View source for Running GEOS-Chem

__FORCETOC__
'''''[[Compiling GEOS-Chem|Previous]] | [[GEOS-Chem output files|Next]] | [[Getting Started with GEOS-Chem]]'''''
#[[Minimum system requirements for GEOS-Chem|Minimum system requirements]]
#[[Downloading GEOS-Chem source code|Downloading source code]]
#[[Downloading GEOS-Chem data directories|Downloading data directories]]
#[[Creating GEOS-Chem run directories|Creating run directories]]
#[[GEOS-Chem input files|Configuring runs]]
#[[Compiling GEOS-Chem|Compiling]]
#<span style="color:blue">'''Running'''</span>
#[[GEOS-Chem output files|Output files]]
#[[Guide_to_visualization_and_analysis_tools_for_GEOS-Chem|Visualizing and processing output]]
#[[GEOS-Chem_coding_and_debugging|Coding and debugging]]
#[[GEOS-Chem_overview#Further_reading|Further reading]]


== Overview ==

This page presents the basic information needed to run GEOS-Chem as well as how to verify a successful run and reuse a run directory.

== Important things to know before you submit your run ==

#Please be aware of several options available for speeding up your GEOS-Chem simulations. See our ''[[Speeding up GEOS-Chem]]'' page for more information.
#The initial restart files do not reflect the actual atmospheric state and should only be used to "spin up" the model. In other words, they should be used as initial values in an initialization simulation to generate more accurate initial conditions for your production runs. See [[GEOS-Chem_basics#Restart_files|this wiki post]] for more information.
#Prior to running with GEOS-FP met fields, please be aware of several caveats regarding that data stream. See the [[GEOS-FP|GEOS-FP]] wiki page for more information.

== Pre-run checklist ==

Prior to running GEOS-Chem, always run through the following checklist to ensure everything is set up properly. 

#Your Unix run-time environment [[Check_if_netCDF_is_already_installed_on_your_system|contains a netCDF library installation]]
#Your run directory contains the [[Compiling_GEOS-Chem|executable <tt>geos</tt>]]
#You have looked through and set all configurable settings in the following files:
##[[GEOS-Chem_input_files#The_input.geos_file|<tt>input.geos</tt>]] (general simulation settings)
##[[GEOS-Chem_input_files#The_HEMCO_Config.rc_file|<tt>HEMCO_Config.rc</tt>]] (emissions settings)
##[[GEOS-Chem_input_files#The_HISTORY.rc_file|<tt>HISTORY.rc</tt>]] (diagnostic output settings)
#You have a run script ([[Running_GEOS-Chem#Running_as_a_Batch_Job|see below]])
#Your run script has the proper environment variables defined for OpenMP parallelization
##[[Setting_Unix_environment_variables_for_GEOS-Chem#OMP_NUM_THREADS|<tt>OMP_NUM_THREADS</tt>]]
##[[Setting_Unix_environment_variables_for_GEOS-Chem#OMP_STACKSIZE|<tt>OMP_STACKSIZE</tt>]]
#You have enough [[Minimum_system_requirements_for_GEOS-Chem#Hardware_Recommendations|memory and computational cores available]]

== How to run GEOS-Chem ==

You can run GEOS-Chem locally from within your run directory (interactively) or by submitting your run to your cluster's job scheduler. 

=== Running Interactively ===

If your computer system allows interactive computational sessions, then you can run GEOS-Chem interactively.  This is useful if you need to run short simulations for debugging or testing.  

''NOTE: If you are working with GEOS-Chem on the Amazon Web Services cloud computing platform, then you can always run GEOS-Chem interactively, because you will not be sharing your computational environment with other users.  See [http://cloud.geos-chem.org '''cloud.geos-chem.org'''] for more information.''

To run GEOS-Chem interactively in your terminal window, 

First, make sure that you have set the proper [[Setting Unix environment variables for GEOS-Chem|Unix environment variables for GEOS-Chem]] in your interactive session.  

Then navigate to your run directory and type:

 ./geos.mp

You may also send the GEOS-Chem output to a log file by using:

 ./geos.mp > GC.log

You may send the GEOS-Chem output to a log file and to your screen using:

 ./geos.mp 2>&1 | tee GC.log

=== Running as a Batch Job ===

You can then submit your GEOS-Chem simulation to your local cluster's queue using a simple script. For example:

 #!/bin/bash
 
 # Load your environment settings
 source ~/.bashrc
 
 # Declare that we would like to run GEOS-Chem with 16 cores
 # (change this for your system)
 export OMP_NUM_THREADS=16
 
 # Max out the stack memory for the simulation.
 # If your system has less than 500 MB then it should still
 # give you the max amount available, which should be sufficient.
 export OMP_STACKSIZE=500m
 
 # Run the GEOS-Chem executable, and pipe output to a log file
 ./geos.mp >> GC.log


A sample run script [https://github.com/geoschem/geos-chem-unittest/blob/master/runs/4x5_benchmark/benchmark.run <tt>benchmark.run</tt>] can also be found in the [[GEOS-Chem Unit Tester]]. This run script is set up for the SLURM scheduler and can be submitted using the command <tt>sbatch benchmark.run</tt>. If your cluster utilizes a different job schedule, you may create your own run script or modify the sample run script as needed.

== Verifying a Successful Run ==

There are several ways to verify that your run was successful. 

# The following output can be found at the end of your GEOS-Chem log file:
#:<code>**************   E N D   O F   G E O S -- C H E M   **************</code>
# NetCDF files (<tt>GEOSChem.*.nc4</tt>) are present in the run directory directory. 
# Your scheduler log (e.g. output from SLURM) does not contain any obvious errors.

If your run stopped with an error, please the following resources:
* [[Common GEOS-Chem error messages]]
* [[GEOS-Chem coding and debugging#GEOS-Chem debugging tips|Tips on how to debug GEOS-Chem effectively]]
* [[Submitting GEOS-Chem support requests]]

== Submitting consecutive runs ==

Often, users will split long simulations into several smaller simulations to stay within their cluster's computational limits. When doing so, make sure you follow these guidelines to minimize differences in model output:

1. Turn off setting initial stratospheric H2O mixing ratios in input.geos:
    => Set initial glob MRs:---
       => strat. H2O?      : F

2. Make sure <tt>GC_RESTART</tt> and <tt>HEMCO_RESTART</tt> options are set to <b><tt>true</tt></b> in HEMCO_Config.rc.

:To ensure you restart files are read and species concentrations are properly initialized, you may check your GEOS-Chem log file for the following output:

   ===============================================================================
   R E S T A R T   F I L E   I N P U T
 
   Min and Max of each species in restart file [mol/mol]:
   Species   1,       NO: Min = 1.000000003E-30  Max = 1.560991691E-08
   Species   2,       O3: Min = 3.135925075E-09  Max = 9.816152669E-06
   Species   3,      PAN: Min = 3.435056848E-25  Max = 1.222619450E-09
   ...

:Actual values may differ. If you see "<tt>Use background = ...</tt>" for most/all species, that suggests your restart file was not found. To avoid using the wrong restart file make sure to use time cycle flag <b><tt>EY</tt></b> in HEMCO_Config.rc to only use a restart file for the exact simulation date.



'''''Please note: As of October 2019, the [[GCST]] is actively investigating differences in model output when running single vs multi-segmented runs. Any issues found will be addressed as soon as possible to minimize these differences.'''''


----
'''''[[Compiling GEOS-Chem|Previous]] | [[GEOS-Chem output files|Next]] | [[Getting Started with GEOS-Chem]]'''''