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 loaded 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 described ​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 version 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)
  
  

For older configurations you may have to source the arch.env file for all the models other than XIOS (applies to IPSLCM5A2 but could be needed for other old configurations).

In that case add . ${arch_path}/arch-X64_IRENE.env; before the command that changes the directory in every models rules except for xios where the previous changes are enough.

• IPSLCM5A2 AA_Make

  oasis3-mct:
      (. ${arch_path}/arch-X64_IRENE.env; cd $(OASIS_DIR)/util/make_dir ; cp $(MYSRC_DIR)/SOURCES/OASIS3-MCT/make_${FCM_ARCH} make.inc ; make -f TopMakefileOasis3 ; )
  
  liborchidee : ../../modeles/ORCHIDEE/
      (. ${arch_path}/arch-X64_IRENE.env; cd ../../modeles/ORCHIDEE/ ; ./makeorchidee_fcm -parallel mpi_omp -arch $(FCM_ARCH) -j 8 -xios2)
  
  ...
  
  lmdz: ../../modeles/LMDZ
      (. ${arch_path}/arch-X64_IRENE.env; cd ../../modeles/LMDZ; ./makelmdz_fcm -d $(RESOL_LMDZ) -arch $(FCM_ARCH) -j 8 ce0l ; cp bin/ce0l_$(RESOL_LMDZ)_phylmd_seq.e ../../bin/create_etat0_limit.e ; )
      (. ${arch_path}/arch-X64_IRENE.env; cd ../../modeles/LMDZ ; ./makelmdz_fcm -d $(RESOL_LMDZ) -mem -cosp false -v true -parallel mpi_omp -io xios -c OMCT -job 8 -arch $(FCM_ARCH) gcm  ; mv bin/gcm_$(RESOL_LMDZ)_phylmd_para_mem_orch_couple.e ../../bin/gcm.e ; )
  
  paleolmdz: ../../modeles/LMDZ
      (. ${arch_path}/arch-X64_IRENE.env; cd ../../modeles/LMDZ; ./makelmdz_fcm -d $(RESOL_LMDZ) -arch $(FCM_ARCH) -j 8 ce0l ; cp bin/ce0l_$(RESOL_LMDZ)_phylmd_seq.e ../../bin/create_etat0_limit.e ; )
      (. ${arch_path}/arch-X64_IRENE.env; cd ../../modeles/LMDZ ; ./makelmdz_fcm -d $(RESOL_LMDZ) -mem -cosp false -v true -parallel mpi_omp -io xios -c OMCT -job 8 -arch $(FCM_ARCH) gcm  ; mv bin/gcm_$(RESOL_LMDZ)_phylmd_para_mem_orch_couple.e ../../bin/gcm.e ; )
  
  ...
  
  orca2lim2:  ../../modeles/NEMOGCM/CONFIG
      (. ${arch_path}/arch-X64_IRENE.env; cd ../../modeles/NEMOGCM/CONFIG; cp ../../../config/IPSLCM5A2/SOURCES/NEMO/arch-${FCM_ARCH}.fcm ../ARCH/. ; cp ../../../config/IPSLCM5A2/SOURCES/NEMO/*.cfg ../TOOLS/COMPILE/. ; ./makenemo -m ${FCM_ARCH} -n ORCA2_LIM_PISCES -e "$(MYSRC_DIR)/SOURCES/NEMO/STANDARD" -j16 add_key "key_lim2_vp key_oasis3 key_diahth key_diaar5 key_xios2" del_key "key_nosignedzero " ; cp ORCA2_LIM_PISCES/BLD/bin/nemo.exe ../../../bin/opa ; )
  
  paleorca2lim2:  ../../modeles/NEMOGCM/CONFIG
      (. ${arch_path}/arch-X64_IRENE.env; cd ../../modeles/NEMOGCM/CONFIG; cp ../../../config/IPSLCM5A2/SOURCES/NEMO/arch-${FCM_ARCH}.fcm ../ARCH/. ; cp ../../../config/IPSLCM5A2/SOURCES/NEMO/PALEO/*.cfg ../TOOLS/COMPILE/. ; ./makenemo -m ${FCM_ARCH} -n ORCA2_LIM_PISCES -e "$(MYSRC_DIR)/SOURCES/NEMO/PALEO" -j16 add_key "key_lim2_vp key_oasis3 key_diahth key_diaar5 key_xios2" del_key "key_nosignedzero " ; cp ORCA2_LIM_PISCES/BLD/bin/nemo.exe ../../../bin/opa ; )
  

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

gmake clean

• compile

Computation

• Extract a new version of libIGCM

  svn co -r 1579 https://forge.ipsl.jussieu.fr/libigcm/svn/trunk/libIGCM libIGCM
  

• Modify config.card file section [UserChoices] to add environment file parameter:

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

• You may have to change the test of compiler version from V17 to V20 in libIGCM/libIGCM_sys/libIGCM_sys_irene.ksh to let the code execute:

  if [ X${compilerVersion} = XV20 ]; then
  IGCM_debug_Print 1 "IGCM_sys_active_variables : Using compiler version ${compilerVersion}"                                                                
  ## EnvFile=/ccc/cont003/home/igcmg/igcmg/MachineEnvironment/irene/env_irene > /dev/null 2>&1
  EnvFile=$( ccc_home -u igcmg)/MachineEnvironment/irene/env_irene > /dev/null 2>&1
  else
  IGCM_debug_Exit "This compiler version is not yet supported : ${compilerVersion}"
  fi