source: BOL/LMDZ_Setup/lmdz_env.sh @ 5447

Last change on this file since 5447 was 5438, checked in by fhourdin, 3 days ago

Automatic installation of SPLA version
File size: 9.5 KB
Line 
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########################################################
9
10# <root_dir> will be set by sed by setup.sh here
11root_dir=/home/hourdin/TMP/TestI
12pub_store=1
13
14function get_hostname {
15  if grep -q "Adastra" /etc/motd 2>/dev/null ; then
16    hostname="adastra"
17  elif which idrquota &> /dev/null; then
18    hostname="jean-zay"
19  else
20    hostname=$(hostname)
21  fi
22}
23
24function set_env {  # Platform-specific
25  case ${hostname:0:5} in
26#-------------------------------------------------------------------------
27    jean-) # Jean-zay, Idris-CNRS super computer
28#-------------------------------------------------------------------------
29      module purge
30      compilo=19.0.4 # available 2013.0, 2017.2
31      module load intel-compilers/$compilo
32      #module load intel-mpi/$compilo
33      module load intel-mkl/$compilo
34      module load hdf5/1.10.5-mpi
35      module load netcdf/4.7.2-mpi
36      module load netcdf-fortran/4.5.2-mpi
37      module load subversion/1.9.7
38      #Pour module gcc, voir : https://trac.lmd.jussieu.fr/LMDZ/wiki/PortageJeanZay
39      #module load gcc/6.5.0
40      module load nco
41      module load cdo
42      # Imputation de la consommation sur le groupe (projet) actif par defaut,
43      #   idrproj indique le groupe (projet) actif par defaut
44      #   idrproj -d newproj   redefinit "newproj" en tant que  projet actif,
45      #        alors $STORE, $WORK etc vont designer les espaces de "newproj")
46      account="lmd"  # $(idrproj | grep active | awk '{ print $1}') doesn't work on compute nodes
47      ARCH="X64_JEANZAY_PBIOIPSL"
48      SIMRUNBASEDIR="$SCRATCH/$(basename $root_dir)"
49      LMDZD="$WORK/LMDZD"
50      LMDZ_INIT="$WORK/LMDZ/pub"
51      NB_MPI_MAX=2000
52      NB_OMP_MAX=20
53      NB_CORE_PER_NODE_MAX=0
54      MPICMD="srun -n"
55      RUNBASHCMD="srun -A $account@cpu --label -n 1 -c"
56      #SUBMITCMD="sbatch -A $account@cpu"
57      submitcmd() {
58         sbatch -A $account@cpu $1
59      }
60      ;;
61#-------------------------------------------------------------------------
62    spiri) # Spirit : IPSL cluster
63#-------------------------------------------------------------------------
64      module purge
65      module load subversion/1.13.0
66      module load gcc/11.2.0
67      module load openmpi/4.0.7
68      module load cdo/2.3.0
69
70      ARCH="X64_MESOIPSL-GNU"
71      SIMRUNBASEDIR="$SCRATCH/$(basename $root_dir)"
72      LMDZD="$root_dir/LMDZD"
73      LMDZ_INIT="$HOME/LMDZ/pub"
74      NB_MPI_MAX=5
75      NB_OMP_MAX=1
76      NB_CORE_PER_NODE_MAX=0
77      N_HYPERTHREADING=1
78      MPICMD="mpirun -np"  # on spirit, we can't run MPI using srun from within sbatch
79      RUNBASHCMD="bash"
80      #SUBMITCMD="sbatch"
81      submitcmd() {
82         sbatch $1
83      }
84      ;;
85#-------------------------------------------------------------------------
86    adast) # Adastra, Cines computing center
87#-------------------------------------------------------------------------
88      module purge
89      module load PrgEnv-gnu  # we need to load the env because lmdz links some shared libraries
90      module load gcc/13.2.0  # required, see https://dci.dci-gitlab.cines.fr/webextranet/user_support/index.html#prgenv-and-compilers
91      export CRAY_CPU_TARGET=x86-64  # to suppress warnings during Cmake netcdf95 build
92      export FI_CXI_RX_MATCH_MODE=hybrid  # 09/24 otherwise we get random SIGABRT e.g. "libfabric:2490616:1725895288::cxi:core:cxip_ux_onload_cb():2657<warn> c1456: RXC (0x5130:21) PtlTE 84:[Fatal] LE resources not recovered during flow control. FI_CXI_RX_MATCH_MODE=[hybrid|software] is required"
93
94      function cdo {  # cdo is available as a spack cmd which requires a specific, incompatible env
95        unset cdo
96        module purge
97        module load develop GCC-CPU-4.0.0 cdo/2.4.2-omp-mpi
98        cdo "$@"
99        set_env
100      }
101
102      function ferret {
103        unset ferret
104        module purge
105        module load GCC-CPU-3.1.0
106        module load ferret
107        ferret "$@"
108        set_env
109      }
110
111      account=$(/usr/sbin/my_project.py -l 2>&1 | head -1 | cut -d " " -f 3- | cut -c 5-)
112      ARCH="X64_ADASTRA-GNU"
113      SIMRUNBASEDIR="$SCRATCHDIR/$(basename $root_dir)"
114      LMDZD="$WORKDIR/LMDZD"
115      LMDZ_INIT="$WORKDIR/LMDZ/pub"
116      NB_MPI_MAX=2000
117      NB_OMP_MAX=200
118      NB_CORE_PER_NODE_MAX=192
119      N_HYPERTHREADING=1  # Adastra has SMT=2 enabled, but we found no actual performance improvement for the latlon model. Maybe useful for Dynamico ?
120      MPICMD="srun -n"
121#      RUNBASHCMD="srun --label --account=$account --constraint=GENOA --ntasks-per-node=1 -n 1 --time=00:15:00 -c"
122      RUNBASHCMD="bash"  # On Adastra the docs says we can use login nodes for compilation
123      #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
124      submitcmd() {
125        env $(env | grep -E "SLURM_|SBATCH_|SRUN_" | cut -d= -f1 | awk '{print "-u " $0}' | tr '\n' ' ' ) sbatch --constraint=GENOA --account=$account $1
126      }  # we need to remove the existing SLURM variables otherwise they may be unexpectedly inherited by the submitted script
127      ;;
128#-------------------------------------------------------------------------
129    *)  # Local machine.
130#-------------------------------------------------------------------------
131      ARCH="local-gfortran-parallel"  # The arch file to use
132      SIMRUNBASEDIR="$root_dir/SCRATCH/"  # Where the simulations will be executed ($SIMRUNBASEDIR/LMDZ_Setup/...)
133      LMDZD="$root_dir/../LMDZD"  # Where the sources will be downloaded and compiled
134      if [[ $pub_store ]] ; then LMDZ_INIT="$HOME/LMDZ/pub" ; else LMDZ_INIT="$root_dir/LMDZ/pub" ; fi
135      NB_MPI_MAX=2  # Max number of MPI cores (only for running simulations)
136      NB_OMP_MAX=2  # Max number of OMP threads (only for running simulations)
137      NB_CORE_PER_NODE_MAX=0  # Max number of cores per node (real cores, not hyperthreading - only for running simulations, cluster-specific)
138      N_HYPERTHREADING=1  # How many hyperthreading threads per physical core
139      MPICMD="mpirun -np" # command to run an mpi executable, as $MPICMD <nprocs> <script>
140      RUNBASHCMD="bash" # command to run a bash job, as $runbashcmd (nthreads) <script> [nthreads only supplied if =/="bash"]
141      #SUBMITCMD="."  # command to sumbit a job, as $submitcmd <script>
142      submitcmd() {
143         nohup bash $1 > out.$$ 2>err.$$ &
144      }
145      ;;
146  esac
147}
148
149#-----------------------------------------------------------------------------------------------------
150function wget_pub() { # geting file from http:lmdz... and saving on $LMDZ_INIT
151#-----------------------------------------------------------------------------------------------------
152  local dir=$1
153  local file=$2
154  local target_dir=$LMDZ_INIT/$dir
155  if [ ! -f $target_dir/$file ] ; then
156     mkdir -p $target_dir
157     cd $target_dir
158     wget --no-check-certificate -nv "http://lmdz.lmd.jussieu.fr/pub/$dir/$file"
159     cd -
160  fi
161}
162
163#-----------------------------------------------------------------------------------------------------
164function cp_from_pub() { # geting file from http:lmdz... and saving on $LMDZ_INIT
165#-----------------------------------------------------------------------------------------------------
166  local dir=$1
167  local file=$2
168  cp -f $LMDZ_INIT/$dir/$file .
169}
170
171#-----------------------------------------------------------------------------------------------------
172function ln_from_pub() { # geting file from http:lmdz... and saving on $LMDZ_INIT
173#-----------------------------------------------------------------------------------------------------
174  local dir=$1
175  local file=$2
176  ln -sf $LMDZ_INIT/$dir/$file .
177}
178
179#-----------------------------------------------------------------------------------------------------
180function get_input_files() {
181#-----------------------------------------------------------------------------------------------------
182  local method=$1
183  local target=$2
184  case $target in
185
186      Orchidee) local files="PFTmap_IPCC_2000.nc cartepente2d_15min.nc routing.nc routing_simple.nc lai2D.nc \
187      alb_bg_modisopt_2D_ESA_v2.nc reftemp.nc \
188      soils_param.nc woodharvest_2000.nc PFTmap_15PFT.v1_2000.nc soil_bulk_and_ph.nc  \
189      ndep_nhx.nc ndep_noy.nc nfert_cropland.nc nfert_pasture.nc nmanure_cropland.nc nmanure_pasture.nc bnf.nc" ;;
190
191      AerChem) local files="aerosols1850_from_inca.nc aerosols9999_from_inca.nc" ;;
192
193      SPLA_WA/emissions) local files="donnees_lisa.nc SOILSPEC.data              \
194         cly.dat $( for i in $(seq -w 1 12 ) ; do echo dust$i.nc ; done ) wth.dat   \
195         carbon_emissions.nc sulphur_emissions_antro.nc sulphur_emissions_nat.nc \
196         sulphur_emissions_volc.nc" ;;
197
198      *) echo target $target non available in get_input_files ; exit 1 ;;
199  esac
200
201  if [[ $method != wget_pub && $method != ln_from_pub ]] ; then
202     echo method $method not available in get_input_files ; exit 1
203  fi
204  for file in $files ; do $method 3DInputData/$target $file ; done
205
206}
207
208get_hostname
209echo "Setting up lmdz_env on $hostname"
210set_env
211
212if [[ ! (-d $root_dir && -f $root_dir/.lmdz_setup_root_dir && -f $root_dir/lmdz_env.sh) ]]; then
213  echo "STOP: root_dir $root_dir not found, either you are running on an unsupported cluster, or the initialisation failed midway"; exit 1
214fi
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