= Namelist Integrity checks = Misplaced or mis-spelt variables in configuration namelist files can be a source of frustration when porting configurations used with older releases of NEMO to more modern versions. The code will report these occurrences and stop during start-up; but only one instance is reported each time. Finding them all this way can be a time-consuming business. Part 1 of this page details a simple Python script which can be used to find mis-matches between a configuration namelist and its reference counterpart before attempting to run the model. For most users, this should be sufficient but developers of new features have the added uncertainty of not knowing if the reference namelist correctly contains all the namelist options available in the code. Part 2 of this page suggests further tools which can can construct a 'pseudo reference namelist' by parsing the fortran code base. The actual reference namelist and the 'pseudo' version can then be used with the integrity checker from part 1. By using the integrity checker twice, with the roles of the two namelists swapped, it is possible to confirm that: * The actual reference namelist is compatible with the code base * The actual reference namelist contains examples of all the namelist variables defined in the code base. All the scripts mentioned are attached to this page. == Part 1 Integrity checker == If we assume the following conventions for NEMO namelists: * namelists are started with ''&name_of_namelist'' appearing as the first non-whitespace on a line (and not followed by anything other than an optional comment) * Only one variable is set on each line * namelists are closed with / appearing as the first non-whitespace on a line then the attached [[attachment:nemo_nml_check.py]] script will: * read supplied namelist files * construct lists of namelist blocks and their contents (the latter being a list of lists) * compare the contents lists for matching named blocks to confirm membership * report any mis-matches together with the line number in the configuration namelist * where possible, suggest close matches that may indicate typos By default, the script will compare ''namelist_cfg'' and ''namelist_ref'' from the current directory. Alternative pairs can be named using the ''-c'' and ''-r'' command-line options: {{{ python nemo_nml_check.py --help usage: nemo_nml_check.py [-h] [--cfg [CFGFILE]] [--ref [REFFILE]] Check for consistency between cfg namelists and ref versions e.g. python nemo_nml_check.py --cfg --ref optional arguments: -h, --help show this help message and exit --cfg [CFGFILE], -c [CFGFILE] configuration namelist --ref [REFFILE], -r [REFFILE] reference namelist --match [MFACTOR], -m [MFACTOR] closeness factor (0-1) }}} A typical example of an error found between the default pairing is: {{{ python nemo_nml_check.py No match in matching blocks for: | Possible close match: rn_rdt in namdom (at line no. 39) | rn_dt }}} and a quick check in the ''namelist_ref'' file will confirm that this is because ''rn_rdt'' has been renamed as ''rn_Dt''. == Part 2 Constructing a pseudo-reference namelist == Parsing the source code to extract information to build a pseudo reference namelist is simpler if we assume adherence to some coding conventions: * The namelist opening declaration: ''namelist / name_of_namelist /'' occurs on one line * The ''name_of_namelist'' string contains only alphanumeric characters and underscores * subsequent continuation lines have a leading ampersand and a trailing ampersand is placed on the preceding line (comments are allowed after the trailing ampersand) With these (seemingly safe) assumptions the attached Perl script: [[attachment:nemo_list_nmls.pl]] can be used to extract namelist templates from the source. For example: {{{ perl nemo_list_nmls.pl OCE/nemogcm.F90 &namctl ln_ctl = sn_cfctl = nn_print = nn_ictls = nn_ictle = nn_isplt = nn_jsplt = nn_jctls = nn_jctle = ln_timing = ln_diacfl = / &namcfg ln_read_cfg = cn_domcfg = ln_closea = ln_write_cfg = cn_domcfg_out = ln_use_jattr = / }}} Combined with a few lines of bash, this can be used to construct a pseudo-namelist_ref: {{{#!bash for f in `find ./OCE -name '*.[Fh]90'` do echo "! "$f >> pseudo_nml_ref perl nemo_list_nmls.pl $f >> pseudo_nml_ref done }}} ''(this does assume scanning OCE is sufficient; how about OFF, SAS etc.?)'' == Part 3 Checking reference namelist and source compatibility == The ''pseudo-namelist_ref'' produced this way should contain all the variables that can be set via namelists (at least for the 'blue ocean'). Treating the actual ''namelist_ref'' as a configuration namelist and checking its integrity against the pseudo version should confirm the validity of everything in the reference namelist. {{{ #!html

Update:There is at least one namelist declared in the code with multiple declarations, namely:

}}} {{{#!fortran NAMELIST/nambdy_dta/ cn_dir, bn_tem, bn_sal, bn_u3d, bn_v3d, bn_ssh, bn_u2d, bn_v2d NAMELIST/nambdy_dta/ bn_a_i, bn_h_i, bn_h_s, bn_t_i, bn_t_s, bn_tsu, bn_s_i, bn_aip, bn_hip NAMELIST/nambdy_dta/ rn_ice_tem, rn_ice_sal, rn_ice_age, rn_ice_apnd, rn_ice_hpnd NAMELIST/nambdy_dta/ ln_full_vel, ln_zinterp }}} The Perl script has been adapted to handle this but each entry will appear in the pseudo file as a separate block. These blocks should be combined by hand into a single block before running the integrity checks. Surprisingly a few variables are flagged even for a fresh copy of r4.0-HEAD (Rev: 13029): {{{ python nemo_nml_check.py -r pseudo_nml_ref -c namelist_ref -m 0.75 No match in matching blocks for: | Possible close match: sn_wnum in namsbc_wave (at line no. 497) | sn_wmp sn_tauwoc in namsbc_wave (at line no. 498) | sn_tauwx in namsbc_wave (at line no. 499) | sn_tauwy in namsbc_wave (at line no. 500) | clname(1) in nam_tide (at line no. 581) | clname tname(1) in nam_diaharm (at line no. 1188) | tname tname(2) in nam_diaharm (at line no. 1189) | tname sn_cfctl%l_config in namctl (at line no. 1322) | sn_cfctl%l_runstat in namctl (at line no. 1323) | sn_cfctl%l_trcstat in namctl (at line no. 1324) | sn_cfctl%l_oceout in namctl (at line no. 1325) | sn_cfctl%l_layout in namctl (at line no. 1326) | sn_cfctl%l_mppout in namctl (at line no. 1327) | sn_cfctl%l_mpptop in namctl (at line no. 1328) | sn_cfctl%procmin in namctl (at line no. 1329) | sn_cfctl%procmax in namctl (at line no. 1330) | sn_cfctl%procincr in namctl (at line no. 1331) | sn_cfctl%ptimincr in namctl (at line no. 1332) | }}} It is probably the case that the structure variables flagged (sn_*) are false positives. This is because only the structure name is declared in the namelist but individual members of the structure may be (and are) set in the ''namelist_ref''. Nonetheless, there are a few normal variables to investigate and this does illustrate the potential usefulness of this tool. Note, the 'possible close matches' are provided by a simple string comparator. By default, only matches exceeding a closeness factor of 0.75 are reported. More (or fewer) possibilities can be provided by decreasing (or increasing) this factor between 0 and 1. This is done by providing the additional command line argument '-m fatc' as shown here (although it was unnecessary since 0.75 is the default value). Secondly, reversing the roles of the input namelists allows a check on whether or not all the available namelist variables have a default setting in ''namelist_ref'': {{{ python nemo_nml_check.py -r namelist_ref -c pseudo_nml_ref No match in matching blocks for: | Possible close match: ln_rnf_icb in namsbc_rnf (at line no. 172) | sn_i_rnf in namsbc_rnf (at line no. 175) | sn_t_rnf clname in nam_tide (at line no. 198) | clname(1) ln_time_average_weight in namberg (at line no. 594) | tname in nam_diaharm (at line no. 826) | tname(2) sn_cfctl in namctl (at line no. 984) | ln_sto_ldf in namsto (at line no. 1100) | rn_ldf_std in namsto (at line no. 1101) | rn_ldf_tcor in namsto (at line no. 1102) | ln_sto_hpg in namsto (at line no. 1103) | rn_hpg_std in namsto (at line no. 1104) | rn_hpg_tcor in namsto (at line no. 1105) | ln_sto_pstar in namsto (at line no. 1106) | rn_pstar_std in namsto (at line no. 1107) | rn_pstar_tcor in namsto (at line no. 1108) | nn_pstar_flt in namsto (at line no. 1109) | nn_pstar_ord in namsto (at line no. 1110) | ln_sto_trd in namsto (at line no. 1111) | rn_trd_std in namsto (at line no. 1112) | rn_trd_tcor in namsto (at line no. 1113) | ln_sto_trc in namsto (at line no. 1122) | nn_sto_trc in namsto (at line no. 1123) | rn_trc_stdxy in namsto (at line no. 1124) | rn_trc_stdz in namsto (at line no. 1125) | rn_trc_tcor in namsto (at line no. 1126) | nn_trc_ord in namsto (at line no. 1127) | nn_trc_flt in namsto (at line no. 1128) | rn_trc_lim in namsto (at line no. 1129) | }}} The same caveats apply but there are a few issues warranting further investigation. Full marks for Clem though since repeating this process for ICE: {{{#!bash for f in `find ./ICE -name '*.[Fh]90'` do echo "! "$f >> pseudo_nml_ice_ref perl nemo_list_nmls.pl $f >> pseudo_nml_ice_ref done python nemo_nml_check.py -c ../cfgs/SHARED/namelist_ice_ref -r pseudo_nml_ice_ref python nemo_nml_check.py -r ../cfgs/SHARED/namelist_ice_ref -c pseudo_nml_ice_ref }}} finds no mismatches For TOP we have to be more selective about which directories to search when building the pseudo file: {{{#!bash for f in `find -f ./TOP ./TOP/TRP -name '*.[Fh]90' -depth 1` do echo "! "$f >> pseudo_nml_top_ref perl nemo_list_nmls.pl $f >> pseudo_nml_top_ref done }}} and the following potential issues are flagged: {{{ python nemo_nml_check.py -c ../cfgs/SHARED/namelist_top_ref -r pseudo_nml_top_ref No match in matching blocks for: | Possible close match: sn_trcdta(1) in namtrc_dta (at line no. 61) | sn_trcdta ln_trdmld_trc_restart in namtrc_trd (at line no. 124) | ln_trdmxl_trc_restart ln_trdmld_trc_instant in namtrc_trd (at line no. 125) | ln_trdmxl_trc_instant ln_trdtrc( 1) in namtrc_trd (at line no. 126) | ln_trdtrc ln_trdtrc( 2) in namtrc_trd (at line no. 127) | ln_trdtrc ln_trdtrc(23) in namtrc_trd (at line no. 128) | ln_trdtrc python nemo_nml_check.py -r ../cfgs/SHARED/namelist_top_ref -c pseudo_nml_top_ref No match in matching blocks for: | Possible close match: sn_trcobc in namtrc_bc (at line no. 4) | rn_trofac in namtrc_bc (at line no. 5) | sn_trcsbc in namtrc_bc (at line no. 7) | rn_trsfac in namtrc_bc (at line no. 8) | sn_trccbc in namtrc_bc (at line no. 10) | rn_trcfac in namtrc_bc (at line no. 11) | sn_tri_tracer in namtrc_ice (at line no. 25) | sn_tracer in namtrc (at line no. 48) | ln_trdmxl_trc_restart in namtrc_trd (at line no. 59) | ln_trdmld_trc_restart ln_trdmxl_trc_instant in namtrc_trd (at line no. 60) | ln_trdmld_trc_instant cn_trdrst_trc_in in namtrc_trd (at line no. 61) | cn_trdrst_trc_out in namtrc_trd (at line no. 62) | ln_trdtrc in namtrc_trd (at line no. 63) | nn_trd_trc sn_trcdta in namtrc_dta (at line no. 67) | sn_trcdta(1) rn_trfac in namtrc_dta (at line no. 69) | }}} and finally for PISCES: {{{#!bash for f in `find ./TOP/PISCES -name '*.[Fh]90'` do echo "! "$f >> pseudo_nml_pisces_ref perl nemo_list_nmls.pl $f >> pseudo_nml_pisces_ref done }}} {{{ python nemo_nml_check.py -c ../cfgs/SHARED/namelist_pisces_ref -r pseudo_nml_pisces_ref No match in matching blocks for: | Possible close match: mprat2 in namp5zmort (at line no. 199) | mpratd xpref2p in namp5zmes (at line no. 233) | xpref2d python nemo_nml_check.py -r ../cfgs/SHARED/namelist_pisces_ref -c pseudo_nml_pisces_ref No match in matching blocks for: | Possible close match: mpratd in namp5zmort (at line no. 357) | mprat2 xpref2n in namp5zmes (at line no. 398) | xpref2c }}}