.. _appendices: *************** Appendices *************** ====================== The configure utility ====================== .. _arguments-to-configure: ---------------------------------------------- Arguments to configure ---------------------------------------------- All configuration options can be specified using command line arguments to CAM's ``configure`` script (a Perl script). Options not specified on the command line will be set to default values which are either hard-coded, or come from the definition file ``components/cam/bld/config_files/definition.xml``. Those that depend on the values of other options are set by logic contained in ``configure``. The user is able to pass arguments to CAM's configure by issuing an ``xlmchange`` command for **CAM_CONFIG_OPTS**. It is important to use the ``--append`` option if a compset's settings are to be maintained. The options may all be specified with either one or two leading dashes, e.g., ``-help`` or ``--help``. A consequence of allowing long names with single leading dashes is that the few options that can be expressed as single letter switches may **not** be bundled, e.g., ``-h -s -v`` may NOT be expressed as ``-hsv``. User supplied values are denoted in angle brackets "<>". Any value that contains white-space must be quoted. For options that can be set from small set of legal values, those values are given as a vertical bar separated list. The arguments to ``configure`` are: :: -[no]age_of_air_trcs Switch on [off] age of air tracers. Default: on for waccm_phys, otherwise off. -analytic_ic Enables the (namelist controlled) dycore testing infrastructure. -aquaplanet Switch on aqua-planet mode. -build_chem_proc Switch forces the build of the chemistry preprocessor (primarily for testing). -cache Name of output cache file which contains all configuration parameters set by configure script. Default: config_cache.xml -cachedir Name of directory where output cache file is written. Default: current working directory -camiop Configure CAM to generate an IOP file that can be used to drive SCAM. This switch only works with the Eulerian dycore. -carma Build CAM with specified CARMA microphysics model [ none (disabled) | bc_strat (Stratospheric Black Carbon) | cirrus (Cirrus Clouds) | cirrus_dust (Cirrus Clouds with dust) | dust (Dust) | meteor_impact (Meteor Impact) | meteor_smoke (Meteor Smoke) | mixed_sulfate (Meteor Smoke and Sulfate) | pmc (Polar Mesospheric Clouds) | pmc_sulfate (PMC and Sulfate) | sea_salt (Sea Salt) | sulfate (Sulfate Aerosols) | tholin (early earth haze) | test_detrain (Detrainment) | test_growth (Particle Growth) | test_passive (Passive Dust) | test_radiative (Radiatively Active Dust) | test_swelling (Sea Salt) | test_tracers (Asian Monsoon) | test_tracers2 (Guam)]. Default: none. -chem Build CAM with specified prognostic chemistry package [ trop_mam3 | trop_mam4 | trop_mam7 | trop_mozart | trop_strat_mam4_vbs | trop_bam | trop_ghg | waccm_ma | waccm_mad_mam4 | waccm_ma_mam4 | waccm_ma_sulfur | waccm_sc | waccm_sc_mam4 | waccm_tsmlt | waccm_tsmlt_mam4 | waccm_tsmlt_sulfur | super_fast_llnl | super_fast_llnl_mam3 | terminator | none ]. Default: trop_mam4 for cam6, trop_mam3 for cam5, otherwise none. -[no]clubb_sgs Switch on [off] CLUBB_SGS. Default: on for cam6, otherwise off. -clubb_opts Comma separated list of CLUBB options to turn on. [clubb_do_adv (Advect CLUBB moments)] -co2_cycle Switch to turn on the carbon cycle code (adds 4 advected constituents) -cosp Enable the COSP simulator. -dyn Dynamical core option. [eul (Eulerian) | fv (Finite Volume)]. -edit_chem_mech Invokes CAMCHEM_EDITOR to allow the user to edit the chemistry mechanism file. -help [or -h] Print usage to STDOUT. -hgrid Specify horizontal grid. For spectral grids use nlatxnlon where nlat and nlon are the number of latitude and longitude grid points respectively in the global Gaussian grid (e.g., T42 is specified 64x128). For FV grids use dlatxdlon where dlat and dlon are the grid cell size in degrees for latitude and longitude respectively (e.g., 1.9x2.5). -ionosphere Ionophere module used in WACCMX [ none | wxi | wxie ]. Default: none -macrophys Override the default macrophysics set by the physics package [rk | park | clubb_sgs | spcam_sam1mom | spcam_m2005] Defaults: clubb_sgs if cam6 park if cam6 and noclubb_sgs, or cam5 rk if cam3 or cam4 -max_n_rad_cnst Maximum number of constituents that are either radiatively active, or in any single diagnostic list for the radiation. Default: 30 -microphys Override the microphysics set by the physics package [mg1 | mg2 | rk | spcam_m2005 | spcam_sam1mom]. Defaults: mg2 if cam6 mg1 if cam5 rk if cam3 or cam4 -nadv Override the total number of advected species set by the physics and chemistry packages. -nadv_tt Set number of advected test tracers. Default: 0 -nlev Override the number of levels set by the physics or chemistry package. Default: 32 if cam6 30 if cam5, simple physics, or spcam_m2005 26 if cam3, cam4, or spcam_sam1mom 66 if waccm and cam4 70 if waccm and cam5 or cam6 81 if waccmx 126 if waccmx and ionosphere is wxie -offline_drv Specify offline unit driver. [rad (PORT)] -offline_dyn Enable offline driver for FV dycore. -ocn Allows build system to inform CAM which ocean component is being used. This information is stored in the cache file and used by build-namelist for selecting the default values of some tuning parameters. [docn | som | socn | aquaplanet | pop]. -pbl Override the PBL scheme set by the physics package. [clubb_sys | uw | hb | spcam_sam1mom | spcam_m2005]. Default PBL schemes: clubb_sgs if cam6 uw if cam5 hb if cam3 or cam4 spacm_m2005 if the physics package is spcam_m2005 spacm_sam1mom if the physics package is spcam_sam1mom -pcols Maximum number of columns in a chunk. Default: 16, or if SCAM mode then 1. -pergro Switch enables building CAM for perturbation growth tests. Only valid with cam3 or cam4 physics. -phys Physics option. [cam3 | cam4 | cam5 | cam6 | held_suarez | adiabatic | kessler | spcam_sam1mom | spcam_m2005]. Default: cam6, or if waccmx then cam4. -prog_species Comma-separate list of prognostic mozart species packages. Currently available: DST,SSLT,SO4,GHG,OC,BC,CARBON16 -psubcols Maximum number of sub-columns in a grid column. Default: 1 -rad Override the radiation scheme set by the physics package. [rrtmg | camrt]. Default radiation scheme: rrtmg if cam5, cam6, or spcam_m2005 camrt if cam3, cam4, or spcam_sam1mom -scam Compiles model in single column (SCAM) mode. Only works with Eulerian dycore. -silent [or -s] Turns on silent mode - only fatal messages issued. -[no]smp Switch on [off] SMP parallelism (OpenMP) -spcam_clubb_sgs Turn on the SPCAM version of CLUBB -spcam_nx SPCAM x-grid. (note the CRM requires spcam_nx to be greater than or equal to 4) Default: 4 -spcam_ny SPCAM y-grid. Default: 1 -spcam_dx SPCAM horizontal grid spacing. -spcam_dt SPCAM timestep in seconds. -[no]spmd Switch on [off] SPMD parallelism (MPI). -unicon Switch to turn on the UNICON scheme. -usr_mech_infile Absolute pathname of the user supplied chemistry mechanism file. -usr_src [,[,[...]]] Directories containing user source code. Note that these directories will also be searched for modified versions of the files needed by the build-namelist script, e.g., the namelist definition, defaults, and use case files. -verbose [or -v] Turn on verbose echoing of settings made by configure. -version Echo the tag name of the CAM component. -waccm_phys Switch enables the use of WACCM physics in any chemistry configuration. Default: off unless one of the waccm chemistry options is chosen. -waccmx Build CAM/WACCM with WACCM upper Thermosphere/Ionosphere extended package. -zmconv_org Enable sub-grid scale convective organization for the ZM deep convective scheme based on Mapes and Neale (2011) =========================== The build-namelist utility =========================== The ``build-namelist`` utility produces namelists for the CAM component (in the file ``atm_in``), and namelists for the control of dry deposition which is shared by CAM and CLM (in the file ``drv_flds_in``). The task of constructing a correct namelist is extremely complex due to the large number of configurations supported by CAM. Editing namelists by hand is a fragile process due to the number of variables that need to be set, and to the many interdependencies among them. **We strongly discourage editing namelists by hand.** All customizations of the CAM namelist are possible by making use of the ``build-namelist`` command line options. The most common way to do this is by adding customized variables to the ``user_nl_cam`` file which is then processed by ``build-namelist`` via the ``-infile`` option. Some of the important features of ``build-namelist`` are: * All valid namelist variables are known to ``build-namelist``. So an invalid variable specified by the user (supplied either by the ``-infile`` or ``-namelist`` options) will cause ``build-namelist`` to fail with an error message telling which namelist variable is invalid. This is a big improvement over a runtime failure caused by an invalid variable which typically gives no hint as to which variable caused the problem. * In addition to knowing all valid variable names and their types, ``build-namelist`` also knows which namelist group each variable belongs to. This means that the user only needs to specify variable names to ``build-namelist`` and not the group names. The ``-infile`` and ``-namelist`` options still require valid namelist syntax as input, but the group name is ignored. So all variables can be put in a single group with an arbitrary name, for example, "&xxx ... /" where "xxx" is the namelist group name. * Since ``build-namelist`` knows all namelist variables specified by the user it is able to do consistency checking. In general however, ``build-namelist`` assumes that the user is the expert and will not override a user specification unless there is a major inconsistency, for example if variables have been set to use parameterizations which can not be run at the same time. * All configurations have namelist variables that must be specified, and ``build-namelist`` has a mechanism to provide default values for these variables. When an appropriate default value cannot be found then ``build-namelist`` will fail with an informative message. * When running a configuration for the first time there are often many input datasets that may not be in the local input data directory. In order to facilitate getting the required datasets ``build-namelist`` has an option, ``-test``, that can be used to produce a complete list of required datasets and report status of whether or not they are present in the local filesystem. This list can then be used to obtain the needed datasets from the CESM SVN input data repository. * One required input for ``build-namelist`` is a configuration cache file produced by a previous invocation of ``configure`` (``config_cache.xml`` by default). ``build-namelist`` looks at this file to determine the features of the CAM executable, such as the dynamical core and horizontal resolution, that affect the default specifications for namelist variables. The default values themselves are specified in the file ``components/cam/bld/namelist_files/namelist_defaults_cam.xml``, and in the use case files located in the directory ``components/cam/bld/namelist_files/use_cases/``. * The other required input for ``build-namelist`` is the root directory for the input datasets. This is required since nearly all input files must be specified using absolute filepaths, but the defaults are stored as filepaths which are relative to the root directory. It is expected that the actual location of the root directory is something that will be resolved at runtime. The way this is done is to either specify it using the ``-csmdata`` argument, or to set the environment variable ``CSMDATA``. The methods for setting the values of namelist variables, listed from highest to lowest precedence, are: 1. using the ``-namelist`` option, 2. setting values in a file specified by ``-infile``, 3. specifying a ``-use_case`` option, 4. setting values in the namelist defaults file. * The first three of these methods for specifying namelist variables are the ones available to the user without requiring code modification. Any namelist variable recognized by CAM can be modified using method 1 or 2. The final two methods represent defaults that are hard coded as part of the code base. ---------------------------------------------- Arguments to build namelist ---------------------------------------------- The options may all be specified with either one or two leading dashes, e.g., ``-help`` or ``--help``. A consequence of allowing long names with single leading dashes is that the few options that can be expressed as single letter switches may **not** be bundled, e.g., ``-h -s -v`` may NOT be expressed as ``-hsv``. User supplied values are denoted in angle brackets "<>". Any value that contains white-space must be quoted. For options that can be set from small set of legal values, those values are given as a vertical bar separated list. :: -config Read the given configuration cache file to determine the configuration of the CAM executable. Default: "config_cache.xml". -csmdata Root directory of CESM input data. Can also be set by using the CSMDATA environment variable. -dir Directory where output namelist files will be written, i.e., atm_in, and drv_flds_in. Default: current working directory. -help [or -h] Print usage to STDOUT. -ignore_ic_date Ignore the date of the initial condition files when determining the default. -ignore_ic_year Ignore just the year part of the date of the initial condition files when determining the default. -infile Specify a file containing namelists to read values from. -inputdata Writes out a list containing pathnames for required input datasets to the specified filepath. -namelist Specify namelist settings directly on the commandline by supplying a string containing FORTRAN namelist syntax, e.g., -namelist "&camexp state_debug_checks=.true. /" -ntasks Specify the number of MPI tasks being used by the run. This is used to set a default decomposition for the FV dycore only (npr_yz). -silent [-s] Turns on silent mode - only fatal messages issued. -test Enable checking that input datasets exist on local filesystem. -use_case Specify a use case. -verbose [or -v] Turn on verbose echoing of informational messages. -version Echo the tag name of the CAM component. ---------------------------------------------- CAM Namelist variables ---------------------------------------------- Follow link for a searchable (or browsable) page containing all `CAM namelist variables `_