We take the first step of downloading, compiling and testing XIOS and NEMO4 code on PSMN (ENS de Lyon; Lyon, France). This is a post based on an installation made by Cerasela Calugaru. Thank you Cerasela ! This post is written by Louis Saddier (louis.saddier@ens-lyon.fr), thanks Louis!
Pre-requisites:
Suggested reading:
Installing XIOS
Log-into PSMN into a E5 partition node. Set-up your environment with:
module use /applis/PSMN/debian11/E5/modules/all/
module load netCDF-Fortran/4.6.1-gompi-2023aGet XIOS :
svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk XIOSNow we need to create arch files to indicate the options we want when we will compile XIOS. First we will create a .path file:
cd XIOS/arch/
vi arch-X64_PSMN_E5.pathand write:
NETCDF_INCDIR="-I$NETCDFF_INCDIR -I$NETCDF_INC_DIR"
NETCDF_LIBDIR="-L$NECDFF_LIBDIR -L$NETCDF_LIB_DIR"
NETCDF_LIB="-lnetcdff -lnetcdf"
MPI_INCDIR=""
MPI_LIBDIR=""
MPI_LIB=""
HDF5_INCDIR="-I$HDF5_INC_DIR"
HDF5_LIBDIR="-L$HDF5_LIB_DIR"
HDF5_LIB="-lhdf5_hl -lhdf5 -lhdf5 -lz"
OASIS_INCDIR="-I$PWD/../../oasis3-mct/BLD/build/lib/psmile.MPI1"
OASIS_LIBDIR="-L$PWD/../../oasis3-mct/BLD/lib"
OASIS_LIB="-lpsmile.MPI1 -lscrip -lmct -lmpeu"Then, we will create a .fcm file:
vi arch-X64_PSMN_E5.fcmand write:
%CCOMPILER mpicc
%FCOMPILER mpif90
%LINKER mpif90
%BASE_CFLAGS -w -std=c++11 -D__XIOS_EXCEPTION
%PROD_CFLAGS -O3 -D BOOST_DISABLE_ASSERTS
%DEV_CFLAGS -g -traceback
%DEBUG_CFLAGS -DBZ_DEBUG -g -traceback -fno-inline
%BASE_FFLAGS -D__NONE__
%PROD_FFLAGS -O3
%DEV_FFLAGS -g -O2 -traceback
%DEBUG_FFLAGS -g -traceback
%BASE_INC -D__NONE__
%BASE_LD -lstdc++
%CPP mpicc -EP
%FPP cpp -P
%MAKE gmakeFinally, we will create a .env file:
vi arch-X64_PSMN_E5.envand then write:
module purge
module use /applis/PSMN/debian11/E5/modules/all/
module load netCDF-Fortran/4.6.1-gompi-2023a
export HDF5_INC_DIR=$HDF5_DIR/include
export HDF5_LIB_DIR=$HDF5_DIR/lib
export NETCDFF_INCDIR=/applis/PSMN/debian11/E5/software/netCDF-Fortran/4.6.1-gompi-2023a/include
export NETCDFF_LIBDIR=/applis/PSMN/debian11/E5/software/netCDF-Fortran/4.6.1-gompi-2023a/lib
export NETCDF_INC_DIR=/applis/PSMN/debian11/E5/software/netCDF/4.9.2-gompi-2023a/include
export NETCDF_LIB_DIR=/applis/PSMN/debian11/E5/software/netCDF/4.9.2-gompi-2023a/libNow we will compile XIOS with the options we just created:
cd ..
./make_xios --arch X64_PSMN_E5To test XIOS:
cd generic_testcase
mpirun -np 4 ../bin/generic_testcase.exeIf no errors appear, XIOS should be well installed.
Installing NEMO
Get NEMO4, in my case I’m using the 4.2.1 version:
git clone --branch 4.2.1 https://forge.nemo-ocean.eu/nemo/nemo.git nemo_4.2.1
cd nemo_4.2.1/If not already done do:
module use /applis/PSMN/debian11/E5/modules/all/
module load netCDF-Fortran/4.6.1-gompi-2023aThen:
source XIOS/bin/fcm_env.shAs in the installation of XIOS, we need to modifiate some arch files that contain Fortran options for the compilation of NEMO:
cd arch
cp arch-linux_gfortran.fcm arch-PSMN_E5.fcm
vi arch-PSMN_E5.fcmUncomment and modify these 4 lines:
Note that you need to specify in the last line the path where you installed XIOS. In my case it was in my home folder
/home/lsaddier
%HDF5_HOME $HDF5_DIR
%NCDF_C_HOME /applis/PSMN/debian11/E5/software/netCDF/4.9.2-gompi-2023a
%NCDF_F_HOME /applis/PSMN/debian11/E5/software/netCDF-Fortran/4.6.1-gompi-2023a
%XIOS_HOME /home/lsaddier/XIOSOn the %FCFLAGS line, add a last argument:
%FCFLAGS -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -ffree-line-length-none -fallow-argument-mismatchThen we are ready to compile NEMO. Let’s try with the GYRE_PISCES configuration:
cd ..
./makenemo -m 'PSMN_E5' -r 'GYRE_PISCES' -n 'MY_GYRE_PISCES'Finally you can test the execution of NEMO (here with 4 processors):
cd /nemo_4.2.1/cfgs/MY_GYRE_PISCES/EXP00
mpirun -n 4 ./nemo