Difference between revisions of "Frequently asked questions about GEOS-Chem"

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=== For new users ===
 
=== For new users ===
  
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* [[GEOS-Chem welcome letter for new users|I am a GEOS-Chem new user.  What is expected of me?]]
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* [https://geos-chem.seas.harvard.edu/geos-welcome I am a GEOS-Chem new user.  What is expected of me?]
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* [[Minimum system requirements for GEOS-Chem|On what types of machines can I run GEOS-Chem?]]
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* [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/related-docs.html Where can I find user manuals for GEOS-Chem and related software?]
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* [http://acmg.seas.harvard.edu/geos/doc/man/appendix_1.html What kind of simulations can I run with GEOS-Chem?]
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* [http://cloud.geos-chem.org Can I use GEOS-Chem on cloud-computing platforms?]
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* What is the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html horizontal resolution] and [http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html vertical resolution] of GEOS-Chem?
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* [[Species in GEOS-Chem|What types of simulations can I run with GEOS-Chem?]]
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* [http://acmg.seas.harvard.edu/geos/doc/man/appendix_4.html Which meteorological data fields can be used by GEOS-Chem?]
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* What is the [[GEOS-Chem horizontal grids|horizontal resolution]] and [[GEOS-Chem vertical grids|vertical resolution]] of GEOS-Chem?
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* [[GEOS-Chem programming staff|To whom can I direct GEOS-Chem-related questions?]]
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* [[Overview of GMAO met data products|Which meteorological data fields can be used by GEOS-Chem?]]
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* [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html What does the GEOS-Chem Steering Committee do?]
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* [[Submitting GEOS-Chem support requests|To whom can I direct GEOS-Chem-related questions?]]
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* [http://acmg.seas.harvard.edu/geos/geos_working_groups.html What do the GEOS-Chem Working Groups do?]
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* [https://geos-chem.seas.harvard.edu/geos-steering-cmte What does the GEOS-Chem Steering Committee do?]
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* [https://geos-chem.seas.harvard.edu/geos-working-groups What do the GEOS-Chem Working Groups do?]
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* [[GEOS-Chem Support Team|What does the GEOS-Chem Support Team do?]]
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* [[Subscribing_to_the_GEOS-Chem_email_lists|I see that there are several GEOS-Chem email lists.  How can I subscribe?]]
  
 
=== Science questions ===
 
=== Science questions ===
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Where can I find information about ...
 
Where can I find information about ...
  
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* [[Chemistry Issues|the Standard chemistry mechanism in GEOS-Chem?]]
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* [[Guide to GEOS-Chem simulations|types of GEOS-Chem simulations that I can run?]]
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* [[Dicarbonyls simulation|the Dicarbonyls mechanism in GEOS-Chem?]]
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* [[Bromine chemistry mechanism|bromine chemistry?]]
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* [[New isoprene scheme|the Caltech isoprene mechanism as implemented in GEOS-Chem?]]
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* [[FlexChem|the KPP chemical solver?]]
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* [[Bromine chemistry mechanism|the bromine chemistry mechanism in GEOS-Chem?]]
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* [[KPP solvers FAQ|the KPP chemical solver?]]
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* [[Linoz stratospheric ozone chemistry|the Linoz stratospheric ozone chemistry scheme?]]
 
* [[Linoz stratospheric ozone chemistry|the Linoz stratospheric ozone chemistry scheme?]]
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* [[Offline chemistry simulations|offline chemistry simulations?]]
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* [[Offline chemistry simulations|Other chemistry simulations such as CO2, CH4, Hg, etc.?]]
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* [[Emissions overview|emissions options in GEOS-Chem?]]
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* [[HEMCO data directories|emissions options in GEOS-Chem?]]
 
* [[Advection scheme TPCORE|the advection scheme in GEOS-Chem?]]
 
* [[Advection scheme TPCORE|the advection scheme in GEOS-Chem?]]
 
* [[Boundary layer mixing|the boundary layer mixing schemes in GEOS-Chem?]]
 
* [[Boundary layer mixing|the boundary layer mixing schemes in GEOS-Chem?]]
 
* [[Cloud convection|the cloud convection schemes in GEOS-Chem?]]
 
* [[Cloud convection|the cloud convection schemes in GEOS-Chem?]]
 
* The [[Dry deposition]] and [[Wet deposition]] schemes in GEOS-Chem?
 
* The [[Dry deposition]] and [[Wet deposition]] schemes in GEOS-Chem?
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* [[GEOS-Chem nested grid simulations]]?
  
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=== Technical questions ===
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:06, 20 September 2022 (UTC)
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=== Technical issues ===
  
 
* [[Using Git with GEOS-Chem#Downloading a new GEOS-Chem version|How do I download the GEOS-Chem source code and run directories?]]
 
* [[Using Git with GEOS-Chem#Downloading a new GEOS-Chem version|How do I download the GEOS-Chem source code and run directories?]]
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* [[Downloading GEOS-Chem source code and data#Data Directory Access|How do I download the GEOS-Chem data directories?]]
 
 
* [[Common GEOS-Chem error messages|What should I do when I encounter an error while running GEOS-Chem]]?
 
* [[Common GEOS-Chem error messages|What should I do when I encounter an error while running GEOS-Chem]]?
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* Do you have any information about [[GEOS-Chem supported platforms and compilers|GEOS-Chem performance]] and [[GEOS-Chem performance|GEOS-Chem Scalability]]?
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* Do you have any information about [[Guide to GEOS-Chem performance|GEOS-Chem performance]] and [[GEOS-Chem scalability]]?
 
* [[GEOS-Chem Makefile Structure|Where can I learn more about the GEOS-Chem Makefiles?]]
 
* [[GEOS-Chem Makefile Structure|Where can I learn more about the GEOS-Chem Makefiles?]]
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* [[Bugs and fixes|Is there a comprehensive list of GEOS-Chem bugs and how they were fixed?]]
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* [https://github.com/geoschem/geos-chem/issues Is there a comprehensive list of GEOS-Chem bug reports?]
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* [[GEOS-Chem programming resources|I am new to programming.  Do you have any online resources or tutorials?]]
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* Do you have any information on how I can [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/debug-guide.html debug GEOS-Chem or HEMCO errors]?
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* [http://acmg.seas.harvard.edu/geos/doc/man/appendix_7.html Is there a recommended programming style that I should use?]
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* Are there any [[Floating point math issues|numerical issues]] or [[Machine issues & portability|machine-dependent issues]] that I should be aware of?
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== Specific questions ==
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=== Parallelization issues ===
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* [[Parallelizing_GEOS-Chem#How_can_I_tell_if_a_variable_has_to_be_declared_with_PRIVATE_or_SHARED.3F|How can I tell if a variable has to be declared with <tt>!$OMP PRIVATE</tt> or <tt>!$OMP SHARED?</tt>]]
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* [[Parallelizing_GEOS-Chem#How_many_CPUs_may_I_use_in_my_GEOS-Chem_simulation.3F|How many CPUs may I use for my GEOS-Chem simulation?]]
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* [[Parallelizing_GEOS-Chem#Why_is_GEOS-Chem_is_not_using_all_the_CPUs_I_requested.3F|Why is GEOS-Chem not using all the CPUs that I requested?]]
  
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=== How long does GEOS-Chem take to run? ===
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=== High-Performance GEOS-Chem (GCHP) ===
  
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It depends on your particular machine.  We have posted several timing results from GEOS-Chem [[GEOS-Chem supported platforms and compilers|4&deg; x 5&deg; (1-month benchmark)]] and [[GEOS-Chem supported platforms and compilers#Performance of 2 x 2.5 simulations|2&deg; x 2.5&deg; (1-year benchmark)]] simulations.
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Please see the GCHP user manual at [https://gchp.readthedocs.io <tt>gchp.readthedocs.io</tt>]for more information.
  
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=== My GEOS-Chem job seems to be running too slowly.  What can I do? ===
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== Where can I get restart files for GEOS-Chem? ==
  
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You should be aware of [[GEOS-Chem Makefile Structure#Compile-time options that can slow down GEOS-Chem|several compile-time options that will slow down GEOS-Chem]].  Use these options only for debugging, but not in your production runs.
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For instructions on how to obtain a set of sample restart files that you can use to spin up your own simulations, [https://geos-chem.readthedocs.io/en/latest/gcc-guide/04-data/restart-files-gc.html#where-can-i-get-a-restart-file-for-my-simulation please visit this link].
  
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Also, the following run-time options may also slow down GEOS-Chem:
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== Running GEOS-Chem ==
  
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; "Normal" diagnostics (e.g. saved out to the ctm.bpch file): The more diagnostic quantities you choose to archive, the more memory and disk I/O operations this will require.
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Please see our ''[[Running GEOS-Chem]]'' wiki page.
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; "Timeseries" diagnostics (ND48, ND49, ND50, ND51, ND51b): If you choose to archive many diagnostic quantities at hourly or bi-hourly intervals, then the increased memory and disk I/O usage can slow down GEOS-Chem.
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To speed up GEOS-Chem, you can try to reduce the number of diagnostics that you are saving to disk.
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=== How long does GEOS-Chem take to run? ===
  
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=== GEOS-Chem died with an error. What can I do? ===
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It depends on your particular computing environment.  We have posted several timing results from GEOS-Chem [[GEOS-Chem 7-day timing tests|7-day time test simulations]].
  
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First, you should try to understand the type of error that has occurred.  There are several different classes of errors, such as:
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=== GEOS-Chem seems to be running too slowly.  What can I do? ===
  
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# [[Common GEOS-Chem error messages#File_I.2FO_errors|File I/O errors]]
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There are several ways to [https://geos-chem.readthedocs.io/en/latest/gcc-guide/05-run/run-speedup.html speed up a slow GEOS-Chem simulation].
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#* Errors caused by incorrect input options
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#* Errors caused by missing data files
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#* Errors caused by corrupted data files
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#* [[Common GEOS-Chem error messages#Error computing F_OF_PBL|Running GEOS-Chem at the wrong resolution for the data files]]
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# [[Common GEOS-Chem error messages#Crashes or abnormal exits|Abnormal exits]]
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#* From the [[KPP solvers FAQ|KPP chemical solver]]
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#* From the SMVGEAR chemical solver
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#* From other areas of GEOS-Chem
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# [[Common GEOS-Chem error messages#General types of errors|Technical errors]]
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#* [[Common GEOS-Chem error messages#Segmentation Fault|Segmentation faults]]
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#* Array-out-of-bounds errors
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#* Out of memory errors
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Once you have understood the type of GEOS-Chem error that has occurred, you can take steps to fix it.  In some cases, the fixes will be simple (i.e. selecting the proper option and starting over, or replacing missing or corrupted data files, etc.).  In other cases, the error may be more difficult to diagnose (such as a [[KPP_solvers_FAQ#How_do_I_choose_the_absolute_and_relative_tolerance.3F|convergence error in the chemical solver]]).  In that case you may have to "dig in" to the code so that you can modify its behavior (e.g. modify convergence criteria, add error checks, etc.).
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If you are archiving many diagnostic quantities are a high temporal resolution (e.g. every hour), then this will increase the run time of your simulation.  You can try saving out less diagnostic quantities, or archiving at a lower temporal resolution (e.g. every day).
  
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Try to isolate the error to a particular GEOS-Chem routine.  You can use a debugger such as idb or Totalview, or you can turn on the ND70 debug printout option.  (ND70 will print debug messages to the log file after key operations have been completed.)  Once you know where the error is occurring, try to print out values for a given grid box and tracer, either in the debugger or by adding PRINT statements to the code.
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== GEOS-Chem errors ==
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In this manner, you will gain great insight into what is happening.
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Try to determine if the error is persistent (i.e. if it always occurs at the same model time/date) or if it occurs at different times and dates in the simulation).  A persistent error could indicate a missing or corrupted data file, or a flaw in the scientific algorithm being used.  Non-persistent errors (i.e. those that don't happen at the same model date & time) may indicate memory errors, such as array-out-of-bounds, segmentation faults, or that the code is using more memory than is available.
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Please also see our ''[[Guide to GEOS-Chem error messages]]'' and ''[https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/debug-guide.html Debug GEOS-Chem and HEMCO errors]'' pages.
  
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Please see our [[Common GEOS-Chem error messages|Common GEOS-Chem errors wiki page]], which contains strategies for recognizing and fixing several commonly-encountered error conditions.  If you still cannot determine the source of your error, please contact the [[GEOS-Chem programming staff|GEOS-Chem Support Team]] and provide a detailed description of your error.
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=== GEOS-Chem died with an error.  What can I do? ===
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=== Can I run two GEOS-Chem jobs simultaneously? ===
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'''''[mailto:timmyf@prl.res.in Timmy Francis] wrote:'''''
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:I would like to know if I can run more than one executables (.geos) by renaming them as .geos1, .geos2 etc. For example using the same restart file, I want to run two simulations, one 'with chemistry' and the other 'without chemistry' after make and rename the executables to geos1 and geos2 and run these in two terminals. Will they interfere with each other and affect the result?
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'''''[mailto:yantosca@seas.harvard.edu Bob Yantosca] replied:'''''
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:I recommend creating separate run directories for each executable.  You can place the identical restart file and input files into each run directory.  Then in one run directory you can turn on chemistry in input.geos, and then in the other run directory, you turn off chemistry in input.geos.  If you run the GEOS-Chem executables in two separate directories, you will ensure that one executable will not overwrite the files that the other executable creates.
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:In theory, you should be able to run two simultaneous GEOS-Chem executables in two separate run directories.  However, I don't know much about your particular machine.  You might find that there is not enough memory to run two simulations at the same time.  That is not a problem with GEOS-Chem, but with your system (and is something that the GEOS-Chem Support Team wouldn't be able to help you with).
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:I would recommend talking with your local IT department to find out how much memory etc. is available to you, and if you would be able to run two simulations at the same time.  I think a 4x5 full chemistry simulation takes 2-3 GB of memory, and a 2x2.5 simulation can take up to 8GB of memory.
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--[[User:Bmy|Bob Y.]] 15:44, 8 November 2010 (EST)
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Please see ''[[Understanding the different categories of errors]]'' section of our ''[[Guide to GEOS-Chem error messages]]''.

Latest revision as of 18:06, 20 September 2022

On this page we shall answer some commonly asked questions about GEOS-Chem.

Basic information about GEOS-Chem

For new users

Science questions

Where can I find information about ...

--Bob Yantosca (talk) 18:06, 20 September 2022 (UTC)

Technical issues

Parallelization issues

High-Performance GEOS-Chem (GCHP)

Please see the GCHP user manual at gchp.readthedocs.iofor more information.

Where can I get restart files for GEOS-Chem?

For instructions on how to obtain a set of sample restart files that you can use to spin up your own simulations, please visit this link.

Running GEOS-Chem

Please see our Running GEOS-Chem wiki page.

How long does GEOS-Chem take to run?

It depends on your particular computing environment. We have posted several timing results from GEOS-Chem 7-day time test simulations.

GEOS-Chem seems to be running too slowly. What can I do?

There are several ways to speed up a slow GEOS-Chem simulation.

If you are archiving many diagnostic quantities are a high temporal resolution (e.g. every hour), then this will increase the run time of your simulation. You can try saving out less diagnostic quantities, or archiving at a lower temporal resolution (e.g. every day).

GEOS-Chem errors

Please also see our Guide to GEOS-Chem error messages and Debug GEOS-Chem and HEMCO errors pages.

GEOS-Chem died with an error. What can I do?

Please see Understanding the different categories of errors section of our Guide to GEOS-Chem error messages.

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