[[TOC(heading=Using libIGCM library with ORCA2_LIM nemo_v3_6, depth=2, libIGCM_nemo_v_3_6/config.card_description, libIGCM_nemo_v_3_6/list_of_possible_errors )]] = '''Using libIGCM library with ORCA2_LIM for nemo_v3_6''' = == Purposes == Through LibIGCM give an example of run of configuration ORCA1_LIM3_PISCES with : * Climatological and Interannual (years from 1948 to 2009) forcing files COREII * outputs: * ocean: 1D 5D 1M 1Y * ice: 1M * biology: 1D 1M 1Y * RESTARTS every year * on Idris ADA machine Official documentation of Libigcm is : https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc == Quick start guide :[https://forge.ipsl.jussieu.fr/nemo/browser/branches/2015/nemo_v3_6_STABLE/NEMOGCM http://www.nemo-ocean.eu/Using-NEMO/Configurations/] == * Create and go into working directory : {{{ cd $WORKDIR ; mkdir TP-NEMO-libIGCM ; cd TP-NEMO-libIGCM }}} * Define the following alias to use SVN : {{{ alias svn_ano='svn co http://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl' }}} * Extract modipsl (modipsl with LibIGCM) {{{ svn_ano }}} * Extract the model "NEMO_v6": {{{ cd modipsl/util ** ./model NEMO_v6 }}} ** verify NEMOGCM revision in ''' modipsl/util/mod.def ''' file: (fixed revision of NEMO: ''' 5618''' ) #-H- NEMO_v6 NEMOGCM for CMIP6 exercise [[BR]] #-H- NEMO_v6 LibIGCM tag libIGCM_v2.6[[BR]] #-M- NEMO_v6 Christian.Ethe@ipsl.jussieu.fr[[BR]] #-C- NEMO_v6 tags/libIGCM_v2.7 HEAD 10 LibIGCM . [[BR]] #-C- NEMO_v6 ''' branches/2015/nemo_v3_6_STABLE/NEMOGCM''' ''' 5618''' 7 . modeles[[BR]] #-C- NEMO_v6 trunk/ORCA1_LIM3_PISCES HEAD 17 . modeles/NEMOGCM/CONFIG[[BR]] #-C- NEMO_v6 CONFIG/UNIFORM/v6/NEMO_v6 HEAD 8 NEMO_v6 config (The OFFICIAL repository for the CONFIG '''ORCA1_LIM3_PISCES''' is the web site '''shaconemo''': https://forge.ipsl.jussieu.fr/shaconemo/wiki/README_ORCA1_LIM3_PISCES ) ''' NOTA BENE''' : ORA1_LIM3_PISCES configuration is by default (in LibIGCM) run with xios_server en detached mode --> so you need to download and compile xios: * Download XIOS ('''branch 1.0 revision 703''') (The documentation of xios is available here: http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation ) * Compile XIOS (on ADA machine): {{{ cd $WORKDIR svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-1.0 XIOS -r 703 cd XIOS }}} {{{ ./make_xios --avail ./make_xios --arch X64_ADA --full --prod --job 8 }}} * Compile ORCA1_LIM3_PISCES configuration (Using ./makenemo -h to see help ( to see list of compilers availables, to see options,...)) {{{ cd ../modeles/NEMOGCM/CONFIG ./makenemo -n ORCA1_LIM3_PISCES -m X64_ADA -j 8 -j8 compile with 8 proc for compilation phase -j0 option create only configuration directory but does not compile it }}} * Copy executable nemo.exe (and xios_server.exe if needed in detached mode) in modipsl : {{{ cd ../../../bin ln -s ../modeles/NEMOGCM/CONFIG/ORCA1_LIM3_PISCES/BLD/bin/nemo.exe nemo.exe (ln -s $WORKDIR/XIOS/bin/xios_server.exe xios_server.exe) }}} ''' NOTA: YOU CAN WANT TO USE MORE THAN ONE EXECUTABLE''' : so you can do, for example, {{{ ln -s ../modeles/NEMOGCM/CONFIG/ORCA1_LIM3_PISCES/BLD/bin/nemo.exe nemo_orca1_lim3_pisces.exe ln -s ../modeles/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/BLD/bin/nemo.exe nemo_orca2_lim3_pisces.exe ln -s ../modeles/NEMOGCM/CONFIG/ORCA2_LIM2_PISCES/BLD/bin/nemo.exe nemo_orca2_lim2_pisces.exe }}} JUST BECAREFUL to use ''' SAME''' executable ''' name''' in config.card * This is the structure of config in modipsl: {{{ modipsl/config/NEMO_v6/ GENERAL EXPERIMENTS/ ORCA1_LIM3_PISCES/ clim/ config.card COMP/ xios.card lim3.card pisces.card opa9.card ia/ config.card COMP/ xios.card lim3.card pisces.card opa9.card ORCA2_LIM2_PISCES/ clim/ config.card COMP/ lim2.card pisces.card opa9.card ORCA2_LIM3_PISCES/ clim/ config.card COMP/ lim3.card pisces.card opa9.card }}} * To create submission directory you have to copy config.card file in config/NEMO-v6 directory: {{{ cd modipsl/config/NEMO_v6 cp EXPERIMENTS/ORCA1_LIM3_PISCES/clim/config.card . }}} * Editing at this point '''modipsl/config/NEMO_v6/config.card''' (according to iodef.xml file) see detailed page for more informations: [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM_nemo_v_3_6/config.card_description page description of config.card] {{{ vi config.card # Modify AT LEAST JobName=eOR1L3P }}} * BE CAREFUL at this point: VERIFY in modipsl/config/NEMO_v6/GENERAL/PARAM/namelist_'''ORCA1'''''clim(ia)''_cfg that you domain decomposition is: * '''jpni = 17 ''' * ''' jpnij = 221''' * ''' jpnj = 13''' if not NEMO makes itself its decomposition like 221 * 1 and THIS DOES NOT WORK (your ocean.output will end with : "dta_tsd: deallocte T & S arrays as they are only use to initialize the run" WITHOUT ERROR MESSAGE * Create Job : (using ins_job in modsipl/lib IGCM directory) {{{ ../../libIGCM/ins_job  ls modipsl/config/NEMO_v6 GENERAL EXPERIMENTS eOR1L3P #new submission directory, config card is now HERE }}} * '''LOOK AT alla parameters of the Job you've created ''': By default is 1 hour ('''@ wall_clock_limit = 1:00:00'''), but for ORCA1-LIM3-PISCES is 1:45 for 1 year {{{ cd eOR1L3P vi Job_eOR1L3P # @ wall_clock_limit = 1:45:00 }}} * Submit Job : {{{ llsubmit Job_eOR1L3P }}} '''***** SPECIAL INFORMATIONS FOR RUN ORCA2-LIM3-PISCES *****''' ORCA2-LIM3-PISCES does not exists between reference configurations in v3_6_STABLE NEMOGCM/CONFIGURATION so you've to: * Create configuration ORCA2_LIM3_PISCES without compile it (with -j0): {{{ ./makenemo -n ORCA2_LIM3_PISCES -r ORCA2_LIM_PISCES -j0 }}} * Edit cfg.txt file by changing ORCA2_LIM3_PISCES definition : {{{ vi cfg.txt ORCA2_LIM3_PISCES OPA_SRC '''LIM_SRC_3''' NST_SRC TOP_SRC }}} * Clean the configuration ORCA2_LIM3_PISCES just created : {{{ ./makenemo -n ORCA2_LIM3_PISCES clean }}} * Change cpp keys: {{{ vi ORCA2_LIM3_PISCES/cpp_ORCA2_LIM3_PISCES.fcm bld::tool::fppkeys key_trabbl '''key_lim3''' key_dynspg_flt key_diaeiv key_ldfslp key_traldf_c2d key_traldf_eiv key_dynldf_c3d key_zdftke key_zdfddm key_zdftmx key_top key_pisces key_iomput key_mpp_mpi }}} * And finally compile the ORCA2_LIM3_PISCES configuration : {{{ ./makenemo -n ORCA2_LIM3_PISCES -j 8 -m X64_ADA }}} If you want to switch from climatological to interannual see [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM_nemo_v_3_6/config.card_description page description of config.card] Simona Flavoni last update: [[Timestamp]]