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

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On this page we shall answer some commonly asked questions about GEOS-Chem.
 
On this page we shall answer some commonly asked questions about GEOS-Chem.
  
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== Basic information about GEOS-Chem ==
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== For new users ==
  
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=== For new users ===
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* [https://geos-chem.seas.harvard.edu/welcome.html I am a GEOS-Chem new user.  What is expected of me?]
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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://cloud.geos-chem.org Can I use GEOS-Chem on cloud-computing platforms?]
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* [[Guide to GEOS-Chem simulations|What types of simulations can I run with 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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* [[Overview of GMAO met data products|Which meteorological data fields can be used by GEOS-Chem?]]
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* [https://geos-chem.readthedocs.io/en/latest/help-and-reference/SUPPORT.html To whom may I direct GEOS-Chem-related questions?]
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* [https://geoschem.github.io/steering-cmte.html What does the GEOS-Chem Steering Committee do?]
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* [https://geoschem.github.io/working-groups.html What do the GEOS-Chem Working Groups do?]
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* [https://geoschem.github.io/support-team What does the GEOS-Chem Support Team do?]
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* [https://geoschem.github.io/email-lists I see that there are several GEOS-Chem email lists.  How can I subscribe?]
  
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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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== Science questions ==
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* [[Minimum system requirements for GEOS-Chem|On what types of machines can I run GEOS-Chem?]]
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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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* 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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* [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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* [[GEOS-Chem programming staff|To whom can I direct GEOS-Chem-related questions?]]
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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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* [http://acmg.seas.harvard.edu/geos/geos_working_groups.html What do the GEOS-Chem Working Groups do?]
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=== 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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* [https://kpp.readthedocs.io The chemical solver used in GEOS-Chem?]
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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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* [[Emissions overview|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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* [https://geos-chem.readthedocs.io/en/latest/supplemental-guides/nested-grid-guide.html GEOS-Chem nested grid simulations]?
  
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=== Technical questions ===
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== Technical issues ==
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* [[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?]]
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* [[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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* [[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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* [[GEOS-Chem programming resources|I am new to programming.  Do you have any online resources or tutorials?]]
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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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=== How long does GEOS-Chem take to run? ===
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It depends on your particular computing environment.  We have posted several timing results from GEOS-Chem [[GEOS-Chem supported platforms and compilers|4° x 5° (1-month benchmark)]] and [[GEOS-Chem supported platforms and compilers#Performance of 2 x 2.5 simulations|2° x 2.5° (1-year benchmark)]] simulations.
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=== GEOS-Chem seems to be running too slowly.  What can I do? ===
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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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Also, the following run-time options may also slow down 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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; "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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=== GEOS-Chem died with an error.  What can I do? ===
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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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# [[Common GEOS-Chem error messages#File_I.2FO_errors|File I/O errors]]
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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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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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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 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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* [https://geos-chem.readthedocs.io/en/latest/gcclassic-user-guide/get-code.html How do I download the GEOS-Chem source code]
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* [https://geos-chem.readthedocs.io/en/latest/gcclassic-user-guide/create-rundir.html How do I create run directories?]
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* [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/error-guide.html What should I do when I encounter an error while running GEOS-Chem]?
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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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* 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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=== Can I run two GEOS-Chem jobs simultaneously? ===
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== Parallelization issues ==
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* [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/parallel-guide.html#how-can-i-tell-what-should-go-into-the-omp-private-clause 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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* [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/parallel-guide.html#how-many-cores-may-i-use-for-geos-chem-or-hemco How many CPU cores may I use for my GEOS-Chem Classic simulation?]
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* [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/parallel-guide.html#why-is-geos-chem-is-not-using-all-the-cores-i-requested Why is GEOS-Chem Classic not using all the CPU cores that I requested?]
  
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'''''[mailto:timmyf@prl.res.in Timmy Francis] wrote:'''''
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== High-Performance GEOS-Chem (GCHP) ==
  
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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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Please see the GCHP user manual at [https://gchp.readthedocs.io <tt>gchp.readthedocs.io</tt>]for more information.
  
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'''''[mailto:yantosca@seas.harvard.edu Bob Yantosca] replied:'''''
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== Where can I get restart files for GEOS-Chem? ==
  
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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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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/gcclassic-user-guide/restart-files-gc.html#where-can-i-get-a-restart-file-for-my-simulation please visit this link].
  
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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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== Running GEOS-Chem ==
  
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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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Please see the [https://geos-chem.readthedocs.io/en/latest/gcclassic-user-guide/run.html Run your simulation] section of [https://geos-chem.readthedocs.io <tt>geos-chem.readthedocs.io.</tt>]. for more information.
  
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--[[User:Bmy|Bob Y.]] 15:44, 8 November 2010 (EST)
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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].  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).

Latest revision as of 17:02, 23 May 2024

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

For new users

Science questions

Where can I find information about ...

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 the Run your simulation section of geos-chem.readthedocs.io.. for more information.

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).

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