PIANO Reference Manual Python Interface for Assimilation in NemO
Contents
1. Parallel run tdir output directories path exe_dir nemofcm_build dir time_dir path to forcing files common_dir path to common files obs_dir path to observation files restart_file path to restart nc file optional bkgnorm_file path to background normalization nc optional optional run_solo run only one executable nemo nemovar nemotam nemohlt optional ndone Start assim cycle from a previous one with nemohlt skip outer run 1 trj_dir path to tam_trajectories optional optional restart_hlt path to restart2 nc file with nemohlt if In_incdx false increments_hlt path to increments file optional with nemohlt if In_incdx true profile_fdbk_file path to profile fbdk file P tional with run_solo nemovar sla_fdbk_file path to sla fbdk file optional with run_solo nemovar optional nvarex_list nvarex list 0 0 1 1 for instance TABLE 1 Available options in descr file Part 1 2 12 Name Description Remark Value optional with nemotam if In_tst_tan true Um Tact isrin pu por optional with nemotam if In_tst_tan true n tlm_start is po in pn por optional with nemotam if In_tst_tan true tlm_loop isnin pn por TABLE 2 Available options in descr file Part 2 2 132. directories called exp and config gt ls block py Python class defining one namelist block blocklist py Python class defining the whole namelist char_handling py Extract strings from a files comments py Python class defining a comment in the namelist config Directory containing the available NEMO configuration descrlist py Python class defining the description file exp Directory containing the user experiments init_run py Method for initialization of PIANO piano py Main param py Python class defining a parameter name value comment lt ps_handling py run_main py hlt_handling py npz2plot tlmdiagmrg py z thods that manage the run of one executable thod to compute RMS coeff corr of lin tgt hyp test thod to convert hlt_handling output to plot thod to merge outputs files from tangent tests zZ g e a y anages processes e e G lt Details on the python code architecture are given in section 77 The directory config contains the following configurations 2 gt ls config GYRE_231 ORCA2_231 POMME_246 SQB_211 Each directory contains two default namelists gt ls GYRE_2Z31 namelist_nemo namelist_nemovar In the following we make a distinction between the namelist the file that contains all the definition of all the parameters needed by a run and a namelist block a section of namelist defined by its name amp n
3. you want to perform 4 outer loops in your assimilation process using 3DFGAT method for the first and the second set of inner loops and then 4DVAR for the thrids and the fourth sets your descr may contain the following lines nvarex_list 0 0 1 1 4 Installation New Configuration 4 1 Input files The management of input files for NEMO NEMOVAR depends on the name list and on convention name defined in the code There are several kind of input files Observation files their name can either be defined by default in case of feed back files for profiles or sla observations or be present as arguments in the namelist block namobs Forcing files surface boundary condition ice cover defined in the namelists namsbc_xxx Their names are defined in the corresponding namelist block when the flag in nam_sbc is activated These kind of files are thus automa tically treated in PIANO Data files for instance the file slaReferences nc needed when there is some SLA observation Files that are not SBC files or that are about specific data need a specific treatment in PIANO Examples are available for ORCA2 5 Available options in descr file Tables and 2 give a list of available options for the descr file R f rences 11 Name Description Remark Value grid configuration name compile compiler name npx x axis subdomain No Parallel run npy y axis subdomain No
4. PIANO Reference Manual Python Interface for Assimilation in NemO Claire CHAUVIN 3 d cembre 2010 Table des mati res 1 First steps with PIANO 1 1 Description of the directory piano L2 Running piao eso asa ee ae he he eA SRY ewes 1 2 1 Running piano general features 1 2 2 Running piano for Tangent Linear Hypothesis HLT test 1 2 3 Running piano for tangent test 2 Managing the input files 2A Forcing bles ame dir gt lt e ee ee RO ee OR RR RS 2 2 Datafiles common_dir e e ee eee 2 3 Observation files obs_dir 0 0 002 000 ee eee Specific features 3 1 NEMOVAR tests 2 2 00 eee eee 3 2 Change Assimilation method between outer loops nvarex_list Installation New Configuration 4 PIES tk ks eg Doe es ag Se es e oe Ge eRe we RS Available options in descr file 10 10 10 11 11 11 1 First steps with PIANO PIANO intends to provide a user friendly interface to a full run of assimilation For the moment PIANO is only about one full cycle of variationnal assimilation Its aims is to manage runs and communications between the model NEMO and the Incremental minimization of the cost function available in NEMOVAR 1 1 Description of the directory piano The software PIANO is available in the VODA development repository in directory UTIL gt cd VODA UTIL python piano This directory contains all the python sources files py and two
5. T test is activated if run_solo is defined as nemohit For instance gt cat exp GYRE HLT descr compile mac_g95 tdir MY_PATH exe _dir MY_EXE PATH npx 1 npy 1 grid GYRE_2Z31 run_solo nemohlt nittrjfrg_hlt 75 increments_hlt MY_INCREMENT_PATH restart_file MY_RESTART_PATH restart_hlt MY_2ND_RESTART_PATH ndone 1 time_dir MY_TIME_PATH common_dir MY_COMMON_PATH The increments 6x is read from an increments file increments_hit or computed from two restart files restart_file and restart_hlt The choice is done through the namelist parameter n_incdx from namhilt namelist block The response time frequency for HLT is controlled with nittrjfrq_hlt Note it will orverwrite nittrjfrq when computing M x 6x and nittrjfrq_tan when computing L 6x If ndone is equal to 1 the driver assumes that M x is already available in outer 7 directory At the end of the process a python compressed file h t_output npz is saved in outer_tam directory For graphical analysis you may use the standalone python routine hlt_npz2plot py python library matplotlib is required It saves a png file hlt_output png in outer_tam 1 2 3 Running piano for tangent test The tangent test refers to the analysis of the tangent behaviour with respect to the direct module when the perturbation evolves as p 6X If p has a geometric progression PIANO is able to perfom the loops on n and concatenate the final results into a s
6. am_block Recall that a NEMO run needs a namelist called namelist in the outer directory and NEMOVAR asks for the namelist namelist nemovar in the inner directory These two namelists contain an exhaustive list of all the existing namelist blocks needed by a run of NEMO or NEMOTAM NEMOVAR The directory exp contains examples of user experiments gt ls exp GYRE ENACT GYRE SGL ORCA2 POMME An experiment is described by three files gt ls GYRE ENACT descr namelist_nemo namelist_nemovar The description file descr contains all the parameters needed by a run that are not in the namelists gt cat exp GYRE ENACT descr Description file for the Experiment T ndays 6 to compute nitend and nwrite grid GYRE_2Z31 Configuration compile mac_intel Compiler npx 1 Parallel run npy 1 not implemented tdir tmp Contains output directories exe_dir tmp Contains nemofcm_build dir time_dir path_to_forcing_dir For forcing files common_dir path_to_common_dir For data files obs_dir path_to_obs_dir Observation files restart_file path_to restart nc If In_rstart okgnorm_file path_to background normalization nc run_solo nemovar Run only one executable ndone 1 Start assim cycle from a previous one trj_dir path_to tam trajectories When only nemovar run This example contains an exhaustive list of all the arguments defined in file descr Some are not implemented yet para
7. ingle file tan_diag global_0000 To do so the user must provide the element to compute py por the initial value po tlm_start the common ratio r tm_fact the number of loops on n tlm_loop The tangent test is activated if run_solo is defined as nemotam and In_tst_tan is set to true plus n_tst_tan_cpd for instance in namtst block namelist For instance gt cat exp GYRE XXX descr compile mac_g95 tdir MY_PATH exe_dir MY_EXE_PATH npx 1 npy 1 grid GYRE_2Z31 run_solo nemotam restart_file MY_RESTART PATH time_dir MY_TIME_PATH common_dir MY_COMMON_PATH tlm_fact 0 1 tlm start 1 tlm loop 1 2 Managing the input files 2 1 Forcing files time_dir The Forcing files are usually time dependent data They will be linked or copy to the outer and inner directories and if needed test directories The directory is identified in the descr file under the name time_dir The forcing files surface boundary conditions ice cover fluxes surface wind are defined in the NEMO namelist namelists namsbc_xxx activated by the logical 1n_xxx in namelist block namsbc Once the time_dir is specified in descr the loading of all the files activated in these namelist blocks should be transparent Note that for the moment only the forcing files for ORCA2 has been implemented the use of other files by then other parts of the namelist has not been tested Since information on files is given in the namel
8. ist note that it is possible to load different forcing files for NEMO and NEMOVAR 2 2 Data files common dir We call Data files files related to the configuration and general forcing file The are usualyy used for realistic configuration such as ORCA2 and their file names are hardcoded into NEMO The directory is identified in the descr file under the name common_dir For the moment they are automatically loaded for the ORCA2 grid by mean of the method init_real in module init_run py def init_orca descrlist common_files grid descrlist get_value grid if grid ORCA2_Z31 forcing_files append data_lm_potential_temperature_nomask nc forcing_files append data_lm_salinity_nomask nc forcing_files append dist coast nc forcing_files append bathy_level nc forcing_files append bathy_meter n G C forcing_files append ahmcoef forcing_files append coordinates nc forcing_files append ssh nc forcing_files append geothermal_heating nc forcing_files append slaReference nc 9 Note 1 treatment of slaReference nc does not rely on a specific configura tion Note 2 For the moment piano works only for one cycle of assimilation no specific treatment is done with respect to the date management and so the storage is done in a very simple way This question will be addressed when the implementation of several cycles of assimilation is done 2 3 Observati
9. llel architecture not managed The following parameters of final namelist are computed from ndays nitend nstock nwrite nstockfl nwritfl and nitiaufin Parameter grid stands for the configuration name piano loads the namelists de fined in config grid Four directories have to be declared in the description file namely tdir exe_dir obs_dir and forcing_dir If needed the name of the restart file and the background normalization file can be provided The two last parameters can be usefull to if the user wants to run only one exe cutable the parameter run_solo has to be specified Also it is possible to ask for piano to start the assimilation cycle from a previous one stopped at iteration ndone Files namelist_nemo and namelist_nemovar contains a subset of the full namelist of aNEMO NEMOVAR NEMOTAM tun Indeed they contain only the modifications made by the user to the default namelists located in config grid 4 For instance gt cat exp GYRE ENACT namelist_nemo nam_asminc In_bkgwri true nitbkg 0 nitdin 0 namtam In_trjwri true amp namobs In_t3d true In_s3d true In_profb true profbfiles profb_01_fdbk_0000 nc piano merges namelist_nemo files loaded from exp GYRE ENACT and config GYRE_Z31 and generates the namelist file that will be used for the NEMO run In this example the experiment asks for NEMO to assimilate an increment from a NE MOVAR run 1n_bkgwri t
10. o generate the new trajectory 1n_trjwri and to write the model equivalent of T and S profile observations parameters set to true in amp namobs and name of the observation file gt cat exp GYRE ENACT namelist_nemovar amp namobs In_prf true In_t3d true In_s3d true namalg noutmax 8 noutit 1 nvarex 1 Here the experiment parameters specify the kind of assimilated observations the number of outer loop of the current loop noutit that can eventually be updated by ndone the kind of assimilation 4D var in this case since nvarex 1 Files namelist_nemo and namelist_nemovar in the exp directory can be empty in this case the namelist used by the run is the one defined in the asso 5 ciated configuration directory for instance GYRE_Z31 in the case of GYRE ENACT experiment 1 2 Running piano 1 2 1 Running piano general features In directory piano run the command gt python piano py exp_name where exp_name is the name of an experiment Depending on your experiment several directories are created in tdir If a full assimilation cycle is asked then an outer and an inner directory are created namely gt cd tdir inner _GYRE ENACT_mac_intel_1x1l outer _GYRE ENACT_mac_intel_1xl outer_tam_GYRE ENACT_ mac_intel_1xl If tangent and adjoint model tests are done parameters ln_tst ln_tst_tam true in namelist_nemovar for instance then the output is located in the outer_tam directory El
11. on files obs_dir It is possible to load observation files of different format as specified in the namelist amp namobs but the communication between NEMO and NEMOVAR is done only with feedback files Note that observations such as sla needs an additional set of data that can be called slaReference nc to work 3 Specific features 3 1 NEMOVAR tests By default feedback files needed by nemovar inner loop is the output of a direct simulation outer loop In a inner loop test context it is possible to specify profiles and or sla feedback files key word profile_fdbk_file and sla_fdbk_file respectively when the key word nemovar is used for run_solo experiment Then your descr may contain the following lines run_solo nemovar profile _fdbk_file SMY_PATH_TO_PROF_FB FILE nc sla_fdbk_file SMY PATH TO SLA FB FILE nc 3 2 Change Assimilation method between outer loops nvarex_list For testing purpose we offer the possibility to change the nvarex value means 3DFGAT or 4DVAR assimilation method for nvar equals 0 or 1 respectively It can be done adding the parameter nvarex_list and the corresponding list in your descr file Parameter nvarex is a list a maximum noutmax maximum number of outer 10 loops elements Each element is separated by a comma If the number ele ments is less than noutmax nvarex is set to the default value specified in name list_nemovar or by default in the default configuration Then if
12. se if run_solo nemo resp nemovar only the outer resp inner directory is created and modified If a full assimilation cycle is done run_solo deactivated then both inner and outer directories are created or overwritten A run is described by two parameters of description file ndone and run_solo e run_solo nemo If ndone not defined in descr or ndone 1 Delete outer directory Outer loop counter nout it ndone e run_solo nemotam Delete outer_tam directory Executable model_tam exe is used to run tests on tangent and adjoint model of NEMO check that lo gical for such tests are activated in namelist namt st ln_tst true and at least one of the following flags has to be set to true In_tst_cpd_tam In_tst_stp_tam ln Lat Lan e run_solo nemovar If ndone not defined in descr or ndone 1 Delete inner directory Outer loop counter noutit ndone 6 e run_solo full_assim default if ndone not defined clean all directo ries Else set noutit ndone In the three last cases the NEMOVAR namelist is initialized For nemovar or full_assim check that nvarex 1 if you want a 4D Var assimilation 1 2 2 Running piano for Tangent Linear Hypothesis HLT test HLT stands for Tangent Linear Hypothesis test The user needs first t define its experiments through namelist_nemo and name list_nemovar and descr in the experiment see NEMOTAM User s Manual Refe rence More particularly blocks namhit and tl_tamtrj The HL
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