= Xios in ORCHIDEE = The interface for XIOS is implemented in ORCHIDEE/trunk rev [https://forge.ipsl.jussieu.fr/orchidee/changeset/1788 rev 1788] for usage of ORCHIDEE offline.[[BR]] 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 : [wiki: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 : {{{ }}} * 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.[[BR]] || operation in histdef || terme in xios_orchidee_send_field || operation in xml [[BR]] || flux_op || one_day/dt(*) || - [[BR]] || flux_scinsec || 1/dt (!**) || - [[BR]] || ave || - || average [[BR]] || once || - || once [[BR]] || tmaxcels || - || maximum [[BR]] || tmincels || - || minimum [[BR]] || sumscatter || - || accumulate [[BR]] (*) 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. [[BR]] (!**) 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]. [[BR]]