Porting on RedHat8

After maintenance of April 11 and 12 all the Irene machines of the TGCC will change OS (it will go from redhat7 to redhat8)

How to install your environment on redhat8 (skl and rome)

We suggest the user to use the igcmg environment (in bash) with a copy of the bashrc in his HOME.

ryyy999@irene: cp ~igcmg/MachineEnvironment/irene_next/bashrc  ~/.bashrc
ryyy999@irene: cp ~igcmg/MachineEnvironment/irene_next/bashrc_irene_next ~/.bashrc_irene_next

Additionally, you can complete the example of bashrc_irene_next file to create your favorite environment (alias, module load ...).

We strongly advice you to add the line module switch dfldatadir dfldatadir/genXXXX in your own .bashrc_irene_next.

WARNING : if you have a ~/.profile file, it's better to remove it to avoid any problem during the execution of a simulation with libIGCM

In this environment is specified:

• the path to the compiler tool fcm and to the rebuild tool which recombines output files from a parallel model:

  export PATH=$(ccc_home -u igcmg)/Tools/fcm/bin:$(ccc_home -u igcmg)/Tools/irene/bin:$PATH
  

• the load of modules giving access to analyze data or post processing libraries and tools needed on our platform (done in ccc_home -u igcmg/MachineEnvironment/irene_next/env_atlas_irene).

WARNING : You cannot load in the same time the intel environment for compilation and models computation, AND ferret software. There are not compatible. It's why by default we propose an environment for post processing. The computation environment will be load by modipsl and libIGCM during the compilation and the running time.

Modifications need to be done in models

LMDZ

modify %BASE_LD in LMDZ/arch/arch-X64_IRENE.fcm

%BASE_LD   -i4 -r8 -auto -L/ccc/products/mkl-20.0.0/system/default/20.0.0/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread

ORCHIDEE

If you are working with a version older than rev 7792, you need to apply modifications describe ​here

INCA

If you are working with a version older than rev 1050, you need to modify lunout parameter to use standard output file. For this in INCA/src/INCA_MOD/print_inca.F90 remove lines from

namefile='inca.out'

(...)

stop 'print_inca'
endif

add line

 lunout = 6

XIOS

If you are working with a veresion on XIOS/branchs/xios-2.5, you need to modify XIOS/arch/arch-X64_IRENE.fcm

%BASE_CFLAGS    -std=gnu++98 -diag-disable 1125 -diag-disable 279 -D__XIOS_EXCEPTION

Modifications for V6.2 configurations

Compilation and computation

Modify ARCH/arch-X64_IRENE.env

# Compile and running environnemnet at Irene Skylake 
  
module purge
module load intel/20.0.0
module load mpi/openmpi/4.1.4
module load flavor/hdf5/parallel
module load hdf5/1.12.0
module load netcdf-fortran/4.5.3
module load mkl/20.0.0
module load feature/bridge/heterogenous_mpmd
module load c++/gnu/8.3.0
module load c/gnu/8.3.0

post-processing

Modify libIGCM/libIGCM_sys/libIGCM_sys_irene.ksh or libIGCM_sys_irene-amd.ksh to source new env_atlas_irene file.

if [ X${TaskType} = Xcomputing ] ; then
  IGCM_debug_Print 1 "Modules will be loaded later in IGCM_sys_activ_variables."
else
  module purge > /dev/null 2>&1
  . $( ccc_home -u igcmg)/MachineEnvironment/irene_next/env_atlas_irene > /dev/null 2>&1

  export PCMDI_MP=/ccc/work/cont003/igcmg/igcmg/PCMDI-MP
  export UVCDAT_ANONYMOUS_LOG=FALSE
fi

Modification for v6.1 configurations and older ones

compilation

• Create a directory config/.../ARCH/ and create in it the file arch-X64_IRENE.env

  # Compile and running environnemnet at Irene Skylake 
    
  module purge
  module load intel/20.0.0
  module load mpi/openmpi/4.1.4
  module load flavor/hdf5/parallel
  module load hdf5/1.12.0
  module load netcdf-fortran/4.5.3
  module load mkl/20.0.0
  module load feature/bridge/heterogenous_mpmd
  module load c++/gnu/8.3.0
  module load c/gnu/8.3.0
  

• Modify AA_make to source this new environment file and indicate to XIOS which environment file it will use

  submitdir=$(shell pwd)
  arch_path=${submitdir}/ARCH/
  
  all :
          if [ -s ./.resol ] ; then $(M_K) `head -1 .resol |cut -c 8-` ; else $(M_K) LMD144142-L79 ; fi
  
  (...)
  
  xios :
        	(cd  ../../modeles/XIOS ; ./make_xios --prod --arch ${FCM_ARCH} --arch_path ${arch_path} --job 4 ; cp bin/xios_server.exe ../../bin/. ; )
  
  
  libioipsl : ../../modeles/IOIPSL/src
  	(. ${arch_path}/arch-X64_IRENE.env; cd ../../modeles/IOIPSL/src ; $(M_K) -f Makefile)
  
  

• create the Makefile as explain ​here
• clean everything on previous compilations :

gmake clean

• compile

Computation

• pour l'exécution il y aura un soucis avec libIGCM qui ne voudra pas lancer un exécutable réaliser avec une version V20 du compilateur. Pour palier cela :
  • récupérer une version récente de libIGCM
  • modifier libIGCM_sys comme indiqué dans le point ​CONFIG V6.2 (si rev inf la rev ​1579)
  • ajouter le paramètre EnvFile dans config.card

    EnvFile=${SUBMIT_DIR}/../ARCH/arch.env
    

• si la simulation a besoin de l'outil rebuild : on peut utiliser l'exécutable ccc_home -u igcmg/igcmg/igcmg/Tools/irene_next/rebuild/modipsl/bin (à indiquer dans le fichier .bashrc du compte)