Changeset 5415 for BOL/LMDZ_Setup/lmdz_env.sh
- Timestamp:
- Dec 17, 2024, 2:02:51 PM (34 hours ago)
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- 1 edited
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BOL/LMDZ_Setup/lmdz_env.sh (modified) (1 diff)
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BOL/LMDZ_Setup/lmdz_env.sh
r4944 r5415 1 #!/bin/bash 2 ######################################################## 3 # This file loads the required modules and sets the paths for simulations 4 # To modify the paths: 5 # 1) In the <set_env> function, find the section corresponding to your machine 6 # 2) Modify the variables, which are documented in the *) section of <set_env> 7 # See the end of <set_env> for the explanation of each 8 ######################################################## 1 9 2 ############################################################## 3 # Gestion des modules 4 ############################################################## 10 # <root_dir> will be set by sed by setup.sh here 11 root_dir=/home/abarral/PycharmProjects/installLMDZ/LMDZ_Setup 5 12 6 hostname=jean-zay-pp2 7 echo lmdz_env $hostname 0:3 ${hostname:0:3} 13 function get_hostname { 14 if grep -q "Adastra" /etc/motd; then 15 hostname="adastra" 16 elif which idrquota &> /dev/null; then 17 hostname="jean-zay" 18 else 19 hostname=$(hostname) 20 fi 21 } 8 22 9 case ${hostname:0:5} in 23 function set_env { # Platform-specific 24 case ${hostname:0:5} in 25 jean-) 26 module purge 27 compilo=19.0.4 # available 2013.0, 2017.2 28 module load intel-compilers/$compilo 29 #module load intel-mpi/$compilo 30 module load intel-mkl/$compilo 31 module load hdf5/1.10.5-mpi 32 module load netcdf/4.7.2-mpi 33 module load netcdf-fortran/4.5.2-mpi 34 module load subversion/1.9.7 35 #Pour module gcc, voir : https://trac.lmd.jussieu.fr/LMDZ/wiki/PortageJeanZay 36 #module load gcc/6.5.0 37 module load nco 38 module load cdo 39 # Imputation de la consommation sur le groupe (projet) actif par defaut, 40 # idrproj indique le groupe (projet) actif par defaut 41 # idrproj -d newproj redefinit "newproj" en tant que projet actif, 42 # alors $STORE, $WORK etc vont designer les espaces de "newproj") 43 account="lmd" # $(idrproj | grep active | awk '{ print $1}') doesn't work on compute nodes 44 ARCH="X64_JEANZAY_PBIOIPSL" 45 SIMRUNBASEDIR="$SCRATCH/" 46 LMDZD="$root_dir/LMDZD" 47 LMDZ_INIT="$root_dir/LMDZ_Init" 48 NB_MPI_MAX=2000 49 NB_OMP_MAX=20 50 NB_CORE_PER_NODE_MAX=0 51 MPICMD="srun -n" 52 RUNBASHCMD="srun -A $account@cpu --label -n 1 -c" 53 SUBMITCMD="sbatch -A $account@cpu" 54 ;; 55 spiri) 56 module purge 57 module load subversion/1.13.0 58 module load gcc/11.2.0 59 module load openmpi/4.0.7 60 module load cdo/2.3.0 10 61 11 jean-) ARCH=X64_JEANZAY 12 module purge 13 compilo=19.0.4 # available 2013.0, 2017.2 14 module load intel-compilers/$compilo 15 #module load intel-mpi/$compilo 16 module load intel-mkl/$compilo 17 module load hdf5/1.10.5-mpi 18 module load netcdf/4.7.2-mpi 19 module load netcdf-fortran/4.5.2-mpi 20 module load subversion/1.9.7 21 #Pour module gcc, voir : https://trac.lmd.jussieu.fr/LMDZ/wiki/PortageJeanZay 22 #module load gcc/6.5.0 23 module load nco 24 module load cdo 25 # Imputation de la consommation sur le groupe (projet) actif par defaut, 26 # idrproj indique le groupe (projet) actif par defaut 27 # idrproj -d newproj redefinit "newproj" en tant que projet actif, 28 # alors $STORE, $WORK etc vont designer les espaces de "newproj") 29 groupe=`idrproj | grep active | awk '{ print $1}'` 30 submit="sbatch -A ${groupe}@cpu " 31 run="srun --label " 32 # Espaces suivants definis par defaut en fonction du groupe actif, 33 # par exemple : SCRATCHD=$SCRATCH is /gpfsstore/rech/$groupe/$login 34 # * On peut aussi ne pas installer les scripts a la racine de STORE, 35 # mais dans STORED=$STORE/your_folder 36 STORED=$STORE 37 SCRATCHD=$SCRATCH 38 LMDZD=$WORK 39 nb_mpi_max=2000 40 nb_omp_max=20 41 #LMDZ_Init sur le $STORE du $groupe 42 LMDZ_Init=$STORE/LMDZ_Init ;; 43 *) ARCH= 44 submit=". " 45 run="mpirun -np " 46 SCRATCHD=~/TMP/SCRATCH 47 STORED=~/TMP/ 48 LMDZD=~/TMP 49 nb_mpi_max=2 50 nb_omp_max=2 51 LMDZ_Init=~/LMDZ/LMDZ_Init 52 esac 62 ARCH="X64_MESOIPSL-GNU" 63 SIMRUNBASEDIR="$SCRATCH/" 64 LMDZD="$root_dir/LMDZD" 65 LMDZ_INIT="$HOME/LMDZ_Init" 66 NB_MPI_MAX=5 67 NB_OMP_MAX=1 68 NB_CORE_PER_NODE_MAX=0 69 N_HYPERTHREADING=1 70 MPICMD="mpirun -np" # on spirit, we can't run MPI using srun from within sbatch 71 RUNBASHCMD="bash" 72 SUBMITCMD="sbatch" 73 ;; 74 adast) 75 module purge 76 module load PrgEnv-gnu # we need to load the env because lmdz links some shared libraries 77 module load gcc/13.2.0 # required, see https://dci.dci-gitlab.cines.fr/webextranet/user_support/index.html#prgenv-and-compilers 78 export CRAY_CPU_TARGET=x86-64 # to suppress warnings during Cmake netcdf95 build 79 export FI_CXI_RX_MATCH_MODE=hybrid # 09/24 otherwise we get random SIGABRT e.g. "libfabric:2490616:1725895288::cxi:core:cxip_ux_onload_cb():2657<warn> c1456: RXC (0x5130:21) PtlTE 84:[Fatal] LE resources not recovered during flow control. FI_CXI_RX_MATCH_MODE=[hybrid|software] is required" 53 80 81 function cdo { # cdo is available as a spack cmd which requires a specific, incompatible env 82 unset cdo 83 module purge 84 module load develop GCC-CPU-4.0.0 cdo/2.4.2-omp-mpi 85 cdo "$@" 86 set_env 87 } 54 88 55 echo LMDZ_Init dans lmdz_env $LMDZ_Init 89 function ferret { 90 unset ferret 91 module purge 92 module load GCC-CPU-3.1.0 93 module load ferret 94 ferret "$@" 95 set_env 96 } 97 98 account=$(/usr/sbin/my_project.py -l 2>&1 | head -1 | cut -d " " -f 3- | cut -c 5-) 99 ARCH="X64_ADASTRA-GNU" 100 SIMRUNBASEDIR="$SCRATCHDIR/" 101 LMDZD="$root_dir/LMDZD" 102 LMDZ_INIT="$WORKDIR/LMDZ_Init" 103 NB_MPI_MAX=2000 104 NB_OMP_MAX=200 105 NB_CORE_PER_NODE_MAX=192 106 N_HYPERTHREADING=1 # Adastra has SMT=2 enabled, but we found no actual performance improvement for the latlon model. Maybe useful for Dynamico ? 107 MPICMD="srun -n" 108 # RUNBASHCMD="srun --label --account=$account --constraint=GENOA --ntasks-per-node=1 -n 1 --time=00:15:00 -c" 109 RUNBASHCMD="bash" # On Adastra the docs says we can use login nodes for compilation 110 SUBMITCMD="env $(env | grep -E "SLURM_|SBATCH_|SRUN_" | cut -d= -f1 | awk '{print "-u " $0}' | tr '\n' ' ' ) sbatch --constraint=GENOA --account=$account" # we need to remove the existing SLURM variables otherwise they may be unexpectedly inherited by the submitted script 111 ;; 112 *) echo "WARNING: RUNNING THIS SCRIPT ON A LOCAL COMPUTER IS DISCOURAGED (lackluster cpus and memory)" 113 ARCH="local-gfortran-parallel" # The arch file to use 114 SIMRUNBASEDIR="/tmp/SCRATCH/" # Where the simulations will be executed ($SIMRUNBASEDIR/LMDZ_Setup/...) 115 LMDZD="$root_dir/LMDZD" # Where the sources will be downloaded and compiled 116 LMDZ_INIT="$HOME/LMDZ_Init" # Where to store shared files used for initialisation. Should be outside the LMDZ_Setup dir since it's shared between several LMDZ_Setup. 117 NB_MPI_MAX=2 # Max number of MPI cores (only for running simulations) 118 NB_OMP_MAX=2 # Max number of OMP threads (only for running simulations) 119 NB_CORE_PER_NODE_MAX=0 # Max number of cores per node (real cores, not hyperthreading - only for running simulations, cluster-specific) 120 N_HYPERTHREADING=1 # How many hyperthreading threads per physical core 121 MPICMD="mpirun -np" # command to run an mpi executable, as $MPICMD <nprocs> <script> 122 RUNBASHCMD="bash" # command to run a bash job, as $runbashcmd (nthreads) <script> [nthreads only supplied if =/="bash"] 123 SUBMITCMD="." # command to sumbit a job, as $submitcmd <script> 124 ;; 125 esac 126 } 127 128 get_hostname 129 echo "Setting up lmdz_env on $hostname" 130 set_env 131 132 if [[ ! (-d $root_dir && -f $root_dir/.lmdz_setup_root_dir && -f $root_dir/lmdz_env.sh) ]]; then 133 echo "STOP: root_dir $root_dir not found, either you are running on an unsupported cluster, or the initialisation failed midway"; exit 1 134 fi
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