDA, REMORA requires versions >= 11.0. For HIP and SYCL, only the latest compilers are supported.
 Prerequisites for building with GNU Make include Python (>= 2.7, including 3) and standard tools available
@@ -18,7 +18,7 @@ in any Unix-like environments (e.g., Perl and sed). For building with CMake, the
       **While REMORA is designed to work with SYCL, we do not make any guarantees that it will build and run on your Intel platform.**
 
 Paradigm
-~~~~~~~~~~
+~~~~~~~~
 
 REMORA uses the paradigm that different executables are built in different subdirectories within the ``Exec`` directory.  When
 using gmake (see below), the user/developer should build in the directory of the selected problem.  When using
@@ -30,6 +30,24 @@ The problem directories within ``Exec`` include ``Upwelling`` a test case demons
 #Rayleigh damping, and 3) tests for features under development in ``Exec/DevTests``, such as moving terrain.  There is a
 #README in each problem directory that describes the purpose/role of that problem.
 
+
+NetCDF (Optional)
+~~~~~~~~~~~~~~~~~
+
+REMORA uses `PnetCDF <https://parallel-netcdf.github.io/>`_ for optional NetCDF support. To build REMORA with PnetCDF, first install PnetCDF as per the instructions. Make a note of the directory where the library is installed, which we will call ``PNETCDF_DIR``. When compiling, add the PnetCDF ``pkgconfig`` directory to the environment variable ``PKG_CONFIG_PATH``, e.g.:
+
+   .. code:: shell
+
+             PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$PNETCDF_DIR/lib/pkgconfig
+
+At run-time, you may need to add PnetCDF to the link path, e.g.:
+
+   .. code:: shell
+
+             LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PNETCDF_DIR/lib
+
+See sections below for compiler-specific instructions for how to enable netCDF support.
+
 GNU Make
 ~~~~~~~~
 
@@ -84,7 +102,7 @@ or if using tcsh,
    +-----------------+----------------------------------+------------------+-------------+
    | DEBUG           | Whether to use DEBUG mode        | TRUE / FALSE     | FALSE       |
    +-----------------+----------------------------------+------------------+-------------+
-   | USE_NETCDF      | Whether to compile with NETCDF   | TRUE / FALSE     | FALSE       |
+   | USE_PNETCDF     | Whether to compile with PnetCDF  | TRUE / FALSE     | FALSE       |
    +-----------------+----------------------------------+------------------+-------------+
    | USE_PARTICLES   | Whether to compile with particle | TRUE / FALSE     | FALSE       |
    |                 | functionality enabled            |                  |             |
@@ -116,6 +134,7 @@ or if using tcsh,
    like ``REMORA3d.gnu.MPI.ex``, indicating that this is a 3-d version of the code, made with
    ``COMP=gnu``, and ``USE_MPI=TRUE``.
 
+
 Job info
 ~~~~~~~~
 
@@ -148,7 +167,7 @@ An example CMake configure command to build REMORA with MPI is listed below:
           -DCMAKE_Fortran_COMPILER:STRING=mpifort \
           .. && make
 
-An example CMake configure command to build REMORA with MPI and particles is listed below:
+An example CMake configure command to build REMORA with MPI, PnetCDF, and particles is listed below:
 
 ::
 
@@ -158,6 +177,7 @@ An example CMake configure command to build REMORA with MPI and particles is lis
           -DCMAKE_C_COMPILER:STRING=mpicc \
           -DCMAKE_Fortran_COMPILER:STRING=mpifort \
           -DREMORA_ENABLE_PARTICLES:BOOL=ON \
+          -DREMORA_ENABLE_PNETCDF:BOOL=ON \
           .. && make
 
 

Exec/Advection/GNUmakefile

@@ -26,7 +26,7 @@ DEBUG = FALSE
 TEST = TRUE
 USE_ASSERTION = TRUE
 
-USE_NETCDF = FALSE
+USE_PNETCDF = FALSE
 
 # GNU Make
 Bpack := ./Make.package

Exec/Channel_Test/GNUmakefile

@@ -23,7 +23,7 @@ DEBUG = FALSE
 TEST = TRUE
 USE_ASSERTION = TRUE
 
-USE_NETCDF = FALSE
+USE_PNETCDF = FALSE
 
 # GNU Make
 Bpack := ./Make.package

Exec/DoubleGyre/GNUmakefile

@@ -23,7 +23,7 @@ DEBUG = FALSE
 TEST = TRUE
 USE_ASSERTION = TRUE
 
-USE_NETCDF = FALSE
+USE_PNETCDF = FALSE
 
 # GNU Make
 Bpack := ./Make.package

Exec/DoublyPeriodic/GNUmakefile

@@ -26,7 +26,7 @@ DEBUG = FALSE
 TEST = TRUE
 USE_ASSERTION = TRUE
 
-USE_NETCDF = FALSE
+USE_PNETCDF = FALSE
 
 # GNU Make
 Bpack := ./Make.package

Exec/IdealMiniGrid/GNUmakefile

@@ -23,7 +23,7 @@ USE_ASSERTION = TRUE
 # Debugging
 DEBUG = FALSE
 
-USE_NETCDF = TRUE
+USE_PNETCDF = TRUE
 
 # GNU Make
 Bpack := ./Make.package

Exec/ParticlesOverSeaMount/GNUmakefile

@@ -23,7 +23,7 @@ DEBUG = FALSE
 TEST = TRUE
 USE_ASSERTION = TRUE
 
-USE_NETCDF    = FALSE
+USE_PNETCDF    = FALSE
 USE_PARTICLES = TRUE
 
 # GNU Make

Exec/Seamount/GNUmakefile

@@ -23,7 +23,7 @@ USE_ASSERTION = TRUE
 # Debugging
 DEBUG = FALSE
 
-USE_NETCDF = FALSE
+USE_PNETCDF = FALSE
 
 # GNU Make
 Bpack := ./Make.package

Exec/Upwelling/GNUmakefile

@@ -24,7 +24,7 @@ DEBUG = FALSE
 TEST = TRUE
 USE_ASSERTION = TRUE
 
-USE_NETCDF = FALSE
+USE_PNETCDF = FALSE
 
 # GNU Make
 Bpack := ./Make.package