8. Appendices

8.1. The configure utility

8.1.1. How configure is called from the CESM scripts

The CESM scripts access CAM’s configure via the script $CAM_ROOT/models/atm/cam/bld/cam.buildnml.csh. The cam.buildnml.csh script acts as the interface between the CESM scripts and CAM’s configure and build-namelist utilities.

8.1.2. Arguments to configure

All configuration options can be specified using command line arguments to configure and this is the recommended practice. Options specified via command line arguments take precedence over options specified any other way.

At the next level of precedence a few options can be specified by setting environment variables. And finally, at the lowest precedence, many options have hard-coded defaults. Most of these are located in the files $CAM_ROOT/models/atm/cam/bld/config_files/defaults_*.xml. A few that depend on the values of other options are set by logic contained in the configure script (a Perl script). The hard-coded defaults are designed to produce the standard production configurations of CAM.

The configure script allows the user to specify compile time options such as model resolution, dynamical core type, additional compiler flags, and many other aspects. The user can type configure --help for a complete list of available options.

The options may all be specified with either one or two leading dashes, e.g., -help or --help. The few options that can be expressed as single letter switches may not be clumped, e.g., -h -s -v may NOT be expressed as -hsv. When multiple options are listed separated by a vertical bar either version may be used.

8.1.2.1. CAM configuration

These options will have an effect whether running CAM as part of CESM or running in a CAM standalone mode:

-[no]age_of_air_trcs

Switch on [off] age of air tracers.

Default: on if -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).
-carma <name>

[ 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) ]

Build CAM with specified CARMA microphysics model

Default: none

-chem <name>

[ 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 ]``.

Build CAM with specified prognostic chemistry package

Default:
  • trop_mam4: if the physics package is cam6
  • trop_mam3: if the physics package is cam5
  • otherwise none
-[no]clubb_sgs

Switch on [off] CLUBB_SGS.

Default: on for cam6, otherwise off.

-clubb_opts [clubb_do_adv (Advect CLUBB moments)]

Comma separated list of CLUBB options to turn on/off.

Default: they are all off.

-co2_cycle

This option is usually used with the -ccsm_seq option as part of the configuration for running biogeochemistry (BGC) compsets. It modifies the CAM configuration by increasing the number of advected constituents by 4.

Default: not set.

-comp_intf [mct | esmf]

Specify the component interfaces

Default: mct

-cosp

Enable the COSP simulator package.

Default: not set.

-cppdefs <string>
A string of user specified CPP defines appended to Makefile defaults. E.g. -cppdefs '-DVAR1 -DVAR2'. Note that a string containing whitespace will need to be quoted.
-dyn [eul | fv | se ]

Build CAM with specified dynamical core.

Default: fv

-edit_chem_mech
Invokes CAMCHEM_EDITOR to allow the user to edit the chemistry mechanism file.
-hgrid <name>
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., 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). For SE grids (cubed sphere) use neNnpM where N is the number of elements on an edge of the cube, and M is the number of Gauss points on the edge of an element (e.g., ne30np4).
-ionosphere [ none | wxi | wxie ].

Ionophere module used in WACCMX

Default: none

-macrophys [ rk , park , clubb_sgs , spcam_sam1mom , spcam_m2005 , none]

Specify the macrophysics option

Default:
  • clubb_sgs: if cam6 and clubb_sgs not explicitly turned off
  • park: if cam6 and noclubb_sgs or cam5
  • rk: if cam3 or cam4
-max_n_rad_cnst <n>
Maximum number of constituents that are either radiatively active, or in any single diagnostic list for the radiation. Default: 30
-microphys [ rk , mg1 , mg2 , spcam_m2005 , spcam_sam1mom , none ]

Specify the microphysics package.

Default:
  • mg2: if the physics package is cam6
  • mg1: if it is cam5
  • rk: if it is cam3 or cam4.
-nadv <n>

Set total number of advected species to <n>. If -nadv is set to a larger number than is required by the selected physics and chemistry schemes, then the remainder will automatically be used for test tracers (N.B. the namelist variable tracers_flag must be set to .true. to enable the test tracer code.)

Default: set to the number required by the selected physics and chemistry schemes.

-nadv_tt <n>

Set number of advected test tracers to <n>. Setting the number of test tracers explicitly with this option allows build-namelist to automatically enable the test tracer code by setting the tracers_flag namelist variable.

Default: 0

-nlev <n>

Set number of vertical layers to <n>.

Default:
  • 32: if the physics package is cam6.
  • 30: if the physics package is cam5, ideal, or adiabatic or spcam_m2005.
  • 26: if the physics package is cam3, cam4 or spcam_sam1mom.
  • 66: if the chemistry package is waccm and physics package is cam4.
  • 70: if the chemistry package is waccm and physics package is not cam4.
  • 81: if -waccmx is set.
  • 126: if -waccmx is set and -ionosphere is wxie
-offline_dyn

Switch enables the use of offline driver for FV dycore.

Default: not set.
-pbl [ clubb_sgs , hb (Holtslag and Boville), hbr (Holtslag, Boville, and Rasch), spcam_sam1mom, spcam_m2005, uw (University of Washington), none ]

PBL package.

Default:
  • clubb_sgs: if the physics package is cam6 or the -clubb_sgs switch is set
  • hb: if the physics package is cam3 or cam4
  • spacm_m2005: if it the physics package is spcam_m2005
  • spacm_sam1mom: if it the physics package is spcam_sam1mom
  • uw: if the physics package is cam5 or cam6 and -noclubb_sgs
  • otherwise none
-pcols <n>

Set maximum number of grid columns in a chunk to <n>.

Default:
  • 1: if -scam is set
  • otherwise 16
-pergro
Switch enables building CAM for perturbation growth tests. Only valid with cam3 and cam4 physics packages.

-phys [ cam3 | cam4 | cam5 | cam6 | adiabatic | held_suarez | kessler | spcam_sam1mom | spcam_m2005 ]

Physics package.

Default:
  • cam6: except
  • cam4: if -waccmx or -chem contains _mam in its setting
-prog_species <list>
Comma separated list of prognostic mozart species packages. Currently available: DST,SSLT,SO4,GHG,OC,BC,CARBON16
-psubcols <n>

Set maximum number of subcolumns in a grid column to <n>.

Default: 1.

-rad [rrtmg | camrt | none]

Radiation package.

Default:
  • rrtmg: if the physics package is cam5, cam6 or spacm_m2005
  • camrt: if the physics package is cam3, cam4 or spacm_sam1mom

-spcam_clubb_sgs Turn on the SPCAM version of CLUBB

-spcam_nx <n> SPCAM x-grid. - defaults to 4 (note the CRM requires spcam_nx to be greater than or equal to 4)

-spcam_ny <n> SPCAM y-grid. - defaults to 1

-spcam_dx <n> SPCAM horizontal grid spacing.

-spcam_dt <n> SPCAM timestep.

-unicon Switch to turn on the UNICON scheme. Default: off.

-usr_mech_infile <name>
Full pathname of the user supplied chemistry mechanism file.
-waccm_phys

Switch enables the use of WACCM physics in any chemistry configuration.

Default:
  • Off: unless one of the waccm chemistry options is chosen, then it’s automatically turned on.
-waccmx
Build CAM/WACCM with WACCM upper Thermosphere/Ionosphere extended package.
-zmconv_org
Include parameterization for sub-grid scale convective organization for the ZM deep convective scheme based on Mapes and Neale (2011)

8.1.2.2. SCAM configuration

-camiop
Configure CAM to generate an IOP file that can be used to drive SCAM. This switch only works with the Eulerian dycore.
-scam
Compiles model in single column mode. Only works with Eulerian dycore.

8.1.2.3. CAM parallelization

-[no]smp
Switch on [off] SMP parallelism (OpenMP). This option can be used when building a model that doesn’t contain CICE. It allows building an executable whose thread count can be set at run time.
-[no]spmd
Switch on [off] SPMD parallelism (MPI). This option can be used when building a model that doesn’t contain CICE. It allows building an executable whose task count can be set at run time.

8.1.2.4. CAM parallelization when running standalone with CICE

-ntasks <n>
This option must be used to specify SPMD parallelism when the CICE component is present. <n> is the number of MPI tasks. Setting ntasks > 0 implies -spmd. Use -nospmd to turn off linking with an MPI library. To configure for pure MPI specify "-ntasks N -nosmp". ntasks is used by CICE to determine default grid decompositions which must be specified at build time.
-nthreads <n>
This option must be used to specify SMP parallelism when the CICE component is present. <n> is the number of OpenMP threads per process. Setting nthreads > 0 implies -smp. Use -nosmp to turn off compilation of OMP directives. For pure OpenMP set "-nthreads N -nospmd". nthreads is used by CICE to determine default grid decomposition which must be specified at build time.

NOTE: When CAM is running standalone with CICE the default CICE decomposition is determined from the values of the -ntasks and -nthreads arguments. The user also has the ability to explicitly set the CICE decomposition using the following four arguments. If any of these arguments is set then ALL FOUR must be set.

-cice_bsizex <n>
CICE block size in longitude dimension. This size must evenly divide the number of longitude points in the global grid.
-cice_bsizey <n>
CICE block size in latitude dimension. This size must evenly divide the number of latitude points in the global grid.
-cice_maxblocks <n>
Maximum number of CICE blocks per process.
-cice_decomptype <name>
CICE decomposition type [ cartesian | spacecurve | roundrobin ].

8.1.2.5. General options to configure

-cache <name>
Name of output cache file. Default: config_cache.xml.
-cachedir <dir>
Name of directory where output cache file is written. Default: CAM build directory.
-ccsm_seq
Switch to specify that CAM is being built from within the CESM scripts. This produces Filepath and CCSM_cppdefs files that contains only the paths and CPP macros needed to build a library for the CAM component.
-help | -h
Print usage to STDOUT.
-silent | -s
Turns on silent mode - only fatal messages printed to STDOUT.
-test
Switch on testing of Fortran compiler and linking to external libraries.
-verbose | -v
Turn on verbose echoing of settings made by configure.
-version
Echo the repository tag name used to check out this CAM source tree.

8.1.2.6. Surface components used in standalone CAM

Options for surface components used in standalone CAM mode:

-ocn [ docn | dom | som | socn | aquaplanet ]``

Specify ocean component. Use data ocean model (docn or dom), stub ocean (socn), or aqua planet ocean (aquaplanet) in cam build. When built from the CESM scripts the value of ocn may be set to pop. This doesn’t impact how CAM is built, only how attributes are matched when searching for namelist defaults. If ocn is set to som then the docn component is used.

Default:
  • aquaplanet: if -aquaplanet set
  • otherwise socn

8.1.2.7. CAM standalone build

Options for building CAM via standalone scripts:

-cam_bld <dir>
Directory where CAM will be built. This is where configure will write the output files it generates (Makefile, Filepath, etc...). Default: ./
-cam_exe <name>
Name of the CAM executable. Default: cam.
-cam_exedir <dir>
Directory where CAM executable will be created. Default: CAM build directory.
-cc <name>
User specified C compiler. Default: Depends on the OS and the Fortran compiler.
-cflags <string>
A string of user specified C compiler options appended to the default options set in Makefile.
-debug
Switch to turn on building CAM with compiler options for debugging. The specific options are compiler dependent. These flags are set in the Makefile.in template file.
-esmf_libdir <dir>
Directory containing ESMF library and the esmf.mk file. If this option is specified then the external ESMF library will be used in place of the ESMF-WRF time manager code which is provided in the CESM source distribution.
-fc <name>
User specified Fortran compiler. Default: Depends on the OS and whether MPI is enabled.
-fc_type [pgi | lahey | intel | pathscale | gnu | xlf]
Type of the Fortran compiler. This argument is used in conjunction with the -fc argument when the name of the fortran compiler refers to a wrapper script (e.g., mpif90 or ftn). In this case the user needs to specify the type of Fortran compiler that is being invoked by the wrapper script. Default: Depends on the name of the Fortran compiler.
-fflags <string>
A string of user specified Fortran compiler options appended to the default options set in the Makefile. See -fopt to override optimization flags.
-fopt <string>
A string of user specified Fortran compiler optimization flags. Overrides Makefile defaults.
-gmake <name>
Name of the GNU make program on your system. Supply the absolute pathname if the program is not in your path (or fix your path). This is only needed by configure for running tests via the -test option.
-lapack_libdir <dir>
Directory containing LAPACK library.
-ldflags <string>
A string of user specified load options. Appended to Makefile defaults.
-linker <name>
User specified linker. Default: use the Fortran compiler.
-mpi_inc <dir>
Directory containing MPI include files.
-mpi_lib <dir>
Directory containing MPI library.
-nc_inc <dir>
Directory containing NetCDF include files.
-nc_lib <dir>
Directory containing NetCDF library.
-nc_mod <dir>
Directory containing NetCDF module files.
-pnc_inc <dir>
Directory containing PnetCDF include files.
-pnc_lib <dir>
Directory containing PnetCDF library.
-rad_driver
Build CAM with the offline radiation driver. This produces an executable that can only be used for offline radiation calculations.
-target_os <name>
Override the OS setting for cross platform compilation from the following list [aix|irix|linux| bgl|bgp ]. Default: OS on which configure is executed as defined by the Perl $OSNAME variable.
-usr_src <dir1>[,<dir2>[,<dir3>[...]]]
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 and use case files.

8.2. The build-namelist utility

The build-namelist utility builds namelists (and on occasion other types of input files) which specify run-time details for CAM and the components it’s running with in standalone mode. When executed from the CESM scripts it only produces a namelist file for the CAM component (in the file atm_in), and a namelist file for control of dry deposition which is shared by CAM and CLM (in the file drv_flds_in).

The task of constructing a correct namelist has become extremely complex due to the large number of configurations supported by CAM. Editing namelists by hand is an extremely 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.

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 directory. 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 $CAM_ROOT/models/atm/cam/bld/namelist_files/namelist_defaults_cam.xml, and in the use case files located in the directory $CAM_ROOT/models/atm/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 specific command-line options, e.g., -case and -runtype,
  2. using the -namelist option,
  3. setting values in a file specified by -infile,
  4. specifying a -use_case option,
  5. setting values in the namelist defaults file.
  • The first four 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 2 or 3. The final two methods represent defaults that are hard coded as part of the code base.

8.2.1. Options to build namelist

To get a list of all available options, type build-namelist --help. Available options are also listed just below.

The following options may all be specified with either one or two leading dashes, e.g., -help or --help. The few options that can be expressed as single letter switches may not be clumped, e.g., -h -s -v may NOT be expressed as -hsv. When multiple options are listed separated by a vertical bar either version may be used.

-case <name>
Case identifier up to 80 characters. This value is used to set the case_name variable in the driver namelist. Default: camrun
-cice_nl <namelist>
Specify namelist settings for CICE directly on the commandline by supplying a string containing FORTRAN namelist syntax, e.g., -cice_nl` "&ice histfreq=1 /". This namelist will be passed to the invocation of the CICE build-namelist via its -namelist argument.
-config <filepath>
Read the specified configuration cache file to determine the configuration of the CAM executable. Default: config_cache.xml.
-config_cice <filepath>
Filepath of the CICE config_cache file. This filepath is passed to the invocation of the CICE build-namelist. Only specify this to override the default filepath which was set when the CICE configure was invoked by the CAM configure.
-csmdata <dir>
Root directory of CESM input data. Can also be set by using the CSMDATA environment variable.
-dir <dir>
Directory where output namelist files for each component will be written, i.e., atm_in, drv_in, ice_in, lnd_in and ocn_in. Default: current working directory.
-help | -h
Print usage to STDOUT.
-ignore_ic_date
Ignore the date attribute of the initial condition files when determining the default.
-ignore_ic_year
Ignore just the year part of the date attribute of the initial condition files when determining the default.
-infile <filepath>
Specify a file containing namelists to read values from.
-inputdata <filepath>
Writes out a list of pathnames for required input datasets to the specified file.
-namelist <namelist>
Specify namelist settings directly on the commandline by supplying a string containing FORTRAN namelist syntax, e.g., -namelist "&atm stop_option='ndays' stop_n=10 /"
-ntasks <n>
Specify the number of MPI tasks to be used by the run. This is only used to set a default decomposition for the FV dycore, i.e., the npr_yz variable.
-runtype [startup|continue|branch]
Type of simulation. Default: startup.
-silent | -s
Turns on silent mode - only fatal messages issued.
-test
Enable checking that input datasets exist on local filesystem. This is also a convenient way to generate a list of the required input datasets for a model run.
-use_case <name>
Specify a use case.
-verbose | -v
Turn on verbose echoing of informational messages.
-version
Echo the source code repository tag name used to check out this CAM distribution.

8.2.2. Environment variables used by build namelist

The environment variables recognized by build-namelist are presented below.

CSMDATA

Root directory of CESM input data. Note that the commandline argument -csmdata takes precedence over the environment variable.

OMP_NUM_THREADS

If values of the specific variables that set the thread count for each component, i.e., atm_nthreads, cpl_nthreads, ice_nthreads, lnd_nthreads, or ocn_nthreads, are set via the -namelist, or -infile options, then these values have highest precedence. The OMP_NUM_THREADS environment variable has next highest precedence for setting any of the component specific thread count variables. Lowest precedence for setting these variables is the value of nthreads from the configure cache file.

8.2.3. CAM Namelist variables

A searchable (or browsable) page containing all CAM namelist variables is here.