WRF.md, corrections to srvx1 configuration

WRF.md

@@ -159,7 +159,7 @@ In most cases, precompiled libraries can be made available to the operating syst
 
 SRVX1:
 ```sh
-module load intel-parallel-studio/composer.2020.4-intel-20.0.4 openmpi/3.1.6-intel-20.0.4 netcdf-fortran/4.5.2-intel-20.0.4-MPI3.1.6 eccodes/2.19.1-intel-20.0.4-MPI3.1.6
+module load intel-parallel-studio/composer.2020.4-intel-20.0.4 openmpi/3.1.6-intel-20.0.4 hdf5/1.10.7-intel-20.0.4-MPI3.1.6 netcdf-c/4.6.3-intel-20.0.4-MPI3.1.6 netcdf-fortran/4.5.2-intel-20.0.4-MPI3.1.6
 ```
 
 JET (GNU Fortran compiler):
@@ -252,7 +252,7 @@ This build of WRF will use NETCDF4 with HDF5 compression
 *****************************************************************************
 ```
 
-But the configuration could also end with a message like this:
+But the configuration could also end with a message like this (it happens for instance on srvx1):
 ```sh
 ************************** W A R N I N G ************************************
 NETCDF4 IO features are requested, but this installation of NetCDF           
@@ -272,10 +272,24 @@ Then re-run this configure script
 
 *****************************************************************************
 ```
-This is actually a misleading error message. The problem has nothing to do with NETCDF4 not being available, but with the operating system not knowing where the NETCDF libraries are. **NOTE: explain solution.**
+This is actually a misleading error message. The problem has nothing to do with NETCDF4 not being available, but with the operating system not detecting correctly all the dependencies of the NETCDF libraries. Solving this problem requires manually editing the configuration files (see below).
 
 The configure script stores the model configuration to a file called `configure.wrf`. This is specific to the source code version, to the server where the source code is compiled, and to the software environment. If you a have a working `configure.wrf` file for a given source code/server/environment, back it up.
 
+To solve the NETCDF4 error on srvx1, these changes to `configure.wrf` are needed:
+```sh
+(base) [serafin@srvx1 WRF]$ diff configure.wrf configure.wrf.dmpar
+98c98
+< DEP_LIB_PATH    = -L/home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/intel-20.0.4/netcdf-c-4.6.3-5netrylc3im76bqg4vlo2ck4qd3jmrdt/lib
+---
+> DEP_LIB_PATH    = -L/home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/intel-20.0.4/netcdf-c-4.6.3-5netrylc3im76bqg4vlo2ck4qd3jmrdt/lib -L/home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/intel-20.0.4/hdf5-1.10.7-nj3ahzinbfiwe5tnteupbfmx4empgh6l/lib
+122c122
+<                       -L$(WRF_SRC_ROOT_DIR)/external/io_netcdf -lwrfio_nf -L/home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/intel-20.0.4/netcdf-fortran-4.5.2-ktet7v73pc74qrx6yc3234zhfo573w23/lib -lnetcdff      
+---
+>                       -L$(WRF_SRC_ROOT_DIR)/external/io_netcdf -lwrfio_nf -L/home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/intel-20.0.4/netcdf-fortran-4.5.2-ktet7v73pc74qrx6yc3234zhfo573w23/lib -lhdf5 -lnetcdff -lnetcdf
+```
+The first file, `configure.wrf`, is the result of the (wrong) automatic configuration. The second file, `configure.wrf.dmpar` is the manually fixed one. In the latter, additional library link directives (`-lnetcdf` and `-lhdf5`) are added to the variable `LIB_EXTERNAL`, and the full paths to these extra libraries are added to the variable `DEP_LIB_PATH`.
+
 #### Compile WRF
 
 You always compile WRF for a specific model configuration. The ones we use most commonly are `em_les` (for large-eddy simulation), `em_quarter_ss` (for idealized mesoscale simulations), `em_real` (for real-case forecasts). So type either of the following, depending on what you want to get: