# Running GCHP: Configuration

## Overview

All GCHP run directories have default simulation-specific run-time settings that are set when you create a run directory. You will likely want to change these settings. This page goes over how to do this.

## Configuration files

GCHP is controlled using a set of configuration files that are included in the GCHP run directory. Files include:

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, bash shell script runConfig.sh is included in all run directories to set the most commonly changed config file settings from one location. Sourcing this script will update multiple config files to use values specified in file.

Sourcing runConfig.sh is done automatically prior to running GCHP if using any of the example run scripts, or you can do it at the command line. Information about what settings are changed and in what files are standard output of the script. To source the script, type the following:

source runConfig.sh


You may also use it in silent mode if you wish to update files but not display settings on the screen:

source runConfig.sh --silent


While using runConfig.sh to configure common settings makes run configure much simpler, it comes with a major caveat. If you manually edit a config file setting that is also set in runConfig.sh then your manual update will be overrided via string replacement. Please get very familiar with the options in runConfig.sh and be conscientious about not updating the same setting elsewhere.

You generally will not need to know more about the GCHP configuration files beyond what is listed on this page. However, for a comprehensive description of all configuration files used by GCHP see the last section of this user manual.

## Commonly Changed Run Options

### Compute Configuration

#### Set Number of Nodes and Cores

To change the number of nodes and cores for your run you must update settings in two places: (1) runConfig.sh, and (2) your run script. The runConfig.sh file contains detailed instructions on how to set resource parameter options and what they mean. Look for the Compute Resources section in the script. Update your resource request in your run script to match the resources set in runConfig.sh.

It is important to be smart about your resource allocation. To do this it is useful to understand how GCHP works with respect to distribution of nodes and cores across the grid. At least one unique core is assigned to each face on the cubed sphere, resulting in a constraint of at least six cores to run GCHP. The same number of cores must be assigned to each face, resulting in another constraint of total number of cores being a multiple of six. Communication between the cores occurs only during transport processes.

While any number of cores is valid as long as it is a multiple of six (although there is an upper limit per resolution), you will typically start to see negative effects due to excessive communication if a core is handling less than around one hundred grid cells or a cluster of grid cells that are not approximately square. You can determine how many grid cells are handled per core by analyzing your grid resolution and resource allocation. For example, if running at C24 with six cores each face is handled by one core (6 faces / 6 cores) and contains 576 cells (24x24). Each core therefore processes 576 cells. Since each core handles one face, each core communicates with four other cores (four surrounding faces). Maximizing squareness of grid cells per core is done automatically within runConfig.sh if variable NXNY_AUTO is set to ON.

#### Split a Simulation Into Multiple Jobs

There is an option to split up a single simulation into separate serial jobs. To use this option, do the following:

1. Update runConfig.sh with your full simulation (all runs) start and end dates, and the duration per segment (single run). Also update the number of runs options to reflect to total number of jobs that will be submitted (NUM_RUNS). Carefully read the comments in runConfig.sh to ensure you understand how it works.
2. Optionally turn on monthly diagnostic (Monthly_Diag). Only turn on monthly diagnostics if your run duration is monthly.
3. Use gchp.multirun.run as your run script, or adapt it if your cluster does not use SLURM. It is located in the runScriptSamples subdirectory of your run directory. As with the regular gchp.run, you will need to update the file with compute resources consistent with runConfig.sh. Note that you should not submit the run script directly. It will be done automatically by the file described in the next step.
4. Use gchp.multirun.sh to submit your job, or adapt it if your cluster does not use SLURM. It is located in the runScriptSamples subdirectory of your run directory. For example, to submit your series of jobs, type: ./gchp.multirun.sh

There is much documentation in the headers of both gchp.multirun.run and gchp.multirun.sh that is worth reading and getting familiar with, although not entirely necessary to get the multi-run option working. If you have not done so already, it is worth trying out a simple multi-segmented run of short duration to demonstrate that the multi-segmented run configuration and scripts work on your system. For example, you could do a 3-hour simulation with 1-hour duration and number of runs equal to 3.

The multi-run script assumes use of SLURM, and a separate SLURM log file is created for each run. There is also log file called multirun.log with high-level information such as the start, end, duration, and job ids for all jobs submitted. If a run fails then all scheduled jobs are cancelled and a message about this is sent to that log file. Inspect this and your other log files, as well as output in the OutputDir/ directory prior to using for longer duration runs.

#### Change Domains Stack Size

For runs at very high resolution or small number of processors you may run into a domains stack size error. This is caused by exceeding the domains stack size memory limit set at run-time and the error will be apparent from the message in your log file. If this occurs you can increase the domains stack size in file input.nml. The default is set to 20000000.

### Basic Run Settings

#### Set Cubed Sphere Grid Resolution

GCHP uses a cubed sphere grid rather than the traditional lat-lon grid used in GEOS-Chem Classic. While regular lat-lon grids are typically designated as ΔLat ⨉ ΔLon (e.g. 4⨉5), cubed sphere grids are designated by the side-length of the cube. In GCHP we specify this as CX (e.g. C24 or C180). The simple rule of thumb for determining the roughly equivalent lat-lon resolution for a given cubed sphere resolution is to divide the side length by 90. Using this rule you can quickly match C24 with about 4x5, C90 with 1 degree, C360 with quarter degree, and so on.

To change your grid resolution in the run directory edit the CS_RES integer parameter in runConfig.sh to the cube side-length you wish to use.

#### Turn On/Off Model Components

You can toggle all primary GEOS-Chem components, including type of mixing, from within runConfig.sh. The settings in that file will update input.geos automatically. Look for section Turn Components On/Off, and other settings in input.geos. Other settings in this section beyond component on/off toggles using CH4 emissions in UCX, and initializing stratospheric H2O in UCX.

#### Change Model Timesteps

Model timesteps, both chemistry and dynamic, are configured within runConfig.sh. They are set to match GEOS-Chem Classic default values for low resolutions for comparison purposes but can be updated, with caution. Timesteps are automatically reduced for high resolution runs. Read the documentation in runConfig.sh section Timesteps for setting them.

#### Set Simulation Start and End Dates

Set simulation start and end in runConfig.sh section Simulation Start, End, Duration, # runs. Read the comments in the file for a complete description of the options. Typically a "CAP" runtime error indicates a problem with start, end, and duration settings. If you encounter an error with the words "CAP" near it then double-check that these settings make sense.

### Inputs

#### Change Initial Restart File

All GCHP run directories come with symbolic links to initial restart files for commonly used cubed sphere resolutions. The appropriate restart file is automatically chosen based on the cubed sphere resolution you set in runConfig.sh.

You may overwrite the default restart file with your own by specifying the restart filename in runConfig.sh section Initial Restart File. Beware that it is your responsibility to make sure it is the proper grid resolution.

Unlike GEOS-Chem Classic, HEMCO restart files are not used in GCHP. HEMCO restart variables may be included in the initial species restart file, or they may be excluded and HEMCO will start with default values. GCHP initial restart files that come with the run directories do not include HEMCO restart variables, but all output restart files do.

#### Turn On/Off Emissions Inventories

Because file I/O impacts GCHP performance it is a good idea to turn off file read of emissions that you do not need. You can turn emissions inventories on or off the same way you would in GEOS-Chem Classic, by setting the inventories to true or false at the top of configuration file HEMCO_Config.rc. All emissions that are turned off in this way will be ignored when GCHP uses ExtData.rc to read files, thereby speeding up the model.

For emissions that do not have an on/off toggle at the top of the file, you can prevent GCHP from reading them by commenting them out in HEMCO_Config.rc. No updates to ExtData.rc would be necessary. If you alternatively comment out the emissions in ExtData.rc but not HEMCO_Config.rc then GCHP will fail with an error when looking for the file information.

Another option to skip file read for certain files is to replace the file path in ExtData.rc with /dev/null. However, if you want to turn these inputs back on at a later time you should preserve the original path by commenting out the original line.

There are two steps for adding new emissions inventories to GCHP:

1. Add the inventory information to HEMCO_Config.rc.
2. Add the inventory information to ExtData.rc.

To add information to HEMCO_Config.rc, follow the same rules as you would for adding a new emission inventory to GEOS-Chem Classic. Note that not all information in HEMCO_Config.rc is used by GCHP. This is because HEMCO is only used by GCHP to handle emissions after they are read, e.g. scaling and applying hierarchy. All functions related to HEMCO file read are skipped. This means that you could put garbage for the file path and units in HEMCO_Config.rc without running into problems with GCHP, as long as the syntax is what HEMCO expects. However, we recommend that you fill in HEMCO_Config.rc in the same way you would for GEOS-Chem Classic for consistency and also to avoid potential format check errors.

Staying consistent with the information that you put into HEMCO_Config.rc, add the inventory information to ExtData.rc following the guidelines listed at the top of the file and using existing inventories as examples. You can ignore all entries in HEMCO_Config.rc that are copies of another entry since putting these in ExtData.rc would result in reading the same variable in the same file twice. HEMCO interprets the copied variables, denoted by having dashes in the HEMCO_Config.rc entry, separate from file read.

A few common errors encountered when adding new input emissions files to GCHP are:

1. Your input file contains integer values. Beware that the MAPL I/O component in GCHP does not read or write integers. If your data contains integers then you should reprocess the file to contain floating point values instead.
2. Your data latitude and longitude dimensions are in the wrong order. Lat must always come before lon in your inputs arrays, a requirement true for both GCHP and GEOS-Chem Classic. For more information about this, see the [Preparing_data_files_for_use_with_HEMCO#Ordering_of_the_data|Preparing Data Files for Use with HEMCO wiki page]].
3. Your 3D input data are mapped to the wrong levels in GEOS-Chem (silent error). If you read in 3D data and assign the resulting import to a GEOS-Chem state variable such as State_Chm or State_Met, then you must flip the vertical axis during the assignment. See files Includes_Before_Run.H and setting State_Chm%Species in Chem_GridCompMod.F90 for examples.
4. You have a typo in either HEMCO_Config.rc or ExtData.rc. Error in HEMCO_Config.rc typically result in the model crashing right away. Errors in ExtData.rc typically result in a problem later on during ExtData read. Always try running with the MAPL debug flags on runConfig.sh (maximizes output to gchp.log) and Warnings and Verbose set to 3 in HEMCO_Config.rc (maximizes output to HEMCO.log) when encountering errors such as this. Another useful strategy is to find config file entries for similar input files and compare them against the entry for your new file. Directly comparing the file metadata may also lead to insights into the problem.

### Outputs

#### Output Diagnostics Data on a Lat-Lon Grid

See documentation in the HISTORY.rc config file for instructions on how to output diagnostic collection on lat-lon grids.

#### Output Restart Files at Regular Frequency

The MAPL component in GCHP has the option to output restart files (also called checkpoint files) at regular intervals. Unlike the final restart file output at the end of a simulation, these regularly output restart files contain the date and time in their filename. Enabling this feature is a good idea if you plan on doing a long simulation and you are not splitting your run into multiple jobs. If the run crashes unexpectedly then you can restart mid-run rather than start over from the beginning. To set the checkpoint frequency, simply update the HHmmSS string for "Checkpoint_Freq" in runConfig.rc. Minutes and seconds must each be two digits but hours can be more than two. Each output checkpoint file will include the timestamp in the filename.

#------------------------------------------------
#    Output Restart Files
#------------------------------------------------
# You can output restart files at regular intervals throughout your
# simulation. These restarts are in addition to the end-of-run restart
# which is always produced. To configure output restart file frequency,
# set the variable below to a string of format HHmmSS. More than 2
# digits for the hours string is permitted (e.g. 1680000 for 7 days).
# Setting the frequency to 000000 will turn off this feature by setting
# it to a very large number.
Checkpoint_Freq="000000"


#### Turn On/Off Diagnostics

All GCHP run directories have four collections on by default: time-averaged species concentrations, instantaneous species concentrations, time-averaged meteorology, and instantaneous meteorology. All species are enabled while only a subset of meteorology variables are enabled. There are several other collections already implemented but they are off by default for the standard and benchmark simulations, and on by default for the RnPbBe simulation.

To turn collections on or off, comment ("#") collection names in the "COLLECTIONS" list at the top of file HISTORY.rc.

#===================================================================
# Declare collection names and toggle on/off
#===================================================================
COLLECTIONS: #'AerosolMass'
#'Aerosols',
#'Budget',
#'CloudConvFlux',
#'ConcAfterChem',
#'DryDep',
'Emissions',
#'JValues',
#'LevelEdgeDiags',
#'ProdLoss',
'SpeciesConc',
#'StateChm',
'StateMet_avg',
'StateMet_inst',
#'WetLossConv',
#'WetLossLS',
::


Once a collection is turned on, you can comment diagnostics within it further down in the file by searching for the collection name with ".fields" suffix. Be aware that you cannot comment out the diagnostic that appears on the same line as the fields keyword. If you wish to suppress that specific diagnostic then move it to the next line and replace it with a diagnostic that you want to output.

#===================================================================
# State_Met array diagnostics - time-averaged
StateMet_avg.template:      '%y4%m2%d2_%h2%n2z.nc4',
StateMet_avg.format:        'CFIO',
StateMet_avg.frequency:     010000
StateMet_avg.duration:      010000
StateMet_avg.mode:          'time-averaged'
#'Met_AIRDEN          ', 'GIGCchem',
#'Met_AIRVOL          ', 'GIGCchem',
#'Met_ALBD            ', 'GIGCchem',
'Met_AREAM2           ', 'GIGCchem',
#'Met_AVGW            ', 'GIGCchem',
'Met_BXHEIGHT         ', 'GIGCchem',
etc


#### Set Diagnostic Frequency, Duration, and Mode

All diagnostic collections that come with the run directory have frequency, duration, and mode defined within runConfig.sh. With the exception of SpeciesConc_inst and StateMet_inst, all collections are time-averaged (mode) with frequency and duration set to the simulation length you specified in CopyRunDirs.input when creating the run directory. Any of these defaults can be over-written by editing runConfig.sh. Be aware that manual updates of HISTORY.rc will be over-written by runConfig.sh settings.

#------------------------------------------------
#    Diagnostics
#------------------------------------------------
# Frequency, duration, and mode used for all default HISTORY.rc diagnostic
# collections are set from within this file. These are defined as:
#
#   Frequency = frequency of diagnostic calculation (HHmmSS)
#   Duration  = frequency of diagnostic file  write (HHmmSS)
#   Mode      = computation of diagnostics (time-averaged or instantaneous)
#
# Edit the frequency, duration, and mode below to change global settings.
# See the list further below of what HISTORY.rc collections will be updated.
#
# NOTES:
#  1. Freq and duration hours may exceed 2 digits, e.g. 7440000 for 31 days
#  2. Freq and duration are ignored if Monthly_Diag is set to 1
#  3. If you do not want settings for certain collections set automatically
#     from this file, comment them out below.
#  4. If you add a collection to HISTORY.rc and want its settings
#     automatically updated from this file, add to the list below.
#  5. To turn off collections completely, comment them out in HISTORY.rc.
#
common_freq="010000"          # Ignore if using multi-run monthly diag option
common_dur="010000"           # Ignore if using multi-run monthly diag option
common_mode="'time-averaged'" # "'time-averaged'" and "'instantaneous'"

SpeciesConc_freq=${common_freq} SpeciesConc_dur=${common_dur}
SpeciesConc_mode=${common_mode} AerosolMass_freq=${common_freq}
AerosolMass_dur=${common_dur} AerosolMass_mode=${common_mode}
Aerosols_freq=${common_freq} Aerosols_dur=${common_dur}
Aerosols_mode=${common_mode} Budget_freq=${common_freq}
etc


#### Add a New Diagnostics Collection

Adding a new diagnostics collection in GCHP is the same as for GEOS-Chem Classic netcdf diagnostics. You must add your collection to the collection list in HISTORY.rc and then define it further down in the file. Any 2D or 3D arrays that are stored within State_Met, State_Chm, or State_Diag, and that are successfully incorporated into the GEOS-Chem Registry may be included as fields in a collection. State_Met variables must be preceded by "met_", State_Chm variables must be preceded by "chm_", and State_Diag variables should not have a prefix. See GeosCore/state_diag_mod.F90 for examples of how existing State_Diag arrays are implemented.

Once implemented, you can either incorporate the new collection settings into runConfig.sh for auto-update, or you can manually configure all settings in HISTORY.rc.

#### Generate Monthly Mean Diagnostics

There is an option to automatically generate monthly diagnostics by submitting month-long simulations as separate jobs. Splitting up the simulation into separate jobs is a requirement for monthly diagnostics because MAPL History requires a fixed number of hours set for diagnostic frequency and file duration. The monthly mean diagnostic option automatically updates HISTORY.rc diagnostic settings each month to reflect the number of days in that month taking into account leap years.

To use the monthly diagnostics option, first read and follow instructions for splitting a simulation into multiple jobs (see separate section on this page). Prior to submitting your run, enable monthly diagnostics in runConfig.sh by searching for variable "Monthly_Diag" and changing its value from 0 to 1. Be sure to always start your monthly diagnostic runs on the first day of the month.

See file GCHP/Shared/MAPL_Base/TeX/HistoryIntro.tex for original MAPL documentation on MAPL History. Please note that we have not tested all of these functionalities and some of them to seem to not work in MAPL. Proceed with caution and let the GEOS-Chem Support Team know what you find. Here is a brief overview of options that may be included for each collection that is taken from that document:

template Character string defining the time stamping template that is appended to collection to create a particular file name. The template uses GrADS convensions. The default value depends on the duration of the file.

descr Character string describing the collection. Defaults to expdsc'.

format Character string to select file format ("CFIO", "CFIOasync", "flat"). "CFIO" uses MAPL_CFIO and produces netcdf output. "CFIOasync" uses MAPL_CFIO but delegates the actual I/O to the MAPL_CFIOServer (see MAPL_CFIOServer documenation for details). Default = "flat".

frequency Integer (HHHHMMSS) for the frequency of time groups in the collection. Default = 060000.

mode Character string equal to instantaneous' or time-averaged'. Default = 'instantaneous'.

acc_interval Integer (HHHHMMSS) for the acculation interval ($\le$ frequency) for time-averaged diagnostics. Default = frequency; ignored if mode is instantaneous'.

ref_date Integer (YYYYMMDD) reference date for {\em frquency}; also the beginning date for the collection. Default is the Start date on the Clock.

ref_time Integer (HHMMSS) Same a ref_date.

end_date Integer (YYYYMMDD) ending date to stop diagnostic output. Default: no end

end_time Integer (HHMMSS) ending time to stop diagnostic output. Default: no end.

duration Integer (HHHHMMSS) for the duration of each file. Default = 00000000 (everything in one file). Duration is not currently functional in GCHP and will be ignored. Frequency is used instead for write frequency.

resolution Optional resolution (IM JM) for the ouput stream. Transforms betwee two regulate LogRect grid in index space. Default is the native resolution.

xyoffset Optional Flag for output grid offset when interpolating. Must be between 0 and 3. (Cryptic Meaning: 0:DcPc, 1:DePc, 2:DcPe, 3:DePe). Ignored when resolution results in no interpolation (native). Default: 0 (DatelineCenterPoleCenter).

levels Optional list of output levels (Default is all levels on Native Grid). If vvars is not specified, these are layer indices. Otherwise see vvars, vunits, vscale.

vvars Optional field to use as the vertical coordinate and functional form of vertical interpolation. A second argument specifies the component the field comes from. Example 1: the entry 'log(PLE)','DYNAMICS' uses PLE from the FV3 advection component as the vertical coordinate and interpolates to levels linearly in its log. Example 2: 'THETA','DYN' a way of producing isentropic output. Only log(*), pow(*), and real number and straight linear interpolation are supported.

vunit Character string to use for units attribute of the vertical coordinate in file. The default is the MAPL_CFIO default. This affects only the name in the file. It does not do the conversion. See vscale

vscale Optional Scaling to convert VVARS units to VUNIT units. Default: no conversion.

regrid_exch Name of the exchange grid that can be used for interpolation between two LogRect grids or from a tile grid to a LogRect grid. Default: no exchange grid interpolation. irregular grid.

regrid_name Name of the Log-Rect grid to interpolate to when going from a tile to Field to a gridde output. regrid_exch must be set, otherwise it is ignored.

conservative Set to a non-zero integer to turn on conservative regridding when going from a native cube-sphere grid to lat-lon output. Default: 0

deflate Set deflate level (0-9) of NETCDF output when format is CFIO or CFIOasync. Default: 0

subset Optional subset (lonMin lonMax latMin latMax) for the output when performing non-conservative cube-sphere to lat-lon regridding of the output.

chunksize Optional user specified chunking of NETCDF output when format is CFIO or CFIOasync, (Lon chunksize, Lat chunksize, Lev chunksize, Time chunksize)

### Debugging

#### Enable Maximum Print Output

Besides compiling with "make compile_debug", there are a few run settings you can configure to boost your chance of successful debugging. All of them involve sending additional print statements to the log files.

1. Change "ND70" in input.geos from 0 to 1 to turn on extra GEOS-Chem print statements in the main log file.
2. Set the "MAPL_DEBUG_LEVEL" variable in runConfig.sh to a number greater than 0 to turn on extra MAPL print statements in MAPL ExtData. This is useful if you are having a problem reading input files. The higher the number the more prints will be sent to the log (and the slower your run will be). Usually 20 is sufficient, although you can go higher. Please be sure to remember to set MAPL_DEBUG back to 0 when you are done so as not to severely slow down your runs!
3. Set the "Verbose" and "Warnings" settings in HEMCO_Config.rc to maximum values of 3 to send the maximum number of prints to HEMCO.log.
4. Set the "MEMORY_DEBUG_LEVEL" option, new in 12.5.0, to 1 to turn on additional memory usage prints per timestep.
#------------------------------------------------
#    Debug Options
#------------------------------------------------
# Set MAPL debug flag to 0 for no extra MAPL debug log output, or 1 to
# print information to log. Using this flag is most helpful for debugging
# issues with file read (MAPL ExtData).
#
# Set memory debug flag to 0 to print memory only once per timestep. Set to
# 1 to enable memory prints at additional locations throughout the run.
#
# For GEOS-Chem debug prints, turn on ND70 in input.geos manually.
#
# WARNING: Turning on debug prints significantly slows down the model!
#
MAPL_DEBUG_LEVEL=0
MEMORY_DEBUG_LEVEL=0


None of these options require recompiling. Be aware that all of them will slow down your simulation. Be sure to set them back to the default values after you are finished debugging.

#### Turn On/Off MAPL Timers and Memory Logging

Your GCHP log file will include timing and memory information by default, and this is usually a good thing. If for some reason you want to turn these features off you can do so in file CAP.rc. Search for "MAPL_ENABLE_TIMERS" and "MAPL_ENABLE_MEMUTILS" and simply change "YES" to "NO". Remember to turn them back on again if you later need to to debug.