Frequently asked questions about GEOS-Chem: Difference between revisions

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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.


== Basic information about GEOS-Chem ==
== For new users ==


=== For new users ===
* [https://geos-chem.seas.harvard.edu/welcome.html I am a GEOS-Chem new user.  What is expected of me?]
 
* [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?]
* [[GEOS-Chem welcome letter for new users|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?]]
* [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?]]
* [[Guide to GEOS-Chem simulations|What types of simulations can I run with GEOS-Chem?]]
* What is the [[GEOS-Chem horizontal grids|horizontal resolution]] and [[GEOS-Chem vertical grids|vertical resolution]] of GEOS-Chem?
* What is the [[GEOS-Chem horizontal grids|horizontal resolution]] and [[GEOS-Chem vertical grids|vertical resolution]] of GEOS-Chem?
* [[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?]]
* [https://geos-chem.readthedocs.io/en/latest/help-and-reference/SUPPORT.html To whom may 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://geoschem.github.io/steering-cmte.html 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://geoschem.github.io/working-groups.html What do the GEOS-Chem Working Groups do?]
* [[GEOS-Chem Support Team|What does the GEOS-Chem Support Team do?]]
* [https://geoschem.github.io/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?]]
* [https://geoschem.github.io/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 ==


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?]]
* [https://kpp.readthedocs.io The chemical solver used in GEOS-Chem?]
* [[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.?]]
* [[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?
* [[GEOS-Chem nested grid simulations]]?
* [https://geos-chem.readthedocs.io/en/latest/supplemental-guides/nested-grid-guide.html GEOS-Chem nested grid simulations]?
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:45, 2 January 2019 (UTC)
 
=== 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?]]
* [[Common GEOS-Chem error messages|What should I do when I encounter an error while running GEOS-Chem]]?
* Do you have any information about [[GEOS-Chem performance]] and [[GEOS-Chem_performance#GEOS-Chem_scalability|GEOS-Chem Scalability]]?
* [[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?]]
* [[GEOS-Chem basics|I am new to programming.  Do you have any online resources or tutorials?]]
* 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)
== Technical issues ==


=== Parallelization issues ===
* [https://geos-chem.readthedocs.io/en/latest/gcclassic-user-guide/get-code.html How do I download the GEOS-Chem source code]
* [[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>]]
* [https://geos-chem.readthedocs.io/en/latest/gcclassic-user-guide/create-rundir.html How do I create run directories?]
* [[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?]]
* [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]?
* [[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?]]
* [https://github.com/geoschem/geos-chem/issues Is there a comprehensive list of GEOS-Chem bug reports?]
* 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]?


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:45, 2 January 2019 (UTC)
== Parallelization issues ==
* [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>]
* [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?]
* [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?]


=== 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/gcclassic-user-guide/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 ==


Please see our ''[[Running GEOS-Chem]]'' wiki page.
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.
 
=== 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]].
 
=== 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.
 
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]]''.
 
=== 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]]''.
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:40, 17 June 2019 (UTC)
 
=== Where does GEOS-Chem error output get printed? ===
 
GEOS-Chem, like all Unix programs, sends its output to two streams:
 
# stdout
# stderr
 
==== The stdout stream ====
 
Most GEOS-Chem output will go to the '''stdout''' stream, which takes I/O from the Fortran WRITE and PRINT commands.  If you run GEOS-Chem by just typing the executable name at the Unix prompt:
 
geos
 
then the stdout stream will be printed to the terminal window.  You can also redirect the stdout stream to a log file with the Unix redirect command:
 
geos > log
 
We recommend that you create GEOS-Chem log files so that you can reexamine the output from your run at a later time.
 
Most GEOS-Chem errors will be printed to stdout (and hence, to the log file). Most errors flagged by GEOS-Chem use a standard error message format, such as:
 
==============================================================
GEOS-CHEM ERROR: No output scheduled on last day of run!
STOP at IS_LAST_DAY_GOOD ("input_mod.f")
==============================================================
 
==== The stderr stream ====
 
The '''stderr''' stream takes I/O from various Unix system commands, including <tt>exit</tt>.  If your GEOS-Chem run died as a result of a system problem (i.e. you ran up against a system time or memory limit, you are over disk quota, etc.), then the error message will more than likely go to stderr instead of stdout.  As a result, these error messages will not be printed to the GEOS-Chem log file output.
 
If you use a queue system then the stderr output may be printed to a file.  For example, if you submit a GEOS-Chem job to the SGE queue system, and your job script is named <tt>run.geos</tt>, SGE will send the stderr output to a file named <tt>run.geos.oXXXXX</tt> (where XXXXX is the job ID #).


--[[User:Bmy|Bob Y.]] 15:44, 8 November 2010 (EST)
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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