wiki:DevelopmentActivities/Xios

Version 19 (modified by jgipsl, 10 years ago) (diff)

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Xios in ORCHIDEE

The interface for XIOS is implemented in ORCHIDEE/trunk rev ​rev 1788 for usage of ORCHIDEE offline.
This page is about the on going work with XIOS in ORCHIDEE. The work with XIOS is done directly in the trunk of ORCHIDEE. Here are some notes during implementation and testing phase. Note ! All tests for now have only been done with ORCHIDEE offline mode. The implementation in ORCHIDEE will need to change when adapting to run with LMDZ.

Validation

The implementation of XIOS interface in ORCHIDEE is uder validation work. See details here : Branches/Xios/Validation

How to install ORCHIDEE with XIOS for offline use : at CURIE

  • Extract 
    > svn co http://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl
> cd modipsl/util

Add extraction of XIOS by adding following line in mod.def : (XIOS revision 446, 455 and 471 have been tested successfully with ORCHIDEE, revision 452 and 472 do not work) :
#-C- ORCHIDEE_trunk  XIOS/trunk                               471     12 XIOS               modeles

> ./model ORCHIDEE_trunk
  • Adapt compiling with netcdf parallel. Since revision [1875] there is no need to modify makefiles or arch files. Only loading parallel netcf and hdf5 is needed. Before compiling do following: 
    module unload netcdf hdf5
module load netcdf/4.2_hdf5_parallel
module load hdf5/1.8.9_parallel
  • Compile using fcm 
    > cd ../config/ORCHIDEE_OL
> gmake with_xios
  • Lance
    • The executable can now be used with XIOS or with IOIPSL or with both at the same time.
      • Activate XIOS by adding XIOS_ORCHIDEE_OK=y
      • Deactivate IOIPSL by setting WRITE_STEP=0 and STOMATE_HIST_DT=0 in run.def
    • This executable must be used with netcdf and hdf5 parallel, add in the job just before exexcution following lines : 
      module unload netcdf hdf5
module load netcdf/4.2_hdf5_parallel
module load hdf5/1.8.9_parallel
    • The executable can be launched in
      • attached mode : this means that the server XIOS is not used. You only launches the orchidee_ol executable.
      • using the server xios : in this case, one or several cores are dedicated to the server and the reste to orchiee_ol.
  • Lance using libIGCM
    • xios files can not have suffix _xios if IOIPSL output is activated as standard. Instead change to use .xios
    • if using multiple_file, add min_digits="4" on the same line in iodef.xml. This can be kept even for one_file : 
      <file_definition type="one_file" par_access="collective" enabled=".TRUE." min_digits="4">
  • Rebuild
    • If using file_definition type="multiple_file" then rebuild must be done. Use this rebuild : /ccc/cont003/home/dsm/p86ipsl/rebuild/src_X64_CURIE/modipsl_v2_2_2_netcdf4.2/bin/rebuild. For exemple : 
      /ccc/cont003/home/dsm/p86ipsl/rebuild/src_X64_CURIE/modipsl_v2_2_2_netcdf4.2/bin/rebuild -o sechiba_history_xios.nc sechiba_history_xios_*
    • If using file_definition type="one_file" then no rebuild is needed.
  • Visulize netcdf output
    • ferret : compatible to all netcdf versions, IOIPSL and XIOS output
    • nco : all versions adapted for IOIPSL output. To vizualize XIOS output, you need to have loaded netcdf and hdf5 parallel.
    • cdo : all versions adapted for IOIPSL output. To vizualize XIOS output, you need to have loaded netcdf and hdf5 parallel and also a newer version of cdo.
    • Load following modules to use interactivly these tools : 
      module unload netcdf hdf5 cdo
module load netcdf/4.2_hdf5_parallel
module load hdf5/1.8.9_parallel
module load cdo/1.6.0

How to install LMDZ-ORCHIDEE with XIOS : at CURIE

  • Extract 
    > svn co http://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl
> cd modipsl/util
  • Add following lines in mod.def : 
    #-H- LMDZOR_v6  LMDZ and ORCHIDEE working version towards IPSLCM6
#-H- LMDZOR_v6  Configuration in developement and test phase
#-M- LMDZOR_v6  Josefine.Ghattas@ipsl.jussieu.fr
#-C- LMDZOR_v6  IOIPSL/tags/v2_2_2/src                HEAD               8  IOIPSL/src modeles
#-C- LMDZOR_v6  trunk/ORCHIDEE                        HEAD		 14 ORCHIDEE   modeles
#-C- LMDZOR_v6  LMDZ5/trunk                           1986               11 LMDZ       modeles
#-C- LMDZOR_v6  XIOS/trunk                            471                12 XIOS       modeles
#-C- LMDZOR_v6  CONFIG/UNIFORM/v6/LMDZOR_v6           HEAD               8  LMDZOR_v6  config
#-C- LMDZOR_v6  trunk/ORCHIDEE_OL                     HEAD		 14 ORCHIDEE_OL config
#-C- LMDZOR_v6  trunk/libIGCM                         990                10 libIGCM    .
  • Extract configuration LMDZOR_v6 
    > ./model LMDZOR_v6
  • Load as for orchidee offline : 
    module unload netcdf hdf5
module load netcdf/4.2_hdf5_parallel
module load hdf5/1.8.9_parallel
  • Compile as usuall 
    cd modipsl/config/LMDZOR_v6
gmake
  • Lance

Use all xml files found in modipsl/modeles/LMDZ/DefLists except iodef.xml.

Implementation

In the definition phase using IOIPSL, in the call to histdef, an operator is declared on the field. Using XIOS, some of these operators will be set in the xml file (which contains the definition phase) and some will be applied to the variables in the call to xios_orchidee_send_field.

operation in histdef terme in xios_orchidee_send_field operation in xml
flux_op one_day/dt(*) -
flux_scinsec 1/dt (**) -
ave - average
once - once
tmaxcels - maximum
tmincels - minimum
sumscatter - accumulate

(*) one_day/dt must be replaced by 48.0 to obtain excactly the same results in double precision between XIOS and IOIPSL output files, for instantaneous output frequency.
(**) 1/dt must be replaced by 0.0005555556 to obtain de same results between XIOS and IOIPSL output files, even in float precision, for instantaneous output frequency. This value is temporary commited in revision [1788] until revision [1877].