Difference between revisions of "GCHP Run Configuration Files"

Revision as of 22:37, 16 November 2020

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Hardware and Software Requirements
Setting Up the GCHP Environment
Downloading Source Code and Data Directories
Compiling
Obtaining a Run Directory
Running GCHP: Basics
Running GCHP: Configuration
Output Data
Developing GCHP
Run Configuration Files

Overview

GCHP is controlled using a set of resource configuration files that are included in the GCHP run directory, most of which are denoted by suffix .rc. These files contain information required by GCHP including hardware allocation, initialization and runtime parameters, locations of necessary files, and where, what and how to read and write data to and from GCHP. Files include:

CAP.rc
ExtData.rc
GCHP.rc
input.geos
HEMCO_Config.rc
HEMCO_Diagn.rc
input.nml
HISTORY.rc

Several run-time settings must be set consistently across multiple files. Inconsistencies may result in your program crashing or yielding unexpected results. To avoid mistakes and make run configuration easier, we therefore include bash shell script runConfig.sh in run directories to update the most commonly used settings in the configuration files. Sourcing this script will update other config files to use values specified in runConfig.sh. This is done automatically at run start if using any of the example run scripts provided with GCHP. The updated settings will be printed to the GCHP log file by default.

Using runConfig.sh to configure common settings makes run configure much simpler, but also comes with peril. If you manually edit a config file setting that is also set in runConfig.sh then the setting in runConfig.sh will be used. For example, most frequency and duration settings for diagnostics in HISTORY.rc are set in runConfig.sh. File runConfig.sh must be edited rather than HISTORY.rc to change frequency and duration of output files. Please get very familiar with the options in runConfig.sh and be conscientious about not updating the same setting elsewhere.

While much of the labor of updating the various configuration files has been eliminated by runConfig.sh, it is still worth understanding what is happening under the hood with the other files. This page details the settings within those other configuration files and what they are used for.

Configuration File Descriptions

The following table lists the core functions of each of the configuration files in the GCHP run directory. See the individual subsections on each file for additional information.

File	Primary function in GCHP
`CAP.rc`	Controls parameters used by the highest level gridded component (CAP). This includes simulation run time information, name of the Root gridded component (GCHP), config filenames for Root and History, and toggles for certain MAPL logging utilities (timers, memory, and import/export name printing).
`ExtData.rc`	Config file for the MAPL ExtData component. Specifies input variable information, including name, regridding method, read frequency, offset, scaling, and file path. All GCHP imports must be specified in this file. Toggles at the top of the file enable MAPL ExtData debug prints and using most recent year if current year of data is unavailable. Default values may be used by specifying file path `/dev/null`.
`GCHP.rc`	Controls high-level aspects of the simulation, including grid type and resolution, core distribution, stretched-grid parameters, timesteps, and restart file configuration.
`input.geos`	Primary config file for GEOS-Chem. Same function as in GEOS-Chem Classic except grid, simulation start/end, met field source, timers, and data directory information are ignored.
`HEMCO_Config.rc`	Contains emissions information used by HEMCO. Same function as in GEOS-Chem Classic except only HEMCO name, species, scale IDs, category, and hierarchy are used. Diagnostic frequency, file path, read frequency, and units are ignored, and are instead stored in GCHP config file `ExtData.rc`. All HEMCO variables listed in `HEMCO_Config.rc` for enabled emissions must also have an entry in `ExtData.rc`.
`HEMCO_Diagn.rc`	Contains information mapping `HISTORY.rc` diagnostic names to HEMCO containers. Same function as in GEOS-Chem Classic except that not all items in `HEMCO_Diagn.rc` will be output; only emissions listed in `HISTORY.rc` will be included in diagnostics. All GCHPctm diagnostics listed in `HISTORY.rc` that start with `Emis`, `Hco`, or `Inv` must have a corresponding entry in `HEMCO_Diagn.rc`.
`input.nml`	Namelist used in advection for domain stack size and stretched grid parameters.
`HISTORY.rc`	Config file for the MAPL History component. Configures diagnostic output from GCHP.

CAP.rc

CAP.rc is the configuration file for the top-level gridded component called CAP. This gridded component can be thought of as the primary driver of GCHP. Its config file handles general runtime settings for GCHP including time parameters, performance profiling routines, and system-wide timestep (hearbeat). Combined with output file cap_restart, CAP.rc configures the exact dates for the next GCHP run.

Parameter	Description
`ROOT_NAME`	Sets the name MAPL uses to initialize the `ROOT` child gridded component component within CAP. CAP uses this name in all operations when querying and interacting with ROOT. It is set to `GCHP`.
`ROOT_CF`	Resource configuration file for the ROOT component. It is set to `GCHP.rc`.
`HIST_CF`	Resource configuration file for the MAPL HISTORY gridded component (another child gridded component of CAP). It is set to `HISTORY.rc`.
`BEG_DATE`	Simulation begin date in format `YYYYMMDD hhmmss`. This parameter is overrided in the presence of output file `cap_restart` containing a different start date.
`END_DATE`	Simulation end date in format `YYYYMMDD hhmmss`. If `BEG_DATE` plus duration (`JOB_SGMT`) is before `END_DATE` then simulation will end at `BEG_DATE + JOB_SGMT`. If it is after then simulation will end at `END_DATE`.
`JOB_SGMT`	Simulation duration in format `YYYYMMDD hhmmss`. The duration must be less than or equal to the difference between start and end date or the model will crash.
`HEARTBEAT_DT`	The timestep of the ESMF/MAPL internal clock, in seconds. All other timesteps in GCHP must be a multiple of `HEARTBEAT_DT`. ESMF queries all components at each heartbeat to determine if computation is needed. The result is based upon individual component timesteps defined in `GCHP.rc`.
`MAPL_ENABLE_TIMERS`	Toggles printed output of runtime MAPL timing profilers. This is set to `YES`. Timing profiles are output at the end of every GCHP run.
`MAPL_ENABLE_MEMUTILS`	Enables runtime output of the programs' memory usage. This is set to `YES`.
`PRINTSPEC`	Allows an abbreviated model run limited to initializat and print of Import and Export state variable names. Options include: `0` (default): Off; `1`: Imports and Exports only; `2`: Imports only; and `3`: Exports only.
`USE_SHMEM`	This setting is deprecated but still has an entry in the file.
`REVERSE_TIME`	Enables running time backwards in CAP. Default is `0` (off).

ExtData.rc

ExtData.rc contains input variable and file read information for GCHP. Explanatory information about the file is located at the top of the configuration file in all run directories. The file format is the same as that used in the GEOS model, and GMAO/NASA documentation for it can be found at the ExtData component page on the GEOS-5 wiki.

The following two parameters are set at the top of the file:

Parameter Name	Description
`Ext_AllowExtrat`	Logical toggle to use data from nearest year available. This is set to true for GCHP. Note that GEOS-Chem Classic accomplishes the same effect but with more flexibility in `HEMCO_Config.rc`. That functionality of `HEMCO_Config.rc` is ignored in GCHP.
`DEBUG_LEVEL`	Turns MAPL ExtData debug prints on/off. This is set to `0` in GCHP (off), but may be set to `1` to enable. Beware that turning on ExtData debug prints greatly slows down the model, and prints are only done from the root thread. Use this when debugging problems with input files.

The rest of the file contains space-delimited lines, one for each variable imported to the model from an external file. Columns are as follows in order as they appear left to right in the file:

Name in Column Header	Description
`Export Name`	Name of imported met field (e.g. `ALBD`) or HEMCO emissions container name (e.g. `GEIA_NH3_ANTH`).
`Units`	Unit string nested within single quotes. `'1'` indicates there is no unit conversion from the native units in the netCDF file.
`Clim`	Enter `Y` if the file is a 12 month climatology, otherwise enter `N`. If you specify it is a climatology ExtData the data can be on either one file or 12 files if they are templated appropriately with one per month.
`Conservative`	Enter `Y` the data should be regridded in a mass conserving fashion through a tile file. `F;{VALUE}` can also be used for fractional regridding. Otherwise enter `N` to use the non-conervative bilinear regridding.
`Refresh Time Template`	Possible values include: `-`: The field will only be updated once the first time ExtData runs `0`: Update the variable at every step. ExtData will do a linear interpolation to the current time using the available data. `%y4-%m2-%h2T%h2:%n2:00`: Set the recurring time to update the file. The file will be updated when the evaluated template changes. For example, a template in the form %y4-%m2-%d2T12:00:00 will cause the variable to be updated at the start of a new day (i.e. when the clock hits 2007-08-02T00:00:00 it will update the variable but the time it will use for reading and interpolation is 2007-08-02T12:00:00).
`Offset Factor`	Factor the variable will be shifted by. Use `none` for no shifting.
`Scale Factor`	Factor the variable will be scaled by. Use `none` for no scaling.
`External File Variable`	The name of the variable in the netCDF data file, e.g. `ALBEDO` in met fields.
`External File Template`	Path to the netCDF data file. If not using the data, specify `/dev/null` to reduce processing time. If there are no tokens in the template name ExtData will assume that all the data is on one file. Note that if the data on file is at a different resolution that the application grid, the underlying I/O library ExtData uses will regrid the data to the application grid.

GCHP.rc

Important Note: This section is not yet updated for GCHP 12.5.0. Several changes to this file occur in that version for compatibility with a newer version of MAPL.

GCHP.rc is resource configuration file for the ROOT component within GCHP. It controls, at a minimum, global model resolution, grid type, parallel sub-domain size, component time steps, and job restart parameters.

Parameter	Description
`NX, NY`	Number of boxes in the two MPI sub-domain dimensions. *`NX NY` must equal your number of CPUs; `NX` or `NY` must be a multiple of 6 (the number of faces); typically `NY` is set as a multiple of 6.**
`IM`	Number of grid cells on the side of a single cubed sphere face. Get a rough idea of equivalent lat/lon resolution by dividing 90 by `IM`. Choose your timestep settings accordingly (see `RUN_DT` below).
`JM`	Number of grid cells times 6, essentially defining the second dimension if all six faces are stacked in a 2-dimensional array. *Must be to equal to `IM6`.**
`LM`	Number of vertical grid cells. The default value is 72. Must be equal to the vertical resolution of the offline meteorological fields since MAPL cannot regrid vertically
`GRIDNAME`	The default grid name is `PE24x144-CF`. The grid name includes how the pole is treated, the face side length, the face side length times six, and whether it is a Cubed Sphere Grid or Lat/Lon. The name `PE24x144-CF` indicates polar edge (PE), 24 cells along one face side, 144 for 246, and a cubed-sphere grid (CF). Many options here are defined in MAPL_Generic. Must be consistent with `IM` and `JM`.*
`GEOChem_CTM`	A toggle that tells FVDycore that it is operating as a transport model rather than a prognostic model if set to 1.
`AdvCore_Advection`	Default is 1.
`DYCORE`	Should either be set to OFF (default) or ON. This value does nothing, but MAPL will crash if it is not declared.
`HEARTBEAT_DT`	The timestep in seconds that the DYCORE Component should be called. Default is 600. Must be a multiple of `HEARTBEAT_DT` in `CAP.rc`.
`SOLAR_DT`	The timestep in seconds that the SOLAR Component should be called. Default is 600. Must be a multiple of `HEARTBEAT_DT` in `CAP.rc`.
`IRRAD_DT`	The timestep in seconds that the IRRAD Component should be called. ESMF checks this value during its timestep check. Default is 600. Must be a multiple of `HEARTBEAT_DT` in `CAP.rc`.
`RUN_DT`	The timestep in seconds that the RUN Component should be called. ESMF checks this value during its timestep check. The recommended timestep [s] per grid resolution (see `IM`) are: 1800 (4x5); 900 (2x2.5); 600 (1x1.25); 600 (1/2 degree); 300 (1/4 degree). Must be a multiple of `HEARTBEAT_DT` in `CAP.rc`.
`GIGCchem_DT`	The timestep in seconds that the GIGCchem Component should be called. ESMF checks this value during its timestep check. Default is 1200. Must be a multiple of `HEARTBEAT_DT` in `CAP.rc`.
`DYNAMICS_DT`	The timestep in seconds that the DYNAMICS Component should be called. ESMF checks this value during its timestep check. Default is 600. Must be a multiple of `HEARTBEAT_DT` in `CAP.rc`.
`SOLARAvrg, IRRADAvrg`	Default is 0.
`GIGCchem_REFERENCE_TIME`
`PRINTRC`	Specifies which resource values to print. Options include 0: Non-Default Values, and 1: All Values. Default setting is 0.
`PARALLEL_READFORCING`	Enables or disables parallel I/O processes when writing the restart files. Default value is 0 (disabled).
`NUM_READERS, NUM_WRITERS`	Number of simultaneous readers. Should divide evenly unto `NY`. Default value is 1.
`BKG_FREQUENCY`	Active observer when desired. Default value is 0.
`GIGCchem_INTERNAL_RESTART_FILE`	The filename of the internal restart file to be written.
`GIGCchem_INTERNAL_RESTART_TYPE`	The format of the internal restart file. Valid types include `pbinary` and `pnc4`.
`GIGCchem_INTERNAL_CHECKPOINT_FILE`	The filename of the internal checkpoint file to be written.
`GIGCchem_INTERNAL_CHECKPOINT_TYPE`	The format of the internal checkstart file. Valid types include `pbinary` and `pnc4`.
`GIGCchem_INTERNAL_HEADER`	Only needed when the file type is set to `pbinary`. Specifies if a binary file is self-describing.
`DYN_INTERNAL_RESTART_FILE`	The filename of the DYNAMICS internal restart file to be written.
`DYN_INTERNAL_RESTART_TYPE`	The format of the DYNAMICS internal restart file. Valid types include `pbinary` and `pnc4`.
`DYN_INTERNAL_CHECKPOINT_FILE`	The filename of the DYNAMICS internal checkpoint file to be written.
`DYN_INTERNAL_CHECKPOINT_TYPE`	The format of the DYNAMICS internal checkpoint file. Valid types include `pbinary` and `pnc4`.
`DYN_INTERNAL_HEADER`	Only needed when the file type is set to `pbinary`. Specifies if a binary file is self-describing.
`MAX_DIAG, MAX_TRCS, MAX_MEMB, MAX_FAMS, MAX_DEP, LINOZ_NFIELDS, LINOZ_NLAT, LINOZ_NLEVELS, LINOZ_NMONTHS, RUN_PHASES`	For reading the `input.geos` file. Default value is 80.
`HEMCO_CONFIG`	Name of the HEMCO configuration file. Default is `HEMCO_Config.rc`.
`STDOUT_LOGFILE`	Log filename template. Default is `PET%%%%%.GEOSCHEMchem.log`.
`STDOUT_LOGLUN`	Logical unit number for stdout. Default value is 6.
`INIT_ZERO`	Default is 0.
`INIT_GCC`	Default is 0.

input.geos

HEMCO_Config.rc

HEMCO_Diagn.rc

input.nml

input.nml controls specific aspects of the FV3 dynamical core used for advection. Entries in input.nml are described below.

Parameter	Description
`&fms_nml`	Header for the FMS namelist which includes all variables directly below the header.
`print_memory_usage`	Toggles memory usage prints to log. However, in practice turning it on or off does not have any effect.
`domain_stack_size`	Domain stack size in bytes. This is set to 20000000 in GCHP to be large enough to use very few cores in a high resolution run. If the domain size is too small then you will get an "mpp domain stack size overflow error" in advection. If this happens, try increasing the domain stack size in this file.
`&fv_core_nml`	Header for the finite-volume dynamical core namelist. This is commented out by default unless running on a stretched grid. Due to the way the file is read, commenting out the header declaration requires an additional comment character within the string, e.g. `#&fv#_core_nml`.
`do_schmidt`	Logical for whether to use Schmidt advection. Set to `.true.` if using stretched grid; otherwise this entry is commented out.
`stretch_fac`	Stretched grid factor, equal to the ratio of grid resolution in targeted high resolution region to the configured run resolution. This is commented out if not using stretched grid.
`target_lat`	Target latitude of high resolution region if using stretched grid. This is commented out if not using stretched grid.
`target_lon`	Target longitude of high resolution region if using stretched grid. This is commented out if not using stretched grid.

HISTORY.rc

The HISTORY.rc configuration file controls the diagnostic files output by GCHP. Information is organized into several sections:

Single parameters set at the top of the file
Grid label declaration list
Definition for each grid in grid label list
Variable collection declaration list
Definition for each collection in collection list.

Single parameters set at the top of HISTORY.rc are as follows and apply to all collections:

Parameter	Description
`EXPID`	Filename prefix concatenated with each collection template string to define file path. It is set to `OutputDir/GCHP` so that all output diagnostic files are output to run subdirectory `OutputDir` and have filename begin with `GCHP`.
`EXPDSC`	Export description included as attribute "Title" in output files
`CoresPerNode`	Number of CPUs per node for your simulation.
`VERSION`	Optional parameter included as attribute in output file.

The grid labels section of HISTORY.rc declares a list of descriptive grid strings followed by a definition for each declared grid label. Grids not in the grid label list may have definitions in the file; however, this will prevent them from being used in output collections. See the HISTORY.rc grid label section for syntax on declaring and defining grid labels.

Keywords that may be used for grid label definitions are in the table below. Note that this list is not exhaustive; MAPL may have additional keywords that may be used that have not yet been explored for use with GCHP.

Grid label keyword	Description
`GRID_TYPE`	Type of grid. May be `Cubed-Sphere` or `LatLon`.
`IM_WORLD`	Side length of one cubed-sphere face, e.g. 24 if grid resolution is C24, or number of longitudinal grid boxes if lat-lon.
`JM_WORLD`	Same as `IM_WORLD` but multiplied by 6 (number of faces), or number of latitudinal grid boxes if lat-lon.
`POLE`	For lat-lon grids only. `PC` if latitudes are pole-centered and `PE` if latitudes are polar edge.
`DATELINE`	For lat-lon grids only. `DC` if longitudes are dateline-centered and `DE` if longitudes are dateline-edge.
`LAT_RANGE`	For lat-lon grids only. Regional grid latitudinal bounds.
`LON_RANGE`	For lat-lon grids only. Regional grid longitudinal bounds.
`LM`	Number of vertical levels.

The collections section of HISTORY.rc declares a list of descriptive strings that define unique collections of output variables and settings. As with grid labels, it is followed by a definition for each declared collection. Collections not in the collection list, or present but commented out, may have definitions in the file; however, this will prevent them from being output. See the HISTORY.rc collection section for syntax on declaring and defining output collections.

Keywords that may be used for collection definitions are in the table below. Note that this list is not exhaustive; MAPL may have additional keywords that may be used that have not yet been explored for use with GCHP.

Collection keyword	Description
`{COLLECTION}.template`	The output filename suffix that is appended to global parameter `EXPID` to define full output file path. Including a date string, such as `'%y4%m2%d2`, will insert the simulation start day following GrADS conventions. The default template for GCHP is set to `%y4%m2%d2_%h2%n2z.nc4`.
`{COLLECTION}.format`	Character string defining the file format. Options include `CFIO` (default) for netCDF-4 or `flat` for binary files. Always output as `CFIO` when using GCHP.
`{COLLECTION}.grid_label`	Declared grid label for output grid. If excluded the collection will be output on the cubed-sphere grid at native resolution, e.g. C24 if you run GCHP with grid resolution C24.
`{COLLECTION}.conservative`	For lat-lon grids only. Set to 1 to conservatively regrid from cubed-sphere to lat-lon upon output. Exclude or set to 0 to use bilinear interpolation instead (not recommended).
`{COLLECTION}.frequency`	The frequency at which output values are computed and archived, in format `HHMMSS`. For example, `010000` will calculate diagnostics every hour. The method of calculation is determined by the `mode` keyword. Unlike GEOS-Chem Classic, you cannot specify number of days, months, or years.
`{COLLECTION}.duration`	The frequency at which files are written, in format `HHMMSS`. For example, `240000` will output daily files. The number of times in the file are determined by the `frequency` keyword. Unlike GEOS-Chem Classic, you cannot specify number of days, months, or years.
`{COLLECTION}.mode`	Method of diagnostic calculation. Options are either `instantaneous` or `time-averaged`.
`{COLLECTION}.fields`	List of character string pairs including diagnostic name and gridded component. All GCHP diagnostics belong to the `GCHPchem` gridded component. Diagnostic names have prefixes that determine where MAPL History will look for them. Prefixes `Emis`, `Inv`, and `Hco` are HEMCO diagnostics and must have definitions in config file `HEMCO_Diagn.rc`. Prefixes `Chem` and `Met` are GEOS-Chem state variables stored in objects `State_Chm` and `State_Met` respectively. Prefix `SPC` corresponds to internal state species, meaning the same arrays that are output to the restart file. Prefix `GEOS` is reserved for use in the `GEOS` model. All other diagnostic name prefixes are interpreted as variables stored in the GEOS-Chem `State_Diag` object.

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Difference between revisions of "GCHP Run Configuration Files"

Revision as of 22:37, 16 November 2020

Contents

Overview

Configuration File Descriptions

CAP.rc

ExtData.rc

GCHP.rc

input.geos

HEMCO_Config.rc

HEMCO_Diagn.rc

input.nml

HISTORY.rc

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@@ Line 15: / Line 15: @@
 GCHP is controlled using a set of resource configuration files that are included in the GCHP run directory, most of which are denoted by suffix <tt>.rc</tt>. These files contain information required by GCHP including hardware allocation, initialization and runtime parameters, locations of necessary files, and where, what and how to read and write data to and from GCHP. Files include:
-#[[#GCHP.rc|GCHP.rc]]
 #[[#CAP.rc|CAP.rc]]
 #[[#ExtData.rc|ExtData.rc]]
+#[[#GCHP.rc|GCHP.rc]]
 #[[#input.geos|input.geos]]
 #[[#HEMCO_Config.rc|HEMCO_Config.rc]]
@@ Line 38: / Line 38: @@
 !width="280px"|File
 !width="720px"|Primary function in GCHP
-|-valign="top"
-| <tt>GCHP.rc</tt>
-| Controls high-level aspects of the simulation, including grid type and resolution, core distribution, stretched-grid parameters, timesteps, and restart file configuration.
 |-valign="top"
@@ Line 50: / Line 46: @@
 | <tt>ExtData.rc</tt>
 | Config file for the MAPL ExtData component. Specifies input variable information, including name, regridding method, read frequency, offset, scaling, and file path. All GCHP imports must be specified in this file. Toggles at the top of the file enable MAPL ExtData debug prints and using most recent year if current year of data is unavailable. Default values may be used by specifying file path <tt>/dev/null</tt>.
+|-valign="top"
+| <tt>GCHP.rc</tt>
+| Controls high-level aspects of the simulation, including grid type and resolution, core distribution, stretched-grid parameters, timesteps, and restart file configuration.
 |-valign="top"
@@ Line 70: / Line 70: @@
 | <tt>HISTORY.rc</tt>
 | Config file for the MAPL History component. Configures diagnostic output from GCHP.
+|}
+=== CAP.rc ===
+<tt>CAP.rc</tt> is the configuration file for the top-level gridded component called <tt>CAP</tt>. This gridded component can be thought of as the primary driver of GCHP. Its config file handles general runtime settings for GCHP including time parameters, performance profiling routines, and system-wide timestep (hearbeat). Combined with output file <tt>cap_restart</tt>, <tt>CAP.rc</tt> configures the exact dates for the next GCHP run.
+{| border=1 cellspacing=0 cellpadding=5
+|-bgcolor="#CCCCCC"
+!width="280px"|Parameter
+!width="720px"|Description
+|-valign="top"
+|<tt>ROOT_NAME</tt>
+|Sets the name MAPL uses to initialize the <tt>ROOT</tt> child gridded component component within CAP. CAP uses this name in all operations when querying and interacting with ROOT. It is set to <tt>GCHP</tt>.
+|-valign="top"
+|<tt>ROOT_CF</tt>
+|Resource configuration file for the ROOT component. It is set to <tt>GCHP.rc</tt>.
+|-valign="top"
+|<tt>HIST_CF</tt>
+|Resource configuration file for the MAPL HISTORY gridded component (another child gridded component of CAP). It is set to <tt>HISTORY.rc</tt>.
+|-valign="top"
+|<tt>BEG_DATE</tt>
+|Simulation begin date in format <tt>YYYYMMDD hhmmss</tt>. This parameter is overrided in the presence of output file <tt>cap_restart</tt> containing a different start date.
+|-valign="top"
+|<tt>END_DATE</tt>
+|Simulation end date in format <tt>YYYYMMDD hhmmss</tt>. If <tt>BEG_DATE</tt> plus duration (<tt>JOB_SGMT</tt>) is before <tt>END_DATE</tt> then simulation will end at <tt>BEG_DATE + JOB_SGMT</tt>. If it is after then simulation will end at <tt>END_DATE</tt>.
+|-valign="top"
+|<tt>JOB_SGMT</tt>
+|Simulation duration in format <tt>YYYYMMDD hhmmss</tt>. The duration must be less than or equal to the difference between start and end date or the model will crash.
+|-valign="top"
+|<tt>HEARTBEAT_DT</tt>
+|The timestep of the ESMF/MAPL internal clock, in seconds. All other timesteps in GCHP must be a multiple of <tt>HEARTBEAT_DT</tt>. ESMF queries all components at each heartbeat to determine if computation is needed. The result is based upon individual component timesteps defined in <tt>GCHP.rc</tt>.
+|-valign="top"
+|<tt>MAPL_ENABLE_TIMERS</tt>
+|Toggles printed output of runtime MAPL timing profilers. This is set to <tt>YES</tt>. Timing profiles are output at the end of every GCHP run.
+|-valign="top"
+|<tt>MAPL_ENABLE_MEMUTILS</tt>
+|Enables runtime output of the programs' memory usage. This is set to <tt>YES</tt>.
+|-valign="top"
+|<tt>PRINTSPEC</tt>
+|Allows an abbreviated model run limited to initializat and print of Import and Export state variable names. Options include: <tt>0</tt> (default): Off; <tt>1</tt>: Imports and Exports only; <tt>2</tt>: Imports only; and <tt>3</tt>: Exports only.
+|-valign="top"
+|<tt>USE_SHMEM</tt>
+| This setting is deprecated but still has an entry in the file.
+|-valign="top"
+|<tt>REVERSE_TIME</tt>
+|Enables running time backwards in CAP. Default is <tt>0</tt> (off).
+|}
+=== ExtData.rc ===
+<tt>ExtData.rc</tt> contains input variable and file read information for GCHP. Explanatory information about the file is located at the top of the configuration file in all run directories. The file format is the same as that used in the <tt>GEOS</tt> model, and GMAO/NASA documentation for it can be found at the [https://geos5.org/wiki/index.php?title=Using_the_ExtData_component ExtData component page on the GEOS-5 wiki].
+The following two parameters are set at the top of the file:
+{| border=1 cellspacing=0 cellpadding=5
+|-bgcolor="#CCCCCC"
+!width="280px"|Parameter Name
+!width="720px"|Description
+|-valign="top"
+|<tt>Ext_AllowExtrat</tt>
+|Logical toggle to use data from nearest year available. This is set to true for GCHP. Note that GEOS-Chem Classic accomplishes the same effect but with more flexibility in <tt>HEMCO_Config.rc</tt>. That functionality of <tt>HEMCO_Config.rc</tt> is ignored in GCHP.
+|-valign="top"
+|<tt>DEBUG_LEVEL</tt>
+|Turns MAPL ExtData debug prints on/off. This is set to <tt>0</tt> in GCHP (off), but may be set to <tt>1</tt> to enable. Beware that turning on ExtData debug prints greatly slows down the model, and prints are only done from the root thread. Use this when debugging problems with input files.
+|}
+The rest of the file contains space-delimited lines, one for each variable imported to the model from an external file. Columns are as follows in order as they appear left to right in the file:
+{| border=1 cellspacing=0 cellpadding=5
+|-bgcolor="#CCCCCC"
+!width="280px"|Name in Column Header
+!width="720px"|Description
+|-valign="top"
+|<tt>Export Name</tt>
+|Name of imported met field (e.g. <tt>ALBD</tt>) or HEMCO emissions container name (e.g. <tt>GEIA_NH3_ANTH</tt>).
+|-valign="top"
+|<tt>Units</tt>
+|Unit string nested within single quotes. <tt>'1'</tt> indicates there is no unit conversion from the native units in the netCDF file.
+|-valign="top"
+|<tt>Clim</tt>
+|Enter <tt>Y</tt> if the file is a 12 month climatology, otherwise enter <tt>N</tt>. If you specify it is a climatology ExtData the data can be on either one file or 12 files if they are templated appropriately with one per month.
+|-valign="top"
+|<tt>Conservative</tt>
+|Enter <tt>Y</tt> the data should be regridded in a mass conserving fashion through a tile file. <tt>F;{VALUE}</tt> can also be used for fractional regridding. Otherwise enter <tt>N</tt> to use the non-conervative bilinear regridding.
+|-valign="top"
+|<tt>Refresh Time Template</tt>
+|Possible values include:
+*<tt>-</tt>: The field will only be updated once the first time ExtData runs
+*<tt>0</tt>: Update the variable at every step. ExtData will do a linear interpolation to the current time using the available data.
+*<tt>%y4-%m2-%h2T%h2:%n2:00</tt>: Set the recurring time to update the file. The file will be updated when the evaluated template changes. For example, a template in the form %y4-%m2-%d2T12:00:00 will cause the variable to be updated at the start of a new day (i.e. when the clock hits 2007-08-02T00:00:00 it will update the variable but the time it will use for reading and interpolation is 2007-08-02T12:00:00).
+|-valign="top"
+|<tt>Offset Factor</tt>
+|Factor the variable will be shifted by. Use <tt>none</tt> for no shifting.
+|-valign="top"
+|<tt>Scale Factor</tt>
+|Factor the variable will be scaled by. Use <tt>none</tt> for no scaling.
+|-valign="top"
+|<tt>External File Variable</tt>
+|The name of the variable in the netCDF data file, e.g. <tt>ALBEDO</tt> in met fields.
+|-valign="top"
+|<tt>External File Template</tt>
+|Path to the netCDF data file. If not using the data, specify <tt>/dev/null</tt> to reduce processing time. If there are no tokens in the template name ExtData will assume that all the data is on one file. Note that if the data on file is at a different resolution that the application grid, the underlying I/O library ExtData uses will regrid the data to the application grid.
 |}
@@ Line 231: / Line 361: @@
 |}
-=== CAP.rc ===
-<tt>CAP.rc</tt> is the configuration file for the top-level gridded component called <tt>CAP</tt>. This gridded component can be thought of as the primary driver of GCHP. Its config file handles general runtime settings for GCHP including time parameters, performance profiling routines, and system-wide timestep (hearbeat). Combined with output file <tt>cap_restart</tt>, <tt>CAP.rc</tt> configures the exact dates for the next GCHP run.
-{| border=1 cellspacing=0 cellpadding=5
-|-bgcolor="#CCCCCC"
-!width="280px"|Parameter
-!width="720px"|Description
-|-valign="top"
-|<tt>ROOT_NAME</tt>
-|Sets the name MAPL uses to initialize the <tt>ROOT</tt> child gridded component component within CAP. CAP uses this name in all operations when querying and interacting with ROOT. It is set to <tt>GCHP</tt>.
-|-valign="top"
-|<tt>ROOT_CF</tt>
-|Resource configuration file for the ROOT component. It is set to <tt>GCHP.rc</tt>.
-|-valign="top"
-|<tt>HIST_CF</tt>
-|Resource configuration file for the MAPL HISTORY gridded component (another child gridded component of CAP). It is set to <tt>HISTORY.rc</tt>.
-|-valign="top"
-|<tt>BEG_DATE</tt>
-|Simulation begin date in format <tt>YYYYMMDD hhmmss</tt>. This parameter is overrided in the presence of output file <tt>cap_restart</tt> containing a different start date.
-|-valign="top"
-|<tt>END_DATE</tt>
-|Simulation end date in format <tt>YYYYMMDD hhmmss</tt>. If <tt>BEG_DATE</tt> plus duration (<tt>JOB_SGMT</tt>) is before <tt>END_DATE</tt> then simulation will end at <tt>BEG_DATE + JOB_SGMT</tt>. If it is after then simulation will end at <tt>END_DATE</tt>.
-|-valign="top"
-|<tt>JOB_SGMT</tt>
-|Simulation duration in format <tt>YYYYMMDD hhmmss</tt>. The duration must be less than or equal to the difference between start and end date or the model will crash.
-|-valign="top"
-|<tt>HEARTBEAT_DT</tt>
-|The timestep of the ESMF/MAPL internal clock, in seconds. All other timesteps in GCHP must be a multiple of <tt>HEARTBEAT_DT</tt>. ESMF queries all components at each heartbeat to determine if computation is needed. The result is based upon individual component timesteps defined in <tt>GCHP.rc</tt>.
-|-valign="top"
-|<tt>MAPL_ENABLE_TIMERS</tt>
-|Toggles printed output of runtime MAPL timing profilers. This is set to <tt>YES</tt>. Timing profiles are output at the end of every GCHP run.
-|-valign="top"
-|<tt>MAPL_ENABLE_MEMUTILS</tt>
-|Enables runtime output of the programs' memory usage. This is set to <tt>YES</tt>.
-|-valign="top"
-|<tt>PRINTSPEC</tt>
-|Allows an abbreviated model run limited to initializat and print of Import and Export state variable names. Options include: <tt>0</tt> (default): Off; <tt>1</tt>: Imports and Exports only; <tt>2</tt>: Imports only; and <tt>3</tt>: Exports only.
-|-valign="top"
-|<tt>USE_SHMEM</tt>
-| This setting is deprecated but still has an entry in the file.
-|-valign="top"
-|<tt>REVERSE_TIME</tt>
-|Enables running time backwards in CAP. Default is <tt>0</tt> (off).
-|}
-=== ExtData.rc ===
-<tt>ExtData.rc</tt> contains input variable and file read information for GCHP. Explanatory information about the file is located at the top of the configuration file in all run directories. The file format is the same as that used in the <tt>GEOS</tt> model, and GMAO/NASA documentation for it can be found at the [https://geos5.org/wiki/index.php?title=Using_the_ExtData_component ExtData component page on the GEOS-5 wiki].
-The following two parameters are set at the top of the file:
-{| border=1 cellspacing=0 cellpadding=5
-|-bgcolor="#CCCCCC"
-!width="280px"|Parameter Name
-!width="720px"|Description
-|-valign="top"
-|<tt>Ext_AllowExtrat</tt>
-|Logical toggle to use data from nearest year available. This is set to true for GCHP. Note that GEOS-Chem Classic accomplishes the same effect but with more flexibility in <tt>HEMCO_Config.rc</tt>. That functionality of <tt>HEMCO_Config.rc</tt> is ignored in GCHP.
-|-valign="top"
-|<tt>DEBUG_LEVEL</tt>
-|Turns MAPL ExtData debug prints on/off. This is set to <tt>0</tt> in GCHP (off), but may be set to <tt>1</tt> to enable. Beware that turning on ExtData debug prints greatly slows down the model, and prints are only done from the root thread. Use this when debugging problems with input files.
-|}
-The rest of the file contains space-delimited lines, one for each variable imported to the model from an external file. Columns are as follows in order as they appear left to right in the file:
-{| border=1 cellspacing=0 cellpadding=5
-|-bgcolor="#CCCCCC"
-!width="280px"|Name in Column Header
-!width="720px"|Description
-|-valign="top"
-|<tt>Export Name</tt>
-|Name of imported met field (e.g. <tt>ALBD</tt>) or HEMCO emissions container name (e.g. <tt>GEIA_NH3_ANTH</tt>).
-|-valign="top"
-|<tt>Units</tt>
-|Unit string nested within single quotes. <tt>'1'</tt> indicates there is no unit conversion from the native units in the netCDF file.
-|-valign="top"
-|<tt>Clim</tt>
-|Enter <tt>Y</tt> if the file is a 12 month climatology, otherwise enter <tt>N</tt>. If you specify it is a climatology ExtData the data can be on either one file or 12 files if they are templated appropriately with one per month.
-|-valign="top"
-|<tt>Conservative</tt>
-|Enter <tt>Y</tt> the data should be regridded in a mass conserving fashion through a tile file. <tt>F;{VALUE}</tt> can also be used for fractional regridding. Otherwise enter <tt>N</tt> to use the non-conervative bilinear regridding.
-|-valign="top"
-|<tt>Refresh Time Template</tt>
-|Possible values include:
-*<tt>-</tt>: The field will only be updated once the first time ExtData runs
-*<tt>0</tt>: Update the variable at every step. ExtData will do a linear interpolation to the current time using the available data.
-*<tt>%y4-%m2-%h2T%h2:%n2:00</tt>: Set the recurring time to update the file. The file will be updated when the evaluated template changes. For example, a template in the form %y4-%m2-%d2T12:00:00 will cause the variable to be updated at the start of a new day (i.e. when the clock hits 2007-08-02T00:00:00 it will update the variable but the time it will use for reading and interpolation is 2007-08-02T12:00:00).
-|-valign="top"
-|<tt>Offset Factor</tt>
-|Factor the variable will be shifted by. Use <tt>none</tt> for no shifting.
-|-valign="top"
-|<tt>Scale Factor</tt>
-|Factor the variable will be scaled by. Use <tt>none</tt> for no scaling.
-|-valign="top"
-|<tt>External File Variable</tt>
-|The name of the variable in the netCDF data file, e.g. <tt>ALBEDO</tt> in met fields.
-|-valign="top"
-|<tt>External File Template</tt>
-|Path to the netCDF data file. If not using the data, specify <tt>/dev/null</tt> to reduce processing time. If there are no tokens in the template name ExtData will assume that all the data is on one file. Note that if the data on file is at a different resolution that the application grid, the underlying I/O library ExtData uses will regrid the data to the application grid.
-|}
 === input.geos ===