Frequently asked questions about GEOS-Chem: Difference between revisions

From Geos-chem
Jump to navigation Jump to search
No edit summary
 
(43 intermediate revisions by 2 users not shown)
Line 1: Line 1:
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?]]
* [[GEOS-Chem Support Team|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?]


=== 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?]]
* [[KPP solvers FAQ|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|offline chemistry simulations?]]
* [[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?
* [[GEOS-Chem nested grid simulations]]?
* [https://geos-chem.readthedocs.io/en/latest/supplemental-guides/nested-grid-guide.html GEOS-Chem nested grid simulations]?
 
=== 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?]]
* [[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]]?
* 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?]]
* [[GEOS-Chem_coding_style_guide|Is there a recommended programming style that I should use?]]
* Are there any [[Floating point math issues|numerical issues]] or [[Machine issues & portability|machine-dependent 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?]]


=== Parallelization issues ===
== Technical issues ==
* [[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>]]
* [[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?]]


=== GEOS-Chem HP ("high-performance") ===
* [https://geos-chem.readthedocs.io/en/latest/gcclassic-user-guide/get-code.html How do I download the GEOS-Chem source code]
* [https://geos-chem.readthedocs.io/en/latest/gcclassic-user-guide/create-rundir.html How do I create run directories?]
* [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]?
* [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]?


<span style="color:red">'''''NOTE: At present GEOS-Chem HP (aka GCHP) is still in the "alpha" stage of development.  If you are interested in assisting with GEOS-Chem HP development, then please contact the [[GEOS-Chem_High_Performance_Working_Group|GEOS-Chem HP working group]].
== 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?]


* [[GEOS-Chem HP|What is GEOS-Chem HP?]]
== High-Performance GEOS-Chem (GCHP) ==
* [[GEOS-Chem_HP_Description|Can you give me an overview of GEOS-Chem HP?]]
* [[GEOS-Chem_HP_Software|What are the hardware and software requirements for GEOS-Chem HP?]]
* [[GEOS-Chem HP Dev Kit|How may I download the GEOS-Chem HP code and run directories?]]
* [[GEOS-Chem_HP_Compiling|How do I compile GEOS-Chem HP?]]
* [[GEOS-Chem_HP_Running|How do I run GEOS-Chem HP?]]
* [[GEOS-Chem_HP_PandE|Have users found any problems with GEOS-Chem HP?]]


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:24, 7 December 2016 (UTC)
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 GEOS-Chem v11-01 and higher versions ===
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].
 
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]].
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:24, 6 January 2017 (UTC)
 
=== For older versions ===
 
[[Image:Obsolete.jpg]]
 
<span style="color:red">'''''NOTE: This information will become obsolete for [[GEOS-Chem v11-01]].'''''</span>
 
For your convenience, we have archived several run directories which contain the various input files and initial conditions (aka "restart files") for GEOS-Chem simulations.  Please see [http://acmg.seas.harvard.edu/geos/doc/man/chapter_2.html#2.3 Chapter 2.3: Downloading the GEOS-Chem run directories] in the GEOS-Chem Online User's Guide for detailed downloading instructions.
 
In general, the GEOS-Chem Support Team does not have the resources to store restart files for multiple years.  Please note:
 
# We have discontinued archiving GEOS-Chem run directories via TARBALL (<tt>*.tar.gz</tt>) files.  You must use the [http://acmg.seas.harvard.edu/geos/doc/man/chapter_8.html Git version control software] to download any of the [http://acmg.seas.harvard.edu/geos/doc/man/chapter_2.html#2.3 GEOS-Chem run directories].
# You can always rename the restart file from one of the GEOS-Chem run directories with a run directory and just rename it (i.e. change <tt>restart.2x25.geos5.2005070100</tt> to <tt>restart.2x25.geos5.2009070100</tt>.)
#For those of you who are running simulations with [[Secondary organic aerosols]], please see this wiki post about the [[Secondary_organic_aerosols#The_SOA_restart_file|SOA restart file]].  This file archives the various quantities.
# Restart files are archived for each of the [http://acmg.seas.harvard.edu/geos/geos_1yr_plots.html GEOS-Chem 1-year benchmark simulations].  You can download any of these via anonymous FTP.  However, these restart files are usually for simulations done at 4&deg; x 5&deg; resolution for model year 2005.
 
Also, we recommend that you do not use the restart files provided in the run directory to initialize any of your "production" GEOS-Chem simulations.  You should "spin-up" GEOS-Chem for at least a year.  Then you can use  the restart file saved out from the "spin-up" run as the initial condition for your production run.
 
--[[User:Bmy|Bob Y.]] 16:05, 22 March 2011 (EDT)


== Running GEOS-Chem ==
== Running GEOS-Chem ==


=== How long does GEOS-Chem take to run? ===
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.
 
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.
 
Also, the following run-time options may also slow down GEOS-Chem:
 
; "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.
; "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.
 
To speed up GEOS-Chem, you can try to reduce the number of diagnostics that you are saving to disk.
 
=== Can I run two GEOS-Chem jobs simultaneously? ===
 
'''''[mailto:timmyf@prl.res.in Timmy Francis] wrote:'''''
 
: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?
 
'''''[mailto:yantosca@seas.harvard.edu Bob Yantosca] replied:'''''
 
: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.
 
: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).
 
: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.
 
== GEOS-Chem errors ==
 
Please also see our [[Common GEOS-Chem error messages]] wiki page.
 
=== GEOS-Chem died with an error.  What can I do? ===
 
First, you should try to understand the type of error that has occurred. There are several different classes of errors, such as:
 
# [[Common GEOS-Chem error messages#File_I.2FO_errors|File I/O errors]]
#* Errors caused by incorrect input options
#* Errors caused by missing data files
#* Errors caused by corrupted data files
#* [[Common GEOS-Chem error messages#Error computing F_OF_PBL|Running GEOS-Chem at the wrong resolution for the data files]]
# [[Common GEOS-Chem error messages#Crashes or abnormal exits|Abnormal exits]]
#* From the [[KPP solvers FAQ|KPP chemical solver]]
#* From the SMVGEAR chemical solver
#* From other areas of GEOS-Chem
# [[Common GEOS-Chem error messages#General types of errors|Technical errors]]
#* [[Common GEOS-Chem error messages#Segmentation faults|Segmentation faults]]
#* [[Common_GEOS-Chem_error_messages#Array-out-of-bounds_error|Array-out-of-bounds errors]]
#* Out of memory errors
 
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.).
 
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.)  You may also try turning off operations (e.g. wet deposition, dry deposition, chemistry) one at a time in the <tt>input.geos</tt> file to isolate the error. 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. You will gain great insight into what is happening by using this technique.
 
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 time and date) may indicate memory errors, such as array-out-of-bounds, segmentation faults, or that the code is using more memory than is available.
 
When you debug, we recommend that you recompile with the <tt>TRACEBACK=yes</tt> compiler option. This will print out the error stack, or list of routines that are called.  The traceback output can often indicate where the error occurs.
 
If you still cannot determine the error from the traceback output, recompile with the <tt>BOUNDS=yes</tt> compiler option.  This will check to see if an array is being accessed incorrectly
 
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 Support Team]] and provide a detailed description of your error.
 
=== 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).

Retrieved from "https://wiki.seas.harvard.edu/geos-chem/index.php?title=Frequently_asked_questions_about_GEOS-Chem&oldid=53736"