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

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Welcome to the GEOS-Chem user community!  Here is a quick guide to getting  
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Welcome to the GEOS-Chem user community!  Here is a quick guide to getting started:
started:
+
  
== GEOS-Chem programming staff ==
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== Mission statement ==
  
[http://people.seas.harvard.edu/~yantosca/ Bob Yantosca] and Claire Carouge are responsible for developing and maintaining the GEOS-Chem source code for the user community.  They are available during regular business hours (M-F, 9AM-5PM ET).
+
<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>
  
The general rule of thumb is that if you have a question about the GEOS-Chem code itself, or if your question deals with a programming or coding matter, then you should ask Bob and Claire.  On the other hand, if you have a question about a scientific matter, a data source, etc., then you should direct your question to the person(s) who have worked on that particular topic.
+
== GEOS-Chem overview ==
  
For a list of GEOS-Chem users and their primary areas of research, please visit the [http://www.as.harvard.edu/ctm/geos/geos_people.html '''GEOS-Chem People & Projects page'''.]
+
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.
  
Of course, if you do not know whom is the best person to ask, then feel free to contact Bob, Philippe or Claire, and they will be happy to forward your query to the proper person.
+
== GEOS-Chem Support Team ==
  
Here is the contact information for Bob and Claire:
+
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'''
  
{| border=1 cellspacing=0 cellpadding=5
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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.
|- bgcolor="#CCCCCC"
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! Name 
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! Title
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! Group email               
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! Individual email
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! Phone
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! FAX     
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|-
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| Bob Yantosca
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| Software Engineer
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| geos-chem-support@as.harvard.edu
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| yantosca@seas.harvard.edu
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| 617-496-9424
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| 617-495-4551
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|-
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| Claire Carouge
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| Research Associate
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| geos-chem-support@as.harvard.edu
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| ccarouge@seas.harvard.edu
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| 617-495-2893
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| 617-495-4551
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|}
+
  
Please send any and all GEOS-Chem related inquiries to the group email [mailto:geos-chem-support@as.harvard.edu '''geos-chem-support@as.harvard.edu'''].  This will send your email to Bob and Claire without you having to address your email to them individually.
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== Expectations and Responsibilities for GEOS-Chem users ==
  
== Expectations and Responsibilities ==
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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 [[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 ===
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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)
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* The Fortran programming language
* IDL (preferred), or other graphics software (e.g. Splus, Matlab)
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* 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
 +
* OPTIONAL, BUT RECOMMENDED: Familiarity with Python
  
We cannot provide you with general instruction in programming languages or answer general programming questions.  We would like to invite you to view to view the list of tutorials and other relevant resources that are listed on the GEOS-Chem web page at [http://www.as.harvard.edu/ctm/geos/geos_resources.html '''GEOS-Chem Resources Page'''.]
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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 invite you to read our document on 
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[http://www.as.harvard.edu/ctm/geos/word_pdf_docs/resources_guidelines_tips.pdf User Resources, Code Development Guidelines, and Debugging Tips].
+
 
+
'''''PLEASE NOTE: GEOS-Chem cannot be used in a Windows (XP/Vista) environment!  You will need a Unix-like operating system (e.g. IRIX, Sun/Solaris, Linux, Ubuntu, Fedora, ...)'''''
+
  
 
=== Being a member of the GEOS-Chem community ===
 
=== Being a member of the GEOS-Chem community ===
  
We would like to ask all new GEOS-Chem user groups to 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.
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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://www.as.harvard.edu/ctm/geos/geos_working_groups.html Working Group] that is most relevant to his/her area of researchThe 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://www.as.harvard.edu/ctm/geos/geos_steering_cmte.html GEOS-Chem Steering Committee].
+
 
+
Each GEOS-Chem user is also expected to adhere to our list of [http://acmg.seas.harvard.edu/geos/geos_best_practices.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!
+
 
+
== Subscribing to the GEOS-Chem email lists ==
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+
There are several GEOS-Chem email lists:
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+
{| border=1 cellspacing=0 cellpadding=5
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|- bgcolor="#cccccc"
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!Email list address
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!Intended audience
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|-
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|<tt>geos-chem@seas.harvard.edu</tt>
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|All GEOS-Chem users and developers<br>'''''NOTE: This is the email list to which information about <br>new model versions, bugs & fixes, etc. will be sent'''''
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|-
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|<tt>geos-chem-adjoint@seas.harvard.edu</tt>
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|Members of the [[GEOS-Chem Adjoint|Adjoint Model and Data Assimilation Working Group]]
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|-
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|<tt>geos-chem-aerosols@seas.harvard.edu</tt>
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|Members of the [[Aerosols_overview:_projects_and_developments|Aerosols Working Group]]
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|-
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||<tt>geos-chem-carbon@seas.harvard.edu</tt>
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|Members of the [[Carbon Gases and Organics Working Group]]
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|-
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|<tt>geos-chem-emissions@seas.harvard.edu</tt>
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|Members of the [[Emissions Working Group]]
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|-
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|<tt>geos-chem-oxidants@seas.harvard.edu</tt>
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|Members of the [[Chemistry Issues|Oxidants and Chemistry Working Group]]
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|-
+
|<tt>geos-chem-regional@seas.harvard.edu</tt>
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|Members of the [[Regional Air Quality Working Group]]
+
|}
+
 
+
To subscribe to any of these lists, please visit the page: https://lists.seas.harvard.edu/mailman/listinfo and then click on the name of the list to which you wish to subscribe.  You will be taken to a page where you can specify your email address and a password and then click SUBMIT.  You will then receive a confirmation email from the system.  Follow the directions in the confirmation email and then you will be added to the list.
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+
'''''PLEASE NOTE: If you wish to send an email to any of the above GEOS-Chem mailing lists, then please be sure to send your email from the same address with which you subscribed to the list.  Otherwise your email may bounce back to you. The GEOS-Chem mailing lists are set up to reject emails from non-list members.  This is done in order to prevent spam.'''''
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== GEOS-Chem website ==
+
 
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The GEOS-Chem website is located at [http://acmg.seas.harvard.edu/geos/ '''http://acmg.seas.harvard.edu/geos/'''].
+
 
+
From this website you may:
+
 
+
* [[Downloading GEOS-Chem source code and data|Download the GEOS-Chem source code and data]]
+
* [http://acmg.seas.harvard.edu/geos/doc/man Read the online '''GEOS-Chem User's Guide''']
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* [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_2007.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 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''']
+
 
+
We also ask that you provide your contact information, a list of people who
+
will be using GEOS-Chem, and a short description of your research for the
+
[http://www.as.harvard.edu/ctm/geos/geos_people.html '''GEOS-Chem People and Projects Page'''.]
+
 
+
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.  This has not been saved into PDF format at this time.'''''
+
 
+
== GEOS-Chem public wiki ==
+
 
+
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/].
+
 
+
This wiki is meant to facilitate communication between GEOS-Chem users and developers.  The following informaton is posted on the wiki:
+
 
+
* General information about GEOS-Chem
+
* Getting started with GEOS-Chem
+
* Technical Information
+
* Information about the specifics of:
+
** Chemistry mechanism
+
** Emissions
+
** Aerosols
+
** Diagnostics
+
** Offline simulations (e.g. Mercury, Tagged CO)
+
* Machine and portability issues
+
* Bugs and fixes
+
* Information about met fields
+
* Data Visualization and Analysis
+
 
+
We invite all GEOS-Chem users to register for the wiki by clicking the "create account" link at the top right corner of the screen.  Only registered users may edit the wiki, but anyone without an account may read the wiki pages.
+
 
+
'''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!''' 
+
 
+
'''''NOTE: Only registered users may edit the wiki.  Please do not  edit wiki pages unless you have new information to contribute!'''''
+
 
+
== GEOS-Chem data directory access ==
+
 
+
=== Primary download site ===
+
 
+
The GEOS-Chem source code, data and meteorological field directories may be accessed by anonymous FTP from
+
 
+
ftp ftp.as.harvard.edu
+
login: anonymous
+
password: your email address
+
cd pub/geos-chem
+
 
+
The geos-chem directory is further divided into the following subdirectories:
+
 
+
HDF/
+
data/
+
evaluation/
+
beta_releases/
+
mean_OH/
+
patches/
+
public_releases/
+
  
Here is a quick look at the contents of these subdirectories:
+
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)]].
  
{| border=1 cellpadding=5 cellspacing=0
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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!
|- bgcolor="#CCCCCC"
+
! Directory                         
+
! Description                               
+
|-
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| <tt>/data</tt>                             
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| Root Data Directory
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|-                         
+
| <tt>/data/GEOS_1x1</tt>                     
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| 1x1 global grid emissions etc. files       
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|-
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| <tt>/data/GEOS_1x1_CH</tt>                 
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| 1x1 China-nested grid emissions etc files 
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|-
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| <tt>/data/GEOS_1x1_CH/GEOS_3</tt>         
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| 1x1 China-nested grid GEOS-3 met fields 
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|- 
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| <tt>/data/GEOS_1x1_NA/</tt>               
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| 1x1 NA-nested grid emissions etc files     
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|-
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| <tt>/data/GEOS_1x1_NA/GEOS_3</tt>         
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| 1x1 NA-nested grid GEOS-3 met fields       
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|-
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| &nbsp;
+
| &nbsp;
+
|-
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| <tt>/data/GEOS_2x2.5/</tt>                 
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| 2x2.5 emissions and other data files 
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|-
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| <tt>/data/GEOS_2x2.5/GEOS_3/YYYY/MM</tt>   
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| GEOS-3 2x2.5 met data               
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|-
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| <tt>/data/GEOS_2x2.5/GEOS_4_v4/YYYY/MM</tt>  
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| GEOS-4 2x2.5 met data (late-look)   
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|-
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| <tt>/data/GEOS_2x2.5/GEOS_4_flk/YYYY/MM</tt>
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| GEOS-4 2x2.5 met data (1st-look)
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|-
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| <tt>/data/GEOS_2x2.5/GEOS_4_5/YYYY/MM</tt>
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| GEOS-5 2x2.5 met data 
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|-
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| &nbsp;
+
| &nbsp;
+
|-
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| <tt>/data/GEOS_4x5/</tt>               
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| 4x5 emissions and other data files                 
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|-
+
| <tt>/data/GEOS_4x5/GEOS_3/YYYY/MM</tt>
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| GEOS-3 4x5 met data               
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|-
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| <tt>/data/GEOS_4x5/GEOS_4_v4/YYYY/MM</tt> 
+
| GEOS-4 4x5 met data (late-look)    
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|-
+
| <tt>/data/GEOS_4x5/GEOS_4_flk/YYYY/MM</tt> 
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| GEOS-4 4x5 met data (1st-look) 
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|-
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| <tt>/data/GEOS_4x5/GEOS_5/YYYY/MM</tt> 
+
| GEOS-5 4x5 met data
+
|-
+
| &nbsp;
+
| &nbsp; 
+
|-
+
| <tt>/evaluation</tt>                       
+
| Plots from 1-yr benchmark simulations
+
|-     
+
| <tt>/HDF</tt>                             
+
| Contains user code for reading HDF and HDF-EOS data files
+
|-     
+
| <tt>/NRT-ARCTAS</tt>                             
+
| Contains output from the [http://coco.atmos.washington.edu/cgi-bin/ion-p?page=arctas.ion GEOS-Chem Near-Real-Time simulations for ARCTAS]
+
|-
+
| <tt>/public_releases</tt>
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| Directory containing TAR file source code and run directories for GEOS-Chem public releases
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|-
+
| <tt>/beta_releases</tt>  
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| Directory containing TAR file source code and run directories for "beta" GEOS-Chem releases
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|-
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| <tt>patches/</tt>
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| Directory containing bug-fix software patches (if necessary)
+
|-
+
| <tt>mean_OH/</tt>
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| Directory containing 3-D mean OH fields archived from previous GEOS-Chem simulations.
+
|}
+
  
NOTE: if you are interested in obtaining the GCAP met fields (at 4x5 resolution), then they are stored in a similar data structure from the root directory:
+
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.
  
ftp ftp.as.harvard.edu
+
Finally, please consider reporting your [[GEOS-Chem_7-day_timing_tests|timing results from a 7-day simulation]] to the GEOS-Chem Support TeamThis will allow us to keep a list of how the model is performing across several different platform/compiler combinations.
  cd pub/gcap/
+
  
=== Alternative download site ===
+
=== Subscribing to the GEOS-Chem email lists ===
  
The GEOS-Chem data and meteorological fields used by Dalhousie University are also available via anonymous FTP from:
+
We use several GEOS-Chem email lists to share information among the user community:
  
ftp rain.ucis.dal.ca
+
* 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.
  
This site has overlap with many of the above directories from the Harvard site, but it is not as extensiveThis site, however, additionally hosts the following unique datasets:
+
We invite you to join the Working Group that is most appropriate to your research, and to subscribe to the relevant email listConsider joining more than one Working Group email list if your research spans several topics.
  
{| border=1 cellpadding=5 cellspacing=0
+
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.
|- bgcolor="#CCCCCC"
+
! Directory                         
+
! Description                               
+
|-
+
| <tt>/GEOS_0.5x0.666_EU/</tt>                             
+
| 1/2 x 2/3 European nested grid emission etc files
+
|-                         
+
| <tt>/GEOS_0.5x0.666_EU.d/</tt>                     
+
| 1/2 x 2/3 European nested grid met fields (GEOS-5)
+
|-
+
| <tt>/GEOS_0.5x0.666_NA/</tt>                 
+
| 1/2 x 2/3 North American nested grid emission etc files
+
|-
+
| <tt>/GEOS_0.5x0.666_NA.d/</tt>         
+
| 1/2 x 2/3 North American nested grid met fields (GEOS-5)
+
|-
+
| &nbsp;
+
| &nbsp;
+
|- 
+
| <tt>/GEOS_1x1.25/</tt>               
+
| 1 x 1.25 Global GEOS4 emission etc files     
+
|-
+
| <tt>/GEOS_1x1.25.d/</tt>         
+
| 1 x 1.25 Global GEOS4 met fields
+
|}
+
  
 +
=== Participating in GEOS-Chem code development ===
  
'''''We recommend using the [[Downloading_GEOS-Chem_source_code_and_data#Using_wget_to_download_files|Unix <tt>wget</tt> utility]] for FTP download.  This has some nice options, including recursive directory download and crontab scheduling.'''''
+
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]].
  
== GEOS-Chem Code development cycle ==
+
Bugs or technical issues should be [[Submitting GEOS-Chem support requests|reported immediately to the GEOS-Chem Support Team]].
  
How GEOS-Chem code development works:  
+
Please also see the following resources:
  
# First download a recent standard code version (public or internal)
+
* [[GEOS-Chem coding and debugging|GEOS-Chem coding]]
# Add your modifications into the code
+
* [[Debugging GEOS-Chem]]
# Test your code thoroughly and make sure that it works
+
# Contact the GEOS-Chem Support Teamand request that your changes be included in the standard code
+
# The GEOS-Chem Support Team will add your changes to the standard code and benchmark it
+
# Daniel approves the benchmark results and declares the version APPROVED
+
# GOTO 1
+
  
== GEOS-Chem debugging tips ==
+
== Where you can find GEOS-Chem documentation ==
  
When your run dies with an error, the most important thing is to try to
+
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.
isolate the place where the error occurs (i.e. does it die in chemistry, in
+
transport, in dry deposition, etc.)  
+
+
Here are a list of things that you can try if your run dies w/ an error:
+
  
# Look at the log file?  Can you tell where the run stopped?
+
<br>----
# If not, re-run with the ND70 diagnostic turned on (debug output)
+
#* This will print debug output and should let you pinpoint the location of the error
+
# Did you run out of time in the queue?
+
# Did you modify the standard code?
+
#* If so, then focus on your most recent changes
+
#* You should keep a *clean* (unmodified) version for comparison
+
# Can you isolate the error to a particular operation?
+
#* Turn off operations (e.g. transport, emissions, etc.) one at a time and run again
+
# Does the error happen consistently?
+
#* If the error happens at the same model date & time, it could indicate bad input data
+
#* If it happened only once, it could be caused by a network problem or other such transient condition
+
# Also check for math errors
+
#* Is there a division by zero, logarithm of negative number, etc?
+
# Recompile with -C (or -CB for IFORT compiler) option to check for array-out-of-bounds errors
+
#* Out-of-bounds errors can produce segmentation faults
+
# When in doubt, print it out!
+
#* Print out the values of variables in the area where you suspect the error lies
+
#* Also use "call flush(6)" to flush the output buffer after writing
+
#* Maybe you will see something wrong in the output
+
# When all else fails, USE THE BRUTE FORCE METHOD!
+
#* Comment out code until you find where the failure occurs
+
  
== Reporting GEOS-Chem bugs and problems ==
+
Happy modeling!
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If you should encounter a bug or a problem running GEOS-Chem, then please send an email to <tt>geos-chem-support@as.harvard.edu</tt> with a description of the problem.  Please include the following information:
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{| border=1 cellpadding=5 cellspacing=0
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Sincerely,<br>[[GEOS-Chem Support Team|The GEOS-Chem Support Team]]
| GEOS-Chem Version Number 
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| (e.g. v8-01-01)
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|-
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| Met field type       
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| (e.g. GEOS-3, GEOS-4, GEOS-5, GCAP)
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|-
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| Horizontal Resolution 
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|(e.g. 4x5, 2x25, 1x1)
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|-
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| Type of Simulation   
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| (e.g. full-chemistry, Hg, Tagged CO )
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|-
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| Platform             
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| (e.g. Altix, SGI-Origin, Linux box)
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|-
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| Compiler             
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| (e.g. IFORT, Sun, SGI Mips, PGI ...)
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|-
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| Number of Processors
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| &nbsp;
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|-
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| Diagnostics Requested 
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| (e.g. ND28, ND43, ND45, etc.)
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|-
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| Description of problem
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| &nbsp;
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|-
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| Error Message
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| &nbsp;
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|}   
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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.
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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.


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Happy modeling!

Sincerely,
The GEOS-Chem Support Team