merge: merge pull request #1 from cryotools/development

feat: COSIPY_DIR environment variable, slim build script
cryotools · Nov 29, 2024 · 8604eb4 · 8604eb4
2 parents ced3746 + 3b170f3
commit 8604eb4
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diff --git a/README.md b/README.md
@@ -26,16 +26,20 @@ module load perl/5.36 perl-path-tiny perl-time-piece
 bash patch_wrfxcspy.sh --install-all -i ./foo/bar/
 ```
 
-2. Install WRF's dependencies and edit ``build_wrf.sh`` to point to the right paths for COSIPY_API, NETCDF, HDF5, and DIR. Make sure WRF's dependencies are correctly installed.
+2. Install WRF's dependencies and edit ``build_wrf.sh`` or ``build_wrf_full.sh`` to point to the right paths for COSIPY_API, COSIPY_DIR, NETCDF, HDF5, and DIR. Alternatively, you can load your own build file, and export COSIPY_API and COSIPY_DIR to your LD_LIBRARY_PATH.
 
-3. Load environment variables, configure and patch WRF:
+3. Load environment variables:
 ```console
-bash patch_wrfxcspy -e -c -p -i ./foo/bar/WRF/
+bash patch_wrfxcspy -e
+source build_wrf.sh  # if the previous command fails
 ```
 
-Depending on your system and access permissions, you may need to run ``build_wrf.sh`` separately.
+4. Configure and patch WRF:
+```console
+bash patch_wrfxcspy -c -p -i ./foo/bar/WRF/
+```
 
-4. Build WRF: ``./compile em_real >& log.compile``
+5. Build WRF: ``./compile em_real >& log.compile``
 
 **Arguments:**
 

diff --git a/src/patch_wrfxcspy/README.md b/src/patch_wrfxcspy/README.md
@@ -26,16 +26,20 @@ module load perl/5.36 perl-path-tiny perl-time-piece
 bash patch_wrfxcspy.sh --install-all -i ./foo/bar/
 ```
 
-2. Install WRF's dependencies and edit ``build_wrf.sh`` to point to the right paths for COSIPY_API, NETCDF, HDF5, and DIR. Make sure WRF's dependencies are correctly installed.
+2. Install WRF's dependencies and edit ``build_wrf.sh`` or ``build_wrf_full.sh`` to point to the right paths for COSIPY_API, COSIPY_DIR, NETCDF, HDF5, and DIR. Alternatively, you can load your own build file, and export COSIPY_API and COSIPY_DIR to your LD_LIBRARY_PATH.
 
-3. Load environment variables, configure and patch WRF:
+3. Load environment variables:
 ```console
-bash patch_wrfxcspy -e -c -p -i ./foo/bar/WRF/
+bash patch_wrfxcspy -e
+source build_wrf.sh  # if the previous command fails
 ```
 
-Depending on your system and access permissions, you may need to run ``build_wrf.sh`` separately.
+4. Configure and patch WRF:
+```console
+bash patch_wrfxcspy -c -p -i ./foo/bar/WRF/
+```
 
-4. Build WRF: ``./compile em_real >& log.compile``
+5. Build WRF: ``./compile em_real >& log.compile``
 
 **Arguments:**
 

diff --git a/src/patch_wrfxcspy/build_wrf.sh b/src/patch_wrfxcspy/build_wrf.sh
@@ -7,16 +7,14 @@ USER_PATH="/home/atuin/<group>/<account>/software"
 
 # Load HPC modules
 module purge
-module load hdf5/1.10.7-impi-intel netcdf-c netcdf-fortran/4.5.3-intel gcc/9.4.0 cmake
-module load mkl/2022.1.0 m4/1.4.19
+module load intelmpi/2021.6.0 intel/2021.4.0
 module load user-spack
 module load time
 
 # Coupler
-export COSIPY_API="${USER_PATH}/WRF/COUPLER"
+export COSIPY_API="${USER_PATH}/path/to/WRF/COUPLER"
+export COSIPY_DIR="${USER_PATH}/path/to/WRF/cosipy"
 export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${COSIPY_API}
-export LIBRARY_PATH=${LIBRARY_PATH}:${COSIPY_API}
-export PATH=${PATH}:${COSIPY_API}
 
 # WRF options
 export WRFIO_NCD_LARGE_FILE_SUPPORT=1
@@ -25,42 +23,21 @@ export WRF_NMM_CORE=0
 export WRF_CHEM=0
 
 # NetCDF
-export NETCDF_LIB="-L${NETCDF_C_ROOT}/lib -lnetcdf -L${NETCDF_FORTRAN_ROOT}/lib -lnetcdff -Wl,-rpath,${NETCDF_C_ROOT}/lib"
-export NETCDF_INC="-I${NETCDF_C_ROOT}/include -I${NETCDF_FORTRAN_ROOT}/include"
-export NETCDF="${USER_PATH}/privat/netcdf"
-export PATH=${NETCDF}/bin:${PATH}
-export LIBRARY_PATH=$NETCDF_C_ROOT/lib:$LIBRARY_PATH
-export LIBRARY_PATH=$NETCDF_FORTRAN_ROOT/lib:$LIBRARY_PATH
+export NETCDF="${USER_PATH}/path/to/netcdf"
+export NETCDF_LIB="-L${NETCDF}/lib -lnetcdf -lnetcdff -Wl,-rpath,${NETCDF}/lib"
+export NETCDF_INC="-I${NETCDF_C_ROOT}/include"
+export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${NETCDF}/lib
 
 # NetCDF options
 export NETCDF_ROOT=$NETCDF
 export NETCDF_classic=1
 export NETCDF4=1
 
 # HDF5
-export HDF5="${USER_PATH}/privat/hdf5"
-export DEP_LIB_PATH=-L${HDF5}/lib
-export PATH=${HDF5}/bin:${PATH}
+export HDF5="${USER_PATH}/path/to/hdf5"
+export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HDF5}/lib
 
 # Libraries
 export DIR="${USER_PATH}/WRF/Build_WRF/LIBRARIES"
 export JASPERLIB=${DIR}/grib2/lib
 export JASPERINC=${DIR}/grib2/include
-export PATH=${DIR}/mpich/bin:${PATH}
-
-# Compilers
-export CC=icc
-export CXX=icpc
-export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
-export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
-
-export F77=ifort
-export FC=ifort
-export F90=ifort
-export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
-
-export CPP='icc -E'
-export CXXCPP='icpc -E'
-
-export LDFLAGS=-L${DIR}/grib2/lib
-export CPPFLAGS=-I${DIR}/grib2/include
diff --git a/src/patch_wrfxcspy/build_wrf_full.sh b/src/patch_wrfxcspy/build_wrf_full.sh
@@ -0,0 +1,67 @@
+#!/bin/bash -l
+# Copyright 2024 WRFxCSPY Contributors
+
+# Ensure COSIPY_API, NETCDF, HDF5, and DIR point to the correct paths.
+
+USER_PATH="/home/atuin/<group>/<account>/software"
+
+# Load HPC modules
+module purge
+module load hdf5/1.10.7-impi-intel netcdf-c netcdf-fortran/4.5.3-intel gcc/9.4.0 cmake
+module load mkl/2022.1.0 m4/1.4.19
+module load user-spack
+module load time
+
+# Coupler
+export COSIPY_API="${USER_PATH}/path/to/WRF/COUPLER"
+export COSIPY_DIR="${USER_PATH}/path/to/WRF/cosipy"
+export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${COSIPY_API}
+export LIBRARY_PATH=${LIBRARY_PATH}:${COSIPY_API}
+export PATH=${PATH}:${COSIPY_API}
+
+# WRF options
+export WRFIO_NCD_LARGE_FILE_SUPPORT=1
+export WRF_EM_CORE=1
+export WRF_NMM_CORE=0
+export WRF_CHEM=0
+
+# NetCDF
+export NETCDF_LIB="-L${NETCDF_C_ROOT}/lib -lnetcdf -L${NETCDF_FORTRAN_ROOT}/lib -lnetcdff -Wl,-rpath,${NETCDF_C_ROOT}/lib"
+export NETCDF_INC="-I${NETCDF_C_ROOT}/include -I${NETCDF_FORTRAN_ROOT}/include"
+export NETCDF="${USER_PATH}/privat/netcdf"
+export PATH=${NETCDF}/bin:${PATH}
+export LIBRARY_PATH=$NETCDF_C_ROOT/lib:$LIBRARY_PATH
+export LIBRARY_PATH=$NETCDF_FORTRAN_ROOT/lib:$LIBRARY_PATH
+
+# NetCDF options
+export NETCDF_ROOT=$NETCDF
+export NETCDF_classic=1
+export NETCDF4=1
+
+# HDF5
+export HDF5="${USER_PATH}/privat/hdf5"
+export DEP_LIB_PATH=-L${HDF5}/lib
+export PATH=${HDF5}/bin:${PATH}
+
+# Libraries
+export DIR="${USER_PATH}/WRF/Build_WRF/LIBRARIES"
+export JASPERLIB=${DIR}/grib2/lib
+export JASPERINC=${DIR}/grib2/include
+export PATH=${DIR}/mpich/bin:${PATH}
+
+# Compilers
+export CC=icc
+export CXX=icpc
+export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
+export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
+
+export F77=ifort
+export FC=ifort
+export F90=ifort
+export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
+
+export CPP='icc -E'
+export CXXCPP='icpc -E'
+
+export LDFLAGS=-L${DIR}/grib2/lib
+export CPPFLAGS=-I${DIR}/grib2/include