[[TOC(heading=Using libIGCM library to run 50 years of ORCA2_LIM3_PISCES nemo_v4_0_alpha, depth=2, libIGCM_nemo_v_4_0_alpha/config.card_description)]] = '''Using libIGCM library with ORCA2_LIM3_PISCES with nemo_v3_4_0_alpha (= dev_merge_2016; revision 7554)''' = == Purposes == Through LibIGCM give an example of 50 years run of ORCA2_LIM3_PISCES configuration, 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 test_O2L3PIS_50years_merge2016 ; cd test_O2L3PIS_50years_merge2016 }}} * 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 }}} * Change mod.def: the model "NEMO_v5": {{{ cd modipsl/util vi mod.def }}} edit mod.def file at ''NEMO_v5'' configuration: change the original with these lines: {{{ #---- NEMO configurations #-H- NEMO_v5 NEMOGCM in forced mode dev_merge_2016 Compilation using FCM #-H- NEMO_v5 libIGCM tag libIGCM_v2.8.2 #-M- NEMO_v5 simona.flavoni@locean.upmc.fr #-C- NEMO_v5 tags/libIGCM_v2.8.2 HEAD 10 libIGCM . #-C- NEMO_v5 branches/2016/dev_merge_2016/NEMOGCM HEAD 7 . modeles #-C- NEMO_v5 CONFIG/UNIFORM/v6/NEMO_v6 HEAD 8 NEMO_v6 config }}} * Extract the model "NEMO_v5": {{{ cd modipsl/util ./model NEMO_v5 }}} * To compile and run NEMO is needed 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 ORCA2_LIM3_PISCES configuration (Using ./makenemo -h to see help ( to see list of compilers availables, to see options,...)) {{{ cd ../modeles/NEMOGCM/CONFIG ./makenemo -n ORCA2_LIM3_PISCES -m X64_ADA -j8 -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/ORCA2_LIM3_PISCES/BLD/bin/nemo.exe nemo.exe (ln -s $WORKDIR/XIOS/bin/xios_server.exe xios_server.exe) }}} ''' NOTA: YOU CAN WANT TO USE MORE THAN ONE EXECUTABLE''' : so you can do, for example, {{{ ln -s ../modeles/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/BLD/bin/nemo.exe nemo_orca2_lim3_pisces.exe ln -s ../modeles/NEMOGCM/CONFIG/ORCA2_LIM2_PISCES/BLD/bin/nemo.exe nemo_orca2_lim2_pisces.exe }}} JUST BECAREFUL to use ''' SAME''' executable ''' name''' in config.card * This is the structure of config in modipsl: {{{ modipsl/config/NEMO_v6/ GENERAL EXPERIMENTS/ ORCA2_LIM3_PISCES/ clim/ config.card COMP/ lim3.card pisces.card opa9.card }}} * To create submission directory you have to copy config.card file in config/NEMO-v6 directory: {{{ cd ../config/NEMO_v6 cp EXPERIMENTS/ORCA2_LIM3_PISCES/clim/config.card . }}} * Editing at this point '''modipsl/config/NEMO_v6/config.card''' (according to iodef.xml file) see detailed page for more informations: [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM_nemo_v_3_6/config.card_description page description of config.card] '''IMPORTANT NOTE''' : in config.card BE CAREFUL TO THESE LINES: [[BR]] Parameters Files in '''opa.card''' List= [[BR]] || (${MODIPSL}/modeles/NEMOGCM/CONFIG/SHARED/namelist_ref, || namelist_ref ), \ || || (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_${RESOL_OCE}${EXPTYPE}_cfg, || namelist_cfg ), \ || || (${SUBMIT_DIR}/PARAM/v4_0_alpha/iodef.xml, || iodef.xml ), \ || || (${SUBMIT_DIR}/PARAM/v4_0_alpha/domain_def.xml, || domain_def.xml), \ || || (${SUBMIT_DIR}/PARAM/v4_0_alpha/field_def.xml, || field_def.xml ) || in '''lim3.card''' || (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_lim3_ref, || namelist_ice_ref), \ || || (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_lim3_cfg, || namelist_ice_cfg) || in '''pisces.card''' || (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_top_ref, || namelist_top_ref), \ || || (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_top_${RESOL_OCE}_cfg, || namelist_top_cfg), \ || || (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_pisces_ref, || namelist_pisces_ref), \ || || (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_pisces_${RESOL_OCE}_cfg, || namelist_pisces_cfg) || here you're coping iodef.xml,field_def.xml and domain_def.xml for '''XIOS1''' {{{ vi config.card # Modify AT LEAST JobName=eOR2L3P }}} * Create Job : (using ins_job in modsipl/lib IGCM directory) {{{ ../../libIGCM/ins_job ls modipsl/config/NEMO_v6 GENERAL EXPERIMENTS eOR2L3P #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 ORCA2-LIM3-PISCES is about '''???? 1:45''' on 32 cpus for 1 year {{{ cd eOR2L3P vi Job_eOR2L3P # @ wall_clock_limit = 2:00:00 }}} * Submit Job : {{{ llsubmit Job_eOR2L3P }}} 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]]