Creating GEOS-Chem run directories

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Revision as of 16:27, 22 December 2015 by Lizzie Lundgren (Talk | contribs) (Generating a GEOS-Chem Run Directory)

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On this page we show you how to use the GEOS-Chem Unit Tester to generate and use fresh copies of run directories for your GEOS-Chem simulations.

Downloading the GEOS-Chem Unit Tester

First, make sure that your system has these software packages installed. (Most of these come standard with your Unix-based operating system.)

Next, clone the GEOS-Chem Unit Tester package with the command:

git clone -b v10-01-Release git://git.as.harvard.edu/bmy/GEOS-Chem-UnitTest UT

This will create a copy of the GEOS-Chem Unit Tester package in a directory named UT for short.

The option

-b v10-01-Release

specifies which branch of the GEOS-Chem Unit Tester that you would like to download. Branches in the GEOS-Chem unit tester correspond to each internal version of GEOS-Chem (i.e. the states of the code for which we run 1-month benchmark simulations), as well as the publicly-released versions. Most likely, you will want to download the v10-01-public branch of the GEOS-Chem Unit Tester, which corresponds to the public release of GEOS-Chem v10-01.

NOTE: The Git clone process may take a few of minutes to complete, depending on your connection speed.

--Bob Y. 12:25, 1 May 2015 (EDT)

Available run directories

Benchmark run directory

The GEOS-Chem Unit Tester includes a run directory called geosfp_4x5_benchmark. As of May 2015, the standard GEOS-Chem benchmark simulation utilizes the GEOS-FP met fields (4° x 5 °, 72 levels) with the UCX tropospheric-stratospheric chemistry mechanism and secondary organic aerosols included.

To reproduce our latest 1-month benchmark simulation for v10-01, you can edit the CopyRunDirs.input file so that the following line is uncommented under RUNS:

 geosfp   4x5         -      benchmark    2013070100   2013080100   UCX=y

Make sure to check the start and end date so that your simulation will run for July 2013. You can then create the GEOS-Chem benchmark run directory by typing gcCopyRunDirs. Navigate to your the newly created geosfp_4x5_benchmark run directory. To compile and run your benchmark simulation, type:

make -j4 mp

To compile only, type:

make -j4 mpbuild

That will create a geos.mp executable file that you can use to submit your GEOS-Chem benchmark simulation to a queue system.

NOTE: If you are compiling GEOS-Chem within the code directory, and not within a run directory created from the GEOS-Chem Unit Tester, you will need to pass the UCX=y option in your make command.

--Melissa Sulprizio (talk) 19:38, 23 June 2015 (UTC)

Other run directories

Run directories are provided for a combination of met field, grid, and simulation type and are named accordingly (e.g. geosfp_4x5_UCX). For more details on the simulation types, please see our GEOS-Chem chemistry mechanism wiki page.

The following table summarizes the run directories that are available in the GEOS-Chem Unit Tester. Please choose the run directory or run directories that are most relevant for your research.

Met field Grid NOx-Ox-
HC-aerosol
UCX RRTMG soa soa_svpoa RnPbBe Hg POPs tagCO tagO3 CH4 CO2 aerosol TOMAS40
geosfp 4x5
geosfp 2x25
geosfp 025x03125
CH
geosfp 025x03125
NA
geos5 4x5
geos5 2x25
geos5 05x0666
CH
geos5 05x0666
NA
merra 4x5
merra 2x25
geos4 4x5
gcap 4x5

LEGEND

Run directory is available
Run directory is in need of updating
Run directory is obsolete
Run directory is not available

--Melissa Sulprizio (talk) 17:36, 26 May 2015 (UTC)

Editing the CopyRunDirs.input file

Once you have downloaded the GEOS-Chem Unit Tester to your disk space, switch to the perl/ directory:

cd UT/perl

In this directory there is a Perl script named gcCopyRunDirs that you will use to generate fresh copies of GEOS-Chem run directories. This script uses an input file named CopyRunDirs.input, which is also located in the perl directory.

Your CopyRunDirs.input file will look something like this:

#------------------------------------------------------------------------------
#                  GEOS-Chem Global Chemical Transport Model                  !
#------------------------------------------------------------------------------
#BOP
#
# !DESCRIPTION: Input file that specifies configuration for creating and
#  copying a run directory from the UnitTester. 
#\\
#\\
# !REMARKS:  
#  Customize the run directory for your system by specifying these values:
#  -------------------------------------------------------------------
#  VERSION     : A tag used to identify this Unit Test (e.g. v10-01h)
#  DESCRIPTION : A short description of this file's run dir copy configuration
#  COPY_PATH   : Local path where run directory will be copied to
#  DATA_ROOT   : Root GEOS-Chem data directory
#  HEMCO_ROOT  : Root directory where HEMCO emissions data files are stored 
#  RUN_ROOT    : Unit test run directories are subdirectories of RUN_ROOT
#  RUN_DIR     : Individual unit test run directory path
#  PERL_DIR    : Unit Test perl script directory (i.e. this directory)
#  COPY_CMD    : Unix copy command with optional tags
#  VERBOSE     : HEMCO verbose level  (0=no output, 3=max output)
#  WARNINGS    : HEMCO warnings level (0=no warnings, 3=max warnings)
#
# !REVISION HISTORY:
#  18 Mar 2015 - R. Yantosca - Initial version
#  19 Mar 2015 - E. Lundgren - Simplify content for only copying run dirs
#EOP
#------------------------------------------------------------------------------
#
# !INPUTS:
#
   VERSION     : v10-01
   DESCRIPTION : Create run directory from UnitTest
   COPY_PATH   : /home/{USER}/GC/rundirs
   DATA_ROOT   : /as/data/geos/ExtData
   HEMCO_ROOT  : {DATAROOT}/HEMCO
   RUN_ROOT    : /home/{USER}/UT/runs
   RUN_DIR     : {RUNROOT}/{RUNDIR}
   PERL_DIR    : /home/{USER}/UT/perl
   COPY_CMD    : cp -rfL
   VERBOSE     : 0
   WARNINGS    : 1
#
# !RUNS:
#  Specify the debugging runs that you want to perform below.
#  Here we provide a few examples, but you may copy additional entries from
#  UnitTest.input and modify the dates as needed. You can deactivate copying
#  run certain directories by commenting them out with "#".
#
#--------|-----------|------|------------|------------|------------|---------|
# MET    | GRID      | NEST | SIMULATION | START DATE | END DATE   | EXTRA?  |
#--------|-----------|------|------------|------------|------------|---------|
  geosfp   4x5         -      fullchem     2013070100   2013070101   -
  geosfp   4x5         -      soa          2013070100   2013070101   -
  geosfp   4x5         -      soa_svpoa    2013070100   2013070101   -
  geosfp   4x5         -      UCX          2013070100   2013070101   UCX=y
  geosfp   4x5         -      RRTMG        2013070100   2013070101   RRTMG=y
  geosfp   4x5         -      RnPbBe       2013070100   2013070101   -
  geosfp   4x5         -      Hg           2013070100   2013070101   -
  geosfp   4x5         -      POPs         2013070100   2013070101   -
  geosfp   4x5         -      CH4          2013070100   2013070101   -
  geosfp   4x5         -      tagO3        2013070100   2013070101   -
  geosfp   4x5         -      tagCO        2013070100   2013070101   -
  geosfp   2x25        -      CO2          2013070100   201307010030 -
  geosfp   4x5         -      aerosol      2013070100   2013070101   - 
  geosfp   025x03125   ch     fullchem     2013070100   201307010010 -
  geosfp   025x03125   na     fullchem     2013070100   201307010010 -
!END OF RUNS:
#EOP
#------------------------------------------------------------------------------

NOTE: Lines starting with a # character will be treated as comments.

The CopyRunDirs.input file has a layout that is very similar to the GEOS-Chem Unit Tester input files (UnitTest.input located within this directory). Like the GEOS-Chem Unit Tester input files, CopyRunDirs.input is composed of an INPUTS section and a RUNS section, which are described below.

Section 1: INPUTS

Under the INPUTS section, you can customize the directory paths and other options for your system. Each configurable input is described in the table below.

Option Description
VERSION An ID tag that will be added to all log files and output files.
DESCRIPTION A short (1-sentence) description of the purpose of this specific file (optional). This may be used to differentiate different input files, such as if you pre-configure several for future re-use.
COPY_PATH Specifies the root directory on your disk server where copies of the GEOS-Chem run directories will be created.
DATA_ROOT Specifies the path for your root-level data directory.
HEMCO_ROOT Specifies the top-level path for the HEMCO data directory tree.
  • The {DATAROOT} token in HEMCO_ROOT will be replaced with the value you specify for RUN_ROOT option.

Leave this as-is.

RUN_ROOT Specifies the top-level unit test run directories.

Leave this as-is.

PERL_DIR Specifies the directory where the unit test Perl scripts are found.

Leave this as-is.

COPY_CMD Specifies the command used to copy run directories from the GEOS-Chem Unit Tester to COPY_PATH.
  • The default setting is cp -rfL. This will create a new copy of the directory, even if the prior copy exists.
  • The -L option to the cp will create "hard" copies of files that are symbolic links. This command may differ slightly depending on the flavor of your Unix-based Operating system.
VERBOSE Specifies the level of debug output that will be sent to the HEMCO log file. (0=no debug output; 3=max debug output)
  • Recommended setting: 0
WARNINGS Specifies the level of warning messages that will be sent to the HEMCO log file. (0=no warnings; 3=max warnings)
  • Recommended setting: 1

--Bob Y. (talk) 22:38, 19 May 2015 (UTC)

Section 2: RUNS

The layout of the RUNS section is identical to the RUNS section in the GEOS-Chem Unit Tester input file. This enables copying and pasting simulation settings text from UnitTest.input into CopyRunDirs.input.

For example, the following line:

#
# !RUNS:
#  Specify the debugging runs that you want to perform below.
#  You can deactivate runs by commenting them out with "#".
#
#--------|-----------|------|------------|------------|------------|---------|
# MET    | GRID      | NEST | SIMULATION | START DATE | END DATE   | EXTRA?  |
#--------|-----------|------|------------|------------|------------|---------|
  geosfp   4x5         -      fullchem     2013070100   2013070101   -

will tell the gcCopyRunDirs script to create a run directory for a GEOS-Chem simulation using:

The date range will be used to initialize the input.geos file that is read during a GEOS-Chem simulation. Once the run directory is created, you may edit these dates within the input.geos file. Note, however, that time ranges must remain within the time range covered by the MET field you are using. You can check the MET field temporal coverage on the GMAO met data products wiki page. Also note that we recommend using the restart files to spin up GEOS-Chem for at least one year prior to your simulation start date. You may use the resulting output restart files as initial values for your simulation.

You can add as many entries to the RUNS section as you wish. Simply comment out the lines containing runs you may wish to copy in the future.

Generating a GEOS-Chem Run Directory

Once you have edited the CopyRunDirs.input script to your liking, you can use that to generate fresh copies of GEOS-Chem run directories. Make sure you are in the perl directory, and then type:

gcCopyRunDirs

If you do not pass a file name to gcCopyRunDirs, then the gcCopyRunDirs script will use the CopyRunDirs.input file that you just created.

If you wish, you can create many customized copies of CopyRunDirs.input. For example, suppose you edit CopyRunDirs.input to generate a full-chemistry run directory. You can then save it as a separate file and use it explicitly with gcCopyRunDirs.

cp CopyRunDirs.input CopyRunDirs.fullchem   # Input file set up to only copy the full-chemistry run directories
 
gcCopyRunDirs CopyRunDirs.Hg                 

Executing gcCopyRunDirs will create a new GEOS-Chem run directory corresponding to each entry that you specified in the input file RUNS. Each run directory will be created as a subdirectory of COPY_PATH that you specified in the input file INPUTS section.

Let's examine the contents of a sample geosfp_4x5_fullchem run directory. Issue the following commands:

cd ~/GC/rundirs/geosfp_4x5_fullchem  # Change to geosfp_4x5_fullchem run dir 
  
make fileclean                       # Remove any files left over from previous unit test runs

ls -l                                # Get detailed directory listing

And you will see this directory listing:

-rw-r--r-- 1 mpayer mpayer     7862 2015-04-03 15:19 FJX_j2j.dat
-rw-r--r-- 1 mpayer mpayer    44808 2015-04-03 15:19 FJX_spec.dat
-rw-r--r-- 1 mpayer mpayer   186359 2015-04-03 15:19 HEMCO_Config.rc
-rw-r--r-- 1 mpayer mpayer     4872 2015-04-03 15:19 Makefile
-rw-r--r-- 1 mpayer mpayer      783 2015-04-03 15:19 README
-rw-r--r-- 1 mpayer mpayer      610 2015-04-03 15:19 chemga.dat
-rw-r--r-- 1 mpayer mpayer    42186 2015-04-03 15:19 dust.dat
-rwxr-xr-x 1 mpayer mpayer     1458 2015-04-03 15:19 getEnd.pl*
-rwxr-xr-x 1 mpayer mpayer     1374 2015-04-03 15:19 getStart.pl*
-rw-r--r-- 1 mpayer mpayer   199632 2015-04-03 15:19 globchem.dat
-rw-r--r-- 1 mpayer mpayer   401972 2015-04-03 15:19 HEMCO_restart.200607010000.nc
-rw-r--r-- 1 mpayer mpayer 41110480 2015-04-03 15:19 initial_trac_rst.geosfp_4x5_fullchem
-rw-r--r-- 1 mpayer mpayer    15913 2015-04-03 15:19 input.geos
-rw-r--r-- 1 mpayer mpayer    26194 2015-04-03 15:19 jv_spec_mie.dat
-rw-r--r-- 1 mpayer mpayer      905 2015-04-03 15:19 mglob.dat
-rw-r--r-- 1 mpayer mpayer    42185 2015-04-03 15:19 org.dat
-rw-r--r-- 1 mpayer mpayer    42185 2015-04-03 15:19 so4.dat
-rw-r--r-- 1 mpayer mpayer    42186 2015-04-03 15:19 soot.dat
-rw-r--r-- 1 mpayer mpayer    42185 2015-04-03 15:19 ssa.dat
-rw-r--r-- 1 mpayer mpayer    42185 2015-04-03 15:19 ssc.dat
-rwxr-xr-x 1 mpayer mpayer     7303 2015-04-03 15:19 validate*

NOTE: Run directories for other simulations may contain other files not pictured here.

The input.geos and HEMCO_Config.rc files have been customized for this particular simulation. They were created from the corresponding template files input.geos.template and HEMCO_Config.template in the Unit Tester. The Perl script getRunInfo is used by the Makefile to extract information about the simulation from input.geos. HEMCO and tracer restart files are also included in every run directory but care must be taken when using them. See the section below for more information about restart files.

Important notes about restart files

  • The date for the two restart files is shown in the filename of the HEMCO restart file (e.g. HEMCO_restart.200607010000.nc).
  • Restart files included in the run directory are for use with spinning up the model to the start date of your production run. We recommend running GEOS-Chem for at least one year to generate new restart files prior to performing your intended simulations. For the case of tagged ozone, we recommend spinning up the model for 10 years.
  • In your spin-up run, you can use the default tracer restart file (initial_trac_rst.{RUNDIR_NAME}) if your start date is a different year but the same month as the original date of the file.
  • In your spin-up run, you can only use the HEMCO restart file (HEMCO_restart.{DATE}.nc) if your start date is exactly the same as the original date of the file. If using a different date, use default emissions values by setting 'HEMCO_RESTART' from 'true' to 'false' in HEMCO_Config.rc. Remember to re-enable the HEMCO restart file after your spin-up run to use the newly generated HEMCO restart file corresponding to your production run start date.

--Lizzie Lundgren (talk) 16:24, 22 December 2015 (UTC)

Tips and tricks for creating run directories

  • In each run directory, we provide a GEOS-Chem restart file that you can use to initialize your simulation. However, it is highly recommended that you not use these restart files for any of your production runs. Rather, you will want to generate your own restart file by spinning up the model for at least a year. See the "Important notes about restart files" section above.
  • You can create a run directory for the nested grid simulations from a 4° x 5° or 2° x 2.5° run directory by following these steps:
    1. Modify the input.geos file for the nested grid simulation. Complete instructions can be found on this wiki page.
    2. Regrid the restart file(s) using the GAMAP regridding routines. For example, REGRIDH_RESTART can be used to regrid the tracer restart file from one horizontal resolution to another. You can then use CREATE_NESTED to crop the restart file to your nested domain (CH, EU, or NA).
  • You can create a MERRA run directory from a GEOS-5 or GEOS-FP run directory, since all three met fields have the same horizontal and vertical resolution. Gabriele Curci found found that the following procedure can be used to create a MERRA run directory from a GEOS-FP run directory (using a geosfp_4x5_UCX run directory as an example).
    1. Create a run directory for GEOS-FP using gcCopyRunDirs
    2. Type cp -R geosfp_4x5_UCX merra_4x5_UCX
    3. Type cd merra_4x5_UCX
    4. Type rename geosfp merra *
    5. Open input.geos in a text editor and change all the occurrences of "geosfp" to "merra"
    6. Type make superclean
    7. Type make distclean in the Code dir
    8. Compile and run
  • If you would like to run a simulation and the run directory is not available in the Unit Tester, you can follow these steps:
    1. Modify the input.geos file for your simulation type following the relevant checklist in Chapter 6 of the GEOS-Chem Manual.
    2. Create a "fake" restart file using GAMAP routine MAKE_RESTART.
    3. Alternatively, you can send an email to the relevant Working Group to see if another member can provide you with a run directory or restart file.

--Melissa Sulprizio (talk) 18:42, 26 August 2015 (UTC)

Compiling and Running GEOS-Chem

Once you have created one or more GEOS-Chem run directories, you may use them for your GEOS-Chem simulations. First, double-check that the settings in the input.geos and HEMCO_Config.rc files are correct for the simulation that you are trying to run. See the GEOS-Chem Manual for more information about setting simulation options. See the "Important notes about restart files" above for important information about use of restart files and spinning up the model.

Next, open the Makefile in a text editor and define the variables CODE_DIR, LOG_DIR, and VERSION specific to your simulation. CODE_DIR is the path to the GEOS-Chem source code you wish to use. LOG_DIR is the path to which you wish to send your log files. VERSION is text you wish to include as a prefix in your output log filename. You can also pass any of these three variables manually to the make command, overwriting the definitions stored in the Makefile.

To start a GEOS-Chem simulation, type the following commands. (We'll use the example of the geosfp_4x5_fullchem simulation, from the previous sections.)

make -j4 TRACEBACK=y mp

The above command turns on traceback for debugging and invokes the mp target in the Makefile. This compiles the source code at path CODE_DIR with OpenMP parallelization and then runs the resultant GEOS-Chem executable using the simulation settings in the configuration files. The suffix .mp is included in each output filename to indicate that you enabled OpenMP parallelization for your GEOS-Chem run.

There are many other targets you may use with make. For example, you can use target sp to compile and run code using a single processor rather than multiple processors. This is useful for generating a baseline from which you can diagnose and debug parallelization errors. Output files will have a .sp rather than .mp suffix to distinguish them from the OpenMP parallelized run output. Alternatively, you can build GEOS-Chem source code without running a simulation (mpbuild or spbuild) or run a simulation without rebuilding (mprun or sprun). There are also several housekeeping targets that clean the run directory (e.g. mpdataclean, mpexeclean, mplogclean, and mpclean) and the source code (e.g. realclean).

See the Makefile for all make options and the GEOS-Chem Makefile Structure wiki page wiki page for more information about compiling GEOS-Chem and using the run directory Makefile.

--Lizzie Lundgren 13:12, 15 April 2015 (EDT)

GEOS-Chem Output Files

Once the GEOS-Chem simulation is complete, you will see several new files in the run directory. Some of these are generated for all simulations while others may be simulation-dependent. For the case of our full-chemistry simulation example, the following files are output:

File Description
trac_avg.geosfp_4x5_fullchem.YYYYMMDDhh.mp or
trac_avg.geosfp_4x5_fullchem.YYYYMMDDhh.sp
Diagnostic output file that contains time-averaged output for diagnostics enabled in input.geos.

Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP.

trac_rst.geosfp_4x5_fullchem.YYYYMMDDhhmm.mp or
trac_rst.geosfp_4x5_fullchem.YYYYMMDDhhmm.sp
Tracer restart file that contains instantaneous tracer concentrations at simulation end time. This file saves instantaneous concentrations of all transported tracers (listed in the Tracer Menu of input.geos) on all levels and may be used to initialize another GEOS-Chem simulation.

Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP.

HEMCO_restart.YYYYMMDDhh.nc.mp or
HEMCO_restart.YYYYMMDDhh.nc.sp
HEMCO restart file containing several quantities tracked by HEMCO for use in initializing another GEOS-Chem simulation. This file includes data used to calculate soil NOx emissions, PARANOX ship plume chemistry, and MEGAN biogenic emissions.

Data in this file are in netcdf format.

v10-01.geosfp_4x5_fullchem.mp or
v10-01.geosfp_4x5_fullchem.sp
GEOS-Chem simulation log file.

Open this file in a text editor to diagnose compile and run errors.

HEMCO.log.mp or
HEMCO.log.sp
HEMCO log file containing detailed information about the emissions read from disk into HEMCO.

Open this file in a text editor to diagnose HEMCO errors.

smv2.log SMVGEAR II log file containing information about reactions and species used by the ND65 prod-loss diagnostic. This file is only produced when SMVGEAR, and thus it will not be created for the specialty simulations.

Open this file in a text editor to see if SMVGEAR read the globchem.dat file properly.

diaginfo.dat File generated by GEOS-Chem that contains diagnostic quantities for use with GAMAP.
tracerinfo.dat File generated by GEOS-Chem that contains tracer name metadata for use with GAMAP.


Additional files may be created by GEOS-Chem, depending on your simulation type and the options specified in the input.geos file. Other optional GEOS-Chem output files include:

File Description
spec_rst.geosfp_4x5_fullchem.YYYYMMDDhh Species restart file that contains instantaneous species concentrations at simulation end time. This file saves instantaneous concentrations of all chemical species (listed in globchem.dat) on all levels and may be used to initialize another GEOS-Chem simulation.

NOTE: If you are going to be running a very long GEOS–Chem simulation and must split your simulation into several stages (i.e. in order to stay within the computational time limits of your system), then you should set LSVCSPEC to T in the Chemistry Menu of input.geos. That will make sure that the chemical species concentrations are preserved when the next run stage starts. Otherwise, GEOS-Chem use the default species concentrations specified in globchem.dat at the beginning of each run.

Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP.

stations.YYYYMMDDhh Diagnostic output file that contains ND48 station timeseries output as specified in input.geos.

Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP. For more information on working with ND48 timeseries output, see our timeseries tutorial.

tsYYYYMMDDhh.bpch Diagnostic output file that contains ND49 instantaneous timeseries output as specified in input.geos.

Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP. For more information on working with ND49 timeseries output, see our timeseries tutorial.

ts_24hr_avg.YYYYMMDDhh.bpch Diagnostic output file that contains ND50 24-hour average timeseries output as specified in input.geos.

Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP.

ts_satellite.YYYYMMDDhh.bpch Diagnostic output file that contains ND51 local-time-average (satellite) timeseries output as specified in input.geos.

Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP.

paranox_ts.YYYYMMDDhh.bpch Diagnostic output file that contains ND63 ship timeseries output as specified in input.geos.

Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP.

ocean_rst.YYYYMMDDhhmm.nc Ocean mercury restart file containing several quantities pertaining to the ocean mercury module saved at the end of the GEOS-Chem simulation. Like the tracer restart file, this file may be used to initialize another GEOS-Chem mercury simulation.

Data in this file are in the in netcdf format.

plane.log.YYYYMMDD</tt?> Diagnostic output file containing planeflight information scheduled via the <tt>Planeflight.dat file. This diagnostic is turned on in the Planeflight Menu of input.geos.

The data in this text file can be read and plotted using GAMAP routines CTM_READ_PLANEFLIGHT and PLANE_PLOT.

--Melissa Sulprizio 15:42, 3 April 2015 (EDT)