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

From Geos-chem
Jump to: navigation, search
(Technical issues)
(Science questions)
 
(11 intermediate revisions by the same user not shown)
Line 5: Line 5:
 
=== For new users ===
 
=== For new users ===
  
* [[GEOS-Chem welcome letter for new users|I am a GEOS-Chem new user.  What is expected of me?]]
+
* [https://geos-chem.seas.harvard.edu/geos-welcome I am a GEOS-Chem new user.  What is expected of me?]
* [[Minimum system requirements for GEOS-Chem|On what types of machines can I run GEOS-Chem?]]
+
* [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?]
 
* [http://cloud.geos-chem.org Can I use GEOS-Chem on cloud-computing platforms?]
 
* [http://cloud.geos-chem.org Can I use GEOS-Chem on cloud-computing platforms?]
 
* [[Species in GEOS-Chem|What types of simulations can I run with GEOS-Chem?]]
 
* [[Species in GEOS-Chem|What types of simulations can I run with GEOS-Chem?]]
Line 12: Line 12:
 
* [[Overview of GMAO met data products|Which meteorological data fields can be used by GEOS-Chem?]]
 
* [[Overview of GMAO met data products|Which meteorological data fields can be used by GEOS-Chem?]]
 
* [[Submitting GEOS-Chem support requests|To whom can I direct GEOS-Chem-related questions?]]
 
* [[Submitting GEOS-Chem support requests|To whom can I direct GEOS-Chem-related questions?]]
* [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html What does the GEOS-Chem Steering Committee do?]
+
* [https://geos-chem.seas.harvard.edu/geos-steering-cmte What does the GEOS-Chem Steering Committee do?]
* [http://acmg.seas.harvard.edu/geos/geos_working_groups.html What do the GEOS-Chem Working Groups do?]
+
* [https://geos-chem.seas.harvard.edu/geos-working-groups What do the GEOS-Chem Working Groups do?]
 
* [[GEOS-Chem Support Team|What does the GEOS-Chem Support Team do?]]
 
* [[GEOS-Chem Support Team|What does the GEOS-Chem Support Team do?]]
 
* [[Subscribing_to_the_GEOS-Chem_email_lists|I see that there are several GEOS-Chem email lists.  How can I subscribe?]]
 
* [[Subscribing_to_the_GEOS-Chem_email_lists|I see that there are several GEOS-Chem email lists.  How can I subscribe?]]
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:45, 2 January 2019 (UTC)
 
  
 
=== Science questions ===
 
=== Science questions ===
Line 23: Line 21:
 
Where can I find information about ...
 
Where can I find information about ...
  
* [[GEOS-Chem chemistry mechanisms|the available chemical mechanisms in GEOS-Chem?]]
+
* [[Guide to GEOS-Chem simulations|types of GEOS-Chem simulations that I can run?]]
* [[Bromine chemistry mechanism|the bromine chemistry mechanism in GEOS-Chem?]]
+
* [[Bromine chemistry mechanism|bromine chemistry?]]
 
* [[FlexChem|the KPP chemical solver?]]
 
* [[FlexChem|the KPP chemical solver?]]
 
* [[Linoz stratospheric ozone chemistry|the Linoz stratospheric ozone chemistry scheme?]]
 
* [[Linoz stratospheric ozone chemistry|the Linoz stratospheric ozone chemistry scheme?]]
* [[GEOS-Chem_chemistry_mechanisms#Stratospheric_chemistry|the stratospheric chemistry mechanism?]]
 
 
* [[Offline chemistry simulations|Other chemistry simulations such as CO2, CH4, Hg, etc.?]]
 
* [[Offline chemistry simulations|Other chemistry simulations such as CO2, CH4, Hg, etc.?]]
 
* [[HEMCO data directories|emissions options in GEOS-Chem?]]
 
* [[HEMCO data directories|emissions options in GEOS-Chem?]]
Line 36: Line 33:
 
* [[GEOS-Chem nested grid simulations]]?
 
* [[GEOS-Chem nested grid simulations]]?
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:45, 2 January 2019 (UTC)
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:06, 20 September 2022 (UTC)
  
 
=== Technical issues ===
 
=== Technical issues ===
Line 44: Line 41:
 
* Do you have any information about [[Guide to GEOS-Chem performance|GEOS-Chem performance]] and [[GEOS-Chem scalability]]?
 
* 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?]]
* [[Bugs and fixes|Is there a comprehensive list of GEOS-Chem bugs and how they were fixed?]]
+
* [https://github.com/geoschem/geos-chem/issues Is there a comprehensive list of GEOS-Chem bug reports?]
* [[GEOS-Chem basics|I am new to programming.  Do you have any online resources or tutorials?]]
+
* 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]?
* Are there any [[Floating point math issues|numerical issues]] that I should be aware of?
+
* Do you have any tools that would help me [[Debugging with the GEOS-Chem unit tester|debug GEOS-Chem more efficiently?]]
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:45, 2 January 2019 (UTC)
+
  
 
=== Parallelization issues ===
 
=== Parallelization issues ===
Line 55: Line 48:
 
* [[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?]]
 
* [[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?]]
 
* [[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?]]
 
* [[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?]]
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:45, 2 January 2019 (UTC)
 
  
 
=== High-Performance GEOS-Chem (GCHP) ===
 
=== High-Performance GEOS-Chem (GCHP) ===
  
Please see the [[GCHP_Main_Page|GCHP main wiki page]] for information about GCHP.
+
Please see the GCHP user manual at [https://gchp.readthedocs.io <tt>gchp.readthedocs.io</tt>]for more information.
  
 
== Where can I get restart files for GEOS-Chem? ==
 
== 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 see [[GEOS-Chem_basics#Restart_files|the ''Restart Files'' section of our ''GEOS-Chem basics'' wiki page]].
+
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].
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:24, 6 January 2017 (UTC)
+
  
 
== Running GEOS-Chem ==
 
== Running GEOS-Chem ==
Line 74: Line 63:
 
=== How long does GEOS-Chem take to run? ===
 
=== How long does GEOS-Chem take to run? ===
  
It depends on your particular computing environment.  We have posted several timing results from GEOS-Chem [[GEOS-Chem_performance#7-day_time_tests|7-day time test simulations]].
+
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]].
  
 
=== GEOS-Chem seems to be running too slowly.  What can I do? ===
 
=== GEOS-Chem seems to be running too slowly.  What can I do? ===
  
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.
+
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).
 
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).
Line 84: Line 73:
 
== GEOS-Chem errors ==
 
== GEOS-Chem errors ==
  
Please also see our ''[[Guide to GEOS-Chem error messages]]'' and ''[[Debugging GEOS-Chem]]'' pages.
+
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.
  
 
=== GEOS-Chem died with an error.  What can I do? ===
 
=== 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]]''.
 
Please see ''[[Understanding the different categories of errors]]'' section of our ''[[Guide to GEOS-Chem error messages]]''.
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:40, 17 June 2019 (UTC)
 

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.