Difference between revisions of "GEOS-Chem welcome letter for new users"

From Geos-chem
Jump to: navigation, search
(GEOS-Chem documentation)
(Being a member of the GEOS-Chem community)
 
(48 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 
Welcome to the GEOS-Chem user community!  Here is a quick guide to getting started:
 
Welcome to the GEOS-Chem user community!  Here is a quick guide to getting started:
  
'''<span style="color:red">Also be sure to see our new [[#GEOS-Chem tutorials|GEOS-Chem tutorials]] section!</span>
+
== Mission statement ==
 +
 
 +
<big>'''GEOS-Chem Community Mission: to advance understanding of human and natural influences on the environment<br>through a comprehensive, state-of-the-science, readily accessible global model of atmospheric composition.'''</big>
 +
 
 +
== GEOS-Chem overview ==
 +
 
 +
Please see the [http://acmg.seas.harvard.edu/geos/geos_overview.html GEOS-Chem overview], [http://acmg.seas.harvard.edu/geos/geos_chem_narrative.html Narrative description of GEOS-Chem], and [http://acmg.seas.harvard.edu/geos/geos_licensing.html GEOS-Chem licensing] web pages.
  
 
== GEOS-Chem Support Team ==
 
== GEOS-Chem Support Team ==
  
The [[GEOS-Chem Support Team]] currently consists of [http://people.seas.harvard.edu/~yantosca/ Bob Yantosca], [http://people.seas.harvard.edu/~mlong/ Michael Long], [http://people.seas.harvard.edu/~mpayer/ Melissa Payer Sulprizio], [http://myweb.dal.ca/sj207331/ Sajeev Philip], Lizzie Lundgren, Matthew Yannetti, and Yanko Davila.  They are responsible for developing and maintaining the [http://acmg.seas.harvard.edu/geos GEOS-Chem] and [[GEOS-Chem Adjoint]] codes for the user community.  They may be reached by email at '''geos-chem-support [at] as.harvard.edu'''.
+
The [[GEOS-Chem Support Team]] (aka GCST) is responsible for developing and maintaining the [http://acmg.seas.harvard.edu/geos GEOS-Chem] and [[GEOS-Chem Adjoint]] codes for the user community.  They may be reached by email at '''geos-chem-support [at] g.harvard.edu'''
 +
 
 +
Please also see [[Submitting GEOS-Chem support requests|our ''Submitting GEOS-Chem support requests'' wiki page]] for a checklist of items that you should include when contacting the GCST for assistance.
  
 
== Expectations and Responsibilities for GEOS-Chem users ==
 
== Expectations and Responsibilities for GEOS-Chem users ==
  
The following sections describe the responsibilities that we expect from each GEOS-Chem user.  Please also see our [http://acmg.seas.harvard.edu/geos/geos_overview.html '''GEOS-Chem overview page'''], which lists some additional information for new GEOS-Chem users.
+
The following sections describe the responsibilities that we expect from each GEOS-Chem user.  
  
 
=== Required hardware and software ===
 
=== Required hardware and software ===
  
We expect that each GEOS-Chem user (or user group, if there are several users at an institution) will have the required [[Minimum system requirements for GEOS-Chem#Hardware Recommendations|hardware]] and [[Minimum system requirements for GEOS-Chem#Software Requirements|software]] available to run GEOS-Chem.  If you are not sure what hardware or software is available to you, then please check with your local IT department.
+
Before getting started with GEOS-Chem, please take a moment to read [[GEOS-Chem basics#Overview|this list of prerequisites on our ''GEOS-Chem basics'' wiki page]].  Some of these items will probably have been already installed along with your operating system build.
 +
 
 +
If you plan to use GEOS-Chem on your local computer system, then make sure that your system has the necessary [[Minimum system requirements for GEOS-Chem#Hardware Recommendations|hardware]] and [[Minimum system requirements for GEOS-Chem#Software Requirements|software]] able to run GEOS-Chem.  If you are not sure what hardware or software is available to you, then please check with your local IT department.
 +
 
 +
If you do not have sufficient local computational resources (or if you require additional computational resources for specific projects), then we invite you to explore how you can run GEOS-Chem on the Amazon Web Services cloud computing environment.  Please see our tutorial [http://cloud.geos-chem.org '''cloud.geos-chem.org'''] for more information.
  
 
=== Computer language proficiency ===
 
=== Computer language proficiency ===
Line 19: Line 31:
 
We expect that each GEOS-Chem user will possess at least some familiarity with the following:
 
We expect that each GEOS-Chem user will possess at least some familiarity with the following:
  
* The Fortran programming language (F77 OK, F90 preferred)
+
* The Fortran programming language
* IDL (preferred), or other graphics software (e.g. Splus, Matlab)
+
 
* The Unix environment (i.e. commands, file paths, etc.)
 
* The Unix environment (i.e. commands, file paths, etc.)
 
* Unix scripts (not strictly required but is very helpful to know!)
 
* Unix scripts (not strictly required but is very helpful to know!)
 
* How [[Version control with Git|version control]] works
 
* How [[Version control with Git|version control]] works
 +
* OPTIONAL, BUT RECOMMENDED: Familiarity with Python
  
While we cannot provide you with general instruction in programming languages or answer general programming questions, we invite you to view the list of tutorials and other relevant resources listed on our '''[[GEOS-Chem basics]]''' page. We also invite you to read our document on 
+
While we cannot provide you with general instruction in programming languages or answer general programming questions, we invite you to view the list of tutorials and other relevant resources listed on our '''[[GEOS-Chem basics]]''' page.
[http://acmg.seas.harvard.edu/geos/word_pdf_docs/resources_guidelines_tips.pdf User Resources, Code Development Guidelines, and Debugging Tips].
+
  
 
=== Being a member of the GEOS-Chem community ===
 
=== Being a member of the GEOS-Chem community ===
Line 32: Line 43:
 
We ask that all new GEOS-Chem user groups submit a short research blurb (1 paragraph) about how you plan to use GEOS-Chem in your research.  We will add this to our [http://acmg.seas.harvard.edu/geos/geos_people.html GEOS-Chem People and Projects] web page.  Please send your research blurb to the  [[GEOS-Chem Support Team]].
 
We ask that all new GEOS-Chem user groups submit a short research blurb (1 paragraph) about how you plan to use GEOS-Chem in your research.  We will add this to our [http://acmg.seas.harvard.edu/geos/geos_people.html GEOS-Chem People and Projects] web page.  Please send your research blurb to the  [[GEOS-Chem Support Team]].
  
We also ask that each GEOS-Chem user join the [http://acmg.seas.harvard.edu/geos/geos_working_groups.html Working Group] that is most relevant to his/her area of research.  The Working Groups are meant to foster communication and information sharing between GEOS-Chem users, as well as to identify [[GEOS-Chem_model_development_priorities|priorities for model development]] to the [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html GEOS-Chem Steering Committee].  Please introduce yourself to the Working Group Chairperson)s) and sign up for the [[#Subscribing to the GEOS-Chem email lists|relevant email list(s)]].
+
We also ask that each GEOS-Chem user join the [http://acmg.seas.harvard.edu/geos/geos_working_groups.html Working Group] that is most relevant to his/her area of research.  The Working Groups are meant to foster communication and information sharing between GEOS-Chem users, as well as to identify [[GEOS-Chem_model_development_priorities|priorities for model development]] to the [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html GEOS-Chem Steering Committee].  Please introduce yourself to the Working Group Chairperson(s) and sign up for the [[#Subscribing to the GEOS-Chem email lists|relevant email list(s)]].
  
 
Each GEOS-Chem user is expected to adhere to our list of [http://acmg.seas.harvard.edu/geos/geos_welcome.html best practices].  In particular, if you should discover a problem (e.g. bugs, missing files, numerical issues, etc.), please bring that to the attention of the GEOS-Chem support team right away.  Other GEOS-Chem users will most certainly benefit from your discovery!
 
Each GEOS-Chem user is expected to adhere to our list of [http://acmg.seas.harvard.edu/geos/geos_welcome.html best practices].  In particular, if you should discover a problem (e.g. bugs, missing files, numerical issues, etc.), please bring that to the attention of the GEOS-Chem support team right away.  Other GEOS-Chem users will most certainly benefit from your discovery!
  
Please consider reporting your [[GEOS-Chem_supported_platforms_and_compilers|timing results from the 1-month benchmark simulation]] to the GEOS-Chem Support Team.  This will allow us to keep a list of how the model is performing across several different platform/compiler combinations.
+
We ask that you read the [http://acmg.seas.harvard.edu/geos/geos_credit_and_refs.html GEOS-Chem Credits and References] containing guidelines for giving appropriate credit to developers through co-authorship or citation. You may also refer to the [http://acmg.seas.harvard.edu/geos/geos_chem_narrative.html Narrative Description of the GEOS-Chem Model] for assistance with correctly citing relevant model components of the [[GEOS-Chem versions|current standard version of GEOS-Chem]] in your publications.
 +
 
 +
Finally, please consider reporting your [[GEOS-Chem_7-day_timing_tests|timing results from a 7-day simulation]] to the GEOS-Chem Support Team.  This will allow us to keep a list of how the model is performing across several different platform/compiler combinations.
  
 
=== Subscribing to the GEOS-Chem email lists ===
 
=== Subscribing to the GEOS-Chem email lists ===
Line 42: Line 55:
 
We use several GEOS-Chem email lists to share information among the user community:
 
We use several GEOS-Chem email lists to share information among the user community:
  
* We send information about new GEOS-Chem releases, bug fixes, and other notices of importance to the the GEOS-Chem "general" email list (<tt>geos-chem@seas.harvard.edu</tt>)
+
* We send information about new GEOS-Chem releases, bug fixes, and other notices of importance to the the GEOS-Chem "general" email list ('''geos-chem [at] g.harvard.edu''')
 
* Each [http://acmg.seas.harvard.edu/geos/geos_working_groups.html GEOS-Chem Working Group] uses its own email list to exchange information between group members.
 
* Each [http://acmg.seas.harvard.edu/geos/geos_working_groups.html GEOS-Chem Working Group] uses its own email list to exchange information between group members.
  
We invite you to join the Working Group that is most appropriate to your research, and to subscribe to the relevant email list.  Consider joining more than one Working Group (and email list) if your research spans several topics.
+
We invite you to join the Working Group that is most appropriate to your research, and to subscribe to the relevant email list.  Consider joining more than one Working Group email list if your research spans several topics.
  
For complete instructions on how to subscribe to (or unsubscribe from) the GEOS-Chem email lists, please see our [[Subscribing to the GEOS-Chem email lists]] wiki page.
+
For complete instructions on how to subscribe to or unsubscribe from the GEOS-Chem email lists, please see our [[Subscribing to the GEOS-Chem email lists]] wiki page.
  
 
=== Participating in GEOS-Chem code development ===
 
=== Participating in GEOS-Chem code development ===
  
As a member of the GEOS-Chem user community, we expect that you will submit your mature code revisions to the [[GEOS-Chem Support Team]] so that they can be included in a future release of GEOS-Chem.  We invite you to read our [[GEOS-Chem code development cycle]] wiki page for more information about the process.
+
As a member of the GEOS-Chem user community, we expect that you will submit your mature code or data updates to the GEOS-Chem Support Team so that they can be included in a future release of GEOS-Chem.  In this way, the entire GEOS-Chem community will benefit from your research.  For more information, please see our [[Submitting updates for inclusion in GEOS-Chem|guidelines for submitting GEOS-Chem code and data updates]].
  
For more detailed information about coding and debugging, see [[#GEOS-Chem coding and debugging|below]].
+
Bugs or technical issues should be [[Submitting GEOS-Chem support requests|reported immediately to the GEOS-Chem Support Team]].
  
== What you need to run GEOS-Chem ==
+
Please also see the following resources:
  
Before getting started with GEOS-Chem, please take a moment to read [[GEOS-Chem basics#Overview|this list of prerequisites on our ''GEOS-Chem basics'' wiki page]].  This is a list of items that you will have to have on your computer system before in order to run GEOS-Chem.
+
* [[GEOS-Chem coding and debugging|GEOS-Chem coding]]
 
+
* [[Debugging GEOS-Chem]]
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:52, 3 November 2016 (UTC)
+
  
 
== Where you can find GEOS-Chem documentation ==
 
== Where you can find GEOS-Chem documentation ==
  
We invite you to read our [[GEOS-Chem_basics#GEOS-Chem_documentation_and_support|summary of GEOS-Chem documentation on our ''GEOS-Chem basics'' wiki page]].  This table lists topics that can be found on the GEOS-Chem web and wiki pages.
+
We invite you to read our [[GEOS-Chem_basics#GEOS-Chem_documentation_and_support|summary of GEOS-Chem documentation on our ''GEOS-Chem basics'' wiki page]].  This table lists topics that can be found on the GEOS-Chem website and wiki.
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:58, 3 November 2016 (UTC)
+
 
+
== GEOS-Chem documentation ==
+
 
+
=== GEOS-Chem website ===
+
 
+
The GEOS-Chem website is located at [http://acmg.seas.harvard.edu/geos/ '''http://acmg.seas.harvard.edu/geos/''')] (aka [http://www.geos-chem.org '''http://www.geos-chem.org''']).
+
 
+
From this website you may:
+
 
+
* [http://acmg.seas.harvard.edu/geos/geos_welcome.html Read a welcome letter which outlines user responsibilities]
+
* [http://acmg.seas.harvard.edu/geos/doc/man Read the online '''GEOS-Chem User's Guide''']
+
* [http://acmg.seas.harvard.edu/geos/geos_sim.html See which '''years of meteorological data''' are available]
+
* [http://acmg.seas.harvard.edu/geos/geos_pub.html Access GEOS-Chem-related publications]
+
* [http://acmg.seas.harvard.edu/geos/geos_meeting_2009.html View online presentations from '''GEOS-Chem user meetings''']
+
* [http://coco.atmos.washington.edu/cgi-bin/ion-p?page=arctas.ion View output from '''GEOS-Chem Near-Real-Time simulations''']
+
* [http://acmg.seas.harvard.edu/geos/geos_people.html See a list of '''who is using GEOS-Chem''' at other institutions]
+
* [http://acmg.seas.harvard.edu/gamap/ Obtain information about the '''GAMAP visualization package''']
+
 
+
Also, please take a minute to read the [http://acmg.seas.harvard.edu/geos/geos_overview.html '''GEOS-Chem overview page'''.]  This document outlines the responsibilities for all GEOS-Chem users.
+
 
+
'''''PLEASE NOTE: At this time, the GEOS-Chem User's Guide is only viewable in HTML.'''''
+
 
+
=== GEOS-Chem public wiki ===
+
 
+
==== Overview ====
+
 
+
The GEOS-Chem public wiki (i.e. this wiki) is located at: [http://wiki.seas.harvard.edu/geos-chem/ http://wiki.seas.harvard.edu/geos-chem/].
+
 
+
The wiki [[Features of the GEOS-Chem public wiki|has many features that are designed to facilitate communication]] between GEOS-Chem users and developers.  The following informaton is posted on the wiki:
+
 
+
* [[GEOS-Chem basics]]
+
* Getting started with GEOS-Chem
+
* Technical Information
+
* Information about the specifics of:
+
** Chemistry mechanism
+
** [[Emissions_overview|Emissions]]
+
** Aerosols
+
** Diagnostics
+
** [[Offline chemistry simulations|Offline simulations]] (e.g. Mercury, Tagged CO)
+
* [[Machine_issues_%26_portability|Machine and portability issues]]
+
* [[Bugs and fixes]]
+
* [[Overview of GMAO met data products|Information about met fields]]
+
* Data Visualization and Analysis
+
 
+
The [[Main Page]] of the wiki contains links to several commonly-read pages.  If you can't find your desired topic, then try typing it into the Search Box on the left hand panel.
+
 
+
==== Wiki Philosophy ====
+
 
+
We encourage all GEOS-Chem code developers and users to check the wiki frequently, as this is the place where the latest information about GEOS-Chem will be posted. The wiki is designed to be a two-way street of communication. Users should feel free to add content to the wiki pages that are most closely related to their research.
+
 
+
In particular, the GEOS-Chem Support Team has started a new effort to make sure that all 3rd-party code and data that is submitted into GEOS-Chem has a corresponding wiki page. This will ensure that all information can be shared transparently.
+
 
+
==== Logistics ====
+
 
+
The best way to find information on the GEOS-Chem wiki is to type in your topic to the search box at the left of your browser window.  The [[Main Page]] has links to several topics on the wiki but it does not link to every single page.
+
 
+
'''You can let the GEOS-Chem wiki inform you of recent updates to the site via RSS. [[Features of the GEOS-Chem public wiki#Let the GEOS-Chem wiki inform you of recent changes!|Click here to find out how]].  You will never miss a discussion!''' 
+
 
+
In general, it is better to create smaller wiki pages that are cross-referenced rather than large wiki pages with a lot of text.  This ensures that individual pages can be more easily navigated and searched.  Also, the MediaWiki system will display a warning message if you try to save a wiki page that contains more than 32 KB of text.  If that happens, you can just simply break up your page into smaller pages. 
+
 
+
All GEOS-Chem wiki posts can be read by anyone.  However, to add or modify wiki pages, you will need to register for a wiki account.  Simply click on the "Log In/Create Account" link at the top right of your browser window.  The GEOS-Chem support team will confirm your account request (this is an anti-spamming measure).
+
 
+
Each wiki page also has a corresponding discussion page.  This is designed as the place to post information (e.g. a long email exchange, user comments, etc.) that would be too cumbersome to post on the front page.
+
 
+
Lastly, we invite all GEOS-Chem users to read our [[Features of the GEOS-Chem public wiki#Wiki culture|post about wiki user culture]].
+
 
+
=== GEOS-Chem online user's guide ===
+
 
+
[http://acmg.seas.harvard.edu/geos/doc/man/ The GEOS-Chem Online User's Guide] provides a wealth of information about how to install and run GEOS-Chem.  The User's Guide is totally rewritten for each GEOS-Chem release.
+
 
+
=== Visualization software ===
+
 
+
==== GAMAP ====
+
 
+
[http://acmg.seas.harvard.edu/gamap/ The GAMAP visualization package] is the standard visualization software that is used with GEOS-Chem.  GAMAP is [http://www.ittvis.com/ProductServices/IDL.aspx Interactive Data Language (IDL)] software and is freely available.  Please see the [http://acmg.seas.harvard.edu/gamap/doc/ Online GAMAP Manual] for more information about how to download and run GAMAP.
+
 
+
==== Other packages ====
+
 
+
Members of the GEOS-Chem User Community are developing visualization software for GEOS-Chem for languages other than IDL.  You can find a full description of available visualization tools on our [http://acmg.seas.harvard.edu/geos/geos_software_tools.html ''Related software tools for use with GEOS-Chem'' web page].
+
 
+
=== GEOS-Chem search engines ===
+
 
+
For your convenience, we have created several search engines that will allow you to search the GEOS-Chem web site, GEOS-Chem wiki, GEOS-Chem manual, and GAMAP manual.  To use these search engines, please visit our '''[http://acmg.seas.harvard.edu/geos/geos_search.html GEOS-Chem Search Page]'''.
+
 
+
=== Frequently asked questions ===
+
 
+
We have also created a wiki page devoted to [[Frequently asked questions about GEOS-Chem]], which is especially geared to new GEOS-Chem users.
+
 
+
== GEOS-Chem coding ==
+
 
+
As a new GEOS-Chem user, you will more than likely be adding your own modifications to GEOS-Chem.  The following sections contain some helpful hints pertaining to source code style and management.
+
 
+
=== Coding style ===
+
 
+
In order to improve the readibility and appearance of the GEOS-Chem source code, we ask all users to conform to the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_7.html '''GEOS-Chem Style Guide'''].  The readability of your code can be greatly enhanced by simple steps, like adding white space between words and by indenting DO loops and IF statements.
+
 
+
=== The more comments, the better! ===
+
 
+
It is good practice to add copious comments to your source code.  This will make sure that current and future GEOS-Chem users will be able to understand the modifications that you have added.
+
 
+
Keep in mind that many GEOS-Chem users (including the [[GEOS-Chem programming staff|GEOS-Chem Support Team]]) will probably not be as familiar with your specific area of research as you are.  While most users will probably get the "big picture" of what you are doing, they will be less knowledgeable about the little details (i.e. why does this reaction rate have a value of X, why is this parameter set to Y, why was this IF statement deleted, etc.).  Providing sufficient source code documentation will eliminate any such guesswork.
+
 
+
=== Automatic documentation with ProTeX ===
+
 
+
Protex is a useful Perl script that can strip information from a standard Fortran document header and save that to a LaTeX file.  The LaTeX file can then be converted into both PostScript and PDF output.
+
(Protex was developed at the Goddard Space Flight Center by Arlindo Da Silva, Will Sawyer, and others.)
+
 
+
Since GEOS-Chem v8-01-03, the [[GEOS-Chem programming staff|GEOS-Chem Support Team]] has been actively replacing the older GEOS-Chem source code documentation with ProTeX documentation headers.  This will allow a "GEOS-Chem Reference Manual" (i.e. a list of all GEOS-Chem routines and their inputs and outputs) to be generated automatically when you invoke the <tt>make doc</tt> Makefile option.
+
 
+
For more information, please see:
+
 
+
# GEOS-Chem wiki: [[Automatic documentation with protex]]
+
# GEOS-Chem User's Guide: [http://acmg.seas.harvard.edu/geos/doc/man/appendix_7.html#A7.2 '''A7.2 Headers, declarations, indentations, and white space''']
+
 
+
=== Get familiar with Git ===
+
 
+
We use the [http://www.git-scm.com Git source code management software] to facilitate the version control for GEOS-Chem.  Git allows us to easily merge and track codes from GEOS-Chem developers into the "mainline" standard source code repository.
+
 
+
When submitting source code updates for GEOS-Chem, we ask that you send us your update in [[Using Git with GEOS-Chem#Sharing your revisions with others_.28and vice versa.29|Git-ready form]].
+
 
+
For more information about Git, please see the following pages:
+
 
+
#[[Version control with Git]]
+
#[[Using Git with GEOS-Chem]]
+
 
+
== GEOS-Chem debugging ==
+
 
+
Please see our wiki page on [[GEOS-Chem Debugging Tips|tips and tricks for debugging GEOS-Chem]].  We expect all GEOS-Chem users to be proactive in debugging.  Please try to do everything possible to solve your problem before contacting the GEOS-Chem Support Team.
+
 
+
If you have access to a debugger such as Totalview, this may help you to diagnose your problem.  Ask your local IT department if you have a debugger installed at your location.
+
 
+
=== GEOS-Chem Unit Tester ===
+
 
+
We have a new tool that you can use to help find many common numerical errors and programming issues.  The GEOS-Chem Unit Tester is an external package that can run several test GEOS-Chem simulations with a set of very strict debugging options.  The debugging options are designed to detect issues such as floating-point math errors, array-out-of-bounds errors, inefficient subroutine calls, and parallelization errors.
+
 
+
For complete instructions on how the GEOS-Chem Unit Tester can assist your debugging efforts, please see our [[Debugging with the GEOS-Chem unit tester|''Debugging with the GEOS-Chem unit tester'' wiki page]].
+
 
+
--[[User:Bmy|Bob Y.]] 09:56, 17 January 2014 (EST)
+
  
=== Reporting GEOS-Chem bugs and problems ===
+
<br>----
+
If you have tried to solve your code problem but cannot, then please report it to the [mailto:geos-chem-support@as.harvard.edu GEOS-Chem Support Team].  Please include the following information:
+
  
{| border=1 cellpadding=5 cellspacing=0
+
Happy modeling!
|GEOS-Chem Version Number 
+
|(e.g. v10-01)
+
|-
+
|Met field type       
+
|(e.g. GEOS-4, GEOS-5, GCAP, GEOS-FP, MERRA)
+
|-
+
|Horizontal Resolution 
+
|(e.g. 4&deg; x 5&deg;, 2&deg; x 2.5&deg;, 0.5&deg; x 0.666&deg;, 0.25&deg; x 0.3125&deg;)
+
|-
+
|Type of Simulation   
+
|(e.g. full-chemistry, Hg, Tagged CO, etc. )
+
|-
+
|Platform & OS     
+
|(e.g. CentOS, MacOS, etc.)
+
|-
+
|Compiler             
+
|(e.g. IFORT, PGI ...)
+
|-
+
|Number of Processors
+
|&nbsp;
+
|-
+
|Diagnostics Requested 
+
|(e.g. ND28, ND43, ND45, etc.)
+
|-
+
|Description of problem
+
|&nbsp;
+
|-
+
|Error Message
+
|&nbsp;
+
|}   
+
  
also, please attach a copy of the log file from the simulation.  It is very difficult for us to diagnose the problem without seeing the log file output.
+
Sincerely,<br>[[GEOS-Chem Support Team|The GEOS-Chem Support Team]]

Latest revision as of 21:20, 3 July 2019

Welcome to the GEOS-Chem user community! Here is a quick guide to getting started:

Mission statement

GEOS-Chem Community Mission: to advance understanding of human and natural influences on the environment
through a comprehensive, state-of-the-science, readily accessible global model of atmospheric composition.

GEOS-Chem overview

Please see the GEOS-Chem overview, Narrative description of GEOS-Chem, and GEOS-Chem licensing web pages.

GEOS-Chem Support Team

The GEOS-Chem Support Team (aka GCST) is responsible for developing and maintaining the GEOS-Chem and GEOS-Chem Adjoint codes for the user community. They may be reached by email at geos-chem-support [at] g.harvard.edu

Please also see our Submitting GEOS-Chem support requests wiki page for a checklist of items that you should include when contacting the GCST for assistance.

Expectations and Responsibilities for GEOS-Chem users

The following sections describe the responsibilities that we expect from each GEOS-Chem user.

Required hardware and software

Before getting started with GEOS-Chem, please take a moment to read this list of prerequisites on our GEOS-Chem basics wiki page. Some of these items will probably have been already installed along with your operating system build.

If you plan to use GEOS-Chem on your local computer system, then make sure that your system has the necessary hardware and software able to run GEOS-Chem. If you are not sure what hardware or software is available to you, then please check with your local IT department.

If you do not have sufficient local computational resources (or if you require additional computational resources for specific projects), then we invite you to explore how you can run GEOS-Chem on the Amazon Web Services cloud computing environment. Please see our tutorial cloud.geos-chem.org for more information.

Computer language proficiency

We expect that each GEOS-Chem user will possess at least some familiarity with the following:

  • The Fortran programming language
  • The Unix environment (i.e. commands, file paths, etc.)
  • Unix scripts (not strictly required but is very helpful to know!)
  • How version control works
  • OPTIONAL, BUT RECOMMENDED: Familiarity with Python

While we cannot provide you with general instruction in programming languages or answer general programming questions, we invite you to view the list of tutorials and other relevant resources listed on our GEOS-Chem basics page.

Being a member of the GEOS-Chem community

We ask that all new GEOS-Chem user groups submit a short research blurb (1 paragraph) about how you plan to use GEOS-Chem in your research. We will add this to our GEOS-Chem People and Projects web page. Please send your research blurb to the GEOS-Chem Support Team.

We also ask that each GEOS-Chem user join the Working Group that is most relevant to his/her area of research. The Working Groups are meant to foster communication and information sharing between GEOS-Chem users, as well as to identify priorities for model development to the GEOS-Chem Steering Committee. Please introduce yourself to the Working Group Chairperson(s) and sign up for the relevant email list(s).

Each GEOS-Chem user is expected to adhere to our list of best practices. In particular, if you should discover a problem (e.g. bugs, missing files, numerical issues, etc.), please bring that to the attention of the GEOS-Chem support team right away. Other GEOS-Chem users will most certainly benefit from your discovery!

We ask that you read the GEOS-Chem Credits and References containing guidelines for giving appropriate credit to developers through co-authorship or citation. You may also refer to the Narrative Description of the GEOS-Chem Model for assistance with correctly citing relevant model components of the current standard version of GEOS-Chem in your publications.

Finally, please consider reporting your timing results from a 7-day simulation to the GEOS-Chem Support Team. This will allow us to keep a list of how the model is performing across several different platform/compiler combinations.

Subscribing to the GEOS-Chem email lists

We use several GEOS-Chem email lists to share information among the user community:

  • We send information about new GEOS-Chem releases, bug fixes, and other notices of importance to the the GEOS-Chem "general" email list (geos-chem [at] g.harvard.edu)
  • Each GEOS-Chem Working Group uses its own email list to exchange information between group members.

We invite you to join the Working Group that is most appropriate to your research, and to subscribe to the relevant email list. Consider joining more than one Working Group email list if your research spans several topics.

For complete instructions on how to subscribe to or unsubscribe from the GEOS-Chem email lists, please see our Subscribing to the GEOS-Chem email lists wiki page.

Participating in GEOS-Chem code development

As a member of the GEOS-Chem user community, we expect that you will submit your mature code or data updates to the GEOS-Chem Support Team so that they can be included in a future release of GEOS-Chem. In this way, the entire GEOS-Chem community will benefit from your research. For more information, please see our guidelines for submitting GEOS-Chem code and data updates.

Bugs or technical issues should be reported immediately to the GEOS-Chem Support Team.

Please also see the following resources:

Where you can find GEOS-Chem documentation

We invite you to read our summary of GEOS-Chem documentation on our GEOS-Chem basics wiki page. This table lists topics that can be found on the GEOS-Chem website and wiki.


----

Happy modeling!

Sincerely,
The GEOS-Chem Support Team