Difference between revisions of "GEOS-Chem basics"

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The [[GEOS-Chem Support Team]] has created this page to assist new GEOS-Chem users to download and run GEOS-Chem on their computer systems.
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This content has been migrated to [https://geos-chem.readthedocs.io <tt>geos-chem.readthedocs.io</tt>]
 
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== Overview ==
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=== GEOS-Chem requirements ===
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This information has been migrated to [https://geos-chem.readthedocs.io <tt>geos-chem.readthedocs.io</tt>].
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=== GEOS-Chem documentation and support ===
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We have compiled a list of resources that will help you get started with GEOS-Chem:
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{| border=1 cellspacing=0 cellpadding=5
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|-valign="top" bgcolor="#CCCCCC"
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!width="325px"|Item
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!width="725px"|Description
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|-valign="top"
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|[[#The GEOS-Chem website|The GEOS-Chem website ('''geos-chem.org''')]]
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|The main GEOS-Chem website, which links to many other resources.
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|-valign="top"
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|[[#The GEOS-Chem wiki|The GEOS-Chem wiki ('''wiki.geos-chem.org''')]]
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|The GEOS-Chem wiki (i.e. this wiki).
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|-valign="top"
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|[https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/related-docs.html GEOS-Chem user manuals]
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|User manuals for GEOS-Chem Classic, GCHP, HEMCO, and related software.
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|-valign="top"
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|[[Frequently asked questions about GEOS-Chem|The GEOS-Chem FAQ]]
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|Answers to the most commonly-asked questions about GEOS-Chem.
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|-valign="top"
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|[[#GEOS-Chem tutorials|GEOS-Chem tutorial presentations]]
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|Several online tutorial presentations about how to use GEOS-Chem
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|-valign="top"
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|[http://www.geos-chem.org/geos_licensing.html GEOS-Chem licensing]
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|Information about the public license under which GEOS-Chem (and related software) are distributed.
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|}
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== Unix resources ==
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GEOS-Chem is designed to run on computers with the '''Unix operating system'''.  There is no single version of Unix; rather, Unix comes packaged in several different '''distributions'''.  Many modern computer clusters use CentOS, which is an open-source Unix implementation.  Other systems may use a proprietary Unix distribution, such as Red Hat Enterprise.  GEOS-Chem will perform in the same way regardless of the specific Unix implementation on your system.
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If you require assistance setting up or customizing your Unix login environment, please contact your local IT staff.  The [[GEOS-Chem Support Team]] can only provide support for GEOS-Chem-related issues.
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You can now run GEOS-Chem on the Amazon Web Services cloud infrastructure.  See our cloud computing tutorial ([http://cloud.geos-chem.org '''cloud.geos-chem.org''']) for more details.
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<span style="color:red">'''''IMPORTANT!'''''</span> Please make sure that your computer system meets the [[Minimum_system_requirements_for_GEOS-Chem|minimum system requirements for memory and disk space in order to run GEOS-Chem]].
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=== Common Unix commands ===
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The resources below cover many common Unix commands.  You will find these useful, particularly if you have never worked on a Unix machine before.
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* [http://www.csd.uoc.gr/~hy255/refcards/unix-command-summary.pdf Summary of Unix commands (PDF doc)]
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* [http://staff.washington.edu/corey/unix-intro%2Bman.html A Brief Introduction to Unix (by Corey Satten)]
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* [http://www.petefreitag.com/item/426.cfm The 15 Essential Unix commands (by Pete Freitag)]
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=== Unix shells and shell scripting ===
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One of the nice features of Unix is that you can highly customize your environment.  You can also write scripts to perform several commands (such as copying files or running programs) sequentially.  This will save you the trouble of having to type the same commands over and over at the command-line prompt. 
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There are several Unix shells that you can use, but we recommend using <tt>bash</tt>.  Here are some resources that you can use to learn more about the <tt>bash</tt> shell:
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*[http://superuser.com/questions/49289/what-is-the-bashrc-file ''What is the .bashrc file'' on SuperUser]
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*[http://www.linuxfromscratch.org/blfs/view/svn/postlfs/profile.html ''The Bash Shell Startup Files'' from <u>Beyond Linux from Scratch</u>]
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*[http://linuxcommand.org/ ''LinuxCommand.org''&mdash;interactive tutorial]
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*[http://www.linfo.org/alias.html How to use the Unix alias command]
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*[http://www.tldp.org/LDP/Bash-Beginners-Guide/html/ Bash Guide for Beginners]
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*[http://www.tldp.org/LDP/abs/html/ Advanced Bash scripting]
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*[http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO.html Bash programming&mdash;Introduction How-To]
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:11, 19 September 2017 (UTC)
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== The GNU Make utility ==
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The GNU Make utility is used to compile GEOS-Chem&mdash;that is, to create an executable file from source code.  GNU Make usually comes pre-packaged with your Unix distribution (e.g. CentOS, Linux, Ubuntu, Fedora, etc.), so you will probably not need to install it yourself.
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GEOS-Chem contains several Makefiles.  A Makefile contains several commands in the GNU Make language direct how the Fortran compiler will build GEOS-Chem.  Makefiles determine the sequence in which individual files are compiled, as well as the options that will be activated.
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Unless you are going to be adding a significant amount of new code into GEOS-Chem, you will probably not need to know the nitty-gritty details of how to create or modify Makefiles.  But if you do have to change an existing Makefile, you can contact the [[GEOS-Chem Support Team]], who will be happy to assist you. 
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If you are interested in learning more about the GNU Make utility, we invite you to consult the following resources:
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*[https://www.gnu.org/software/make/manual/make.html ''The GNU Make manual'']
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*[http://opensourceforu.com/2012/06/gnu-make-in-detail-for-beginners/ ''GNU Make in detail for beginners'' at OpenSource.com]
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*[https://www.cs.swarthmore.edu/~newhall/unixhelp/howto_makefiles.html ''Using Make and writing makefiles'' at Swarthmore U.]
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*[https://en.wikibooks.org/wiki/Make ''Make'' at wikibooks.org]
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*[https://notendur.hi.is/jonasson/software/make-book/ ''Managing projects with GNU Make'' by O'Reilly]
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For specific information about compiling GEOS-Chem, see:
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*[[Compiling GEOS-Chem]]
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*''[[Guide to compilers for GEOS-Chem]]''
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:40, 19 December 2016 (UTC)
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== The Git source code management system ==
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Please see our ''[[Guide to using Git with GEOS-Chem]]'' for more information about how to use Git with GEOS-Chem.
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:28, 21 June 2019 (UTC)
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== Fortran resources ==
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Please see our ''[[Guide to compilers for GEOS-Chem]]'' wiki page for more information about the compilers that you can use to build GEOS-Chem, as well as some Fortran-language resources.
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:58, 14 June 2019 (UTC)
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== The netCDF library ==
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Please see our ''[[Guide to netCDF in GEOS-Chem]]'' for more information about how to install netCDF on your system (or check if it is already installed).
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:58, 13 June 2019 (UTC)
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== The GEOS-Chem source code ==
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The '''GEOS-Chem model source code''' is kept in a publicly-accessible [[#The Git source code management system|Git repository]].  You must '''compile''' the source code into an '''executable file''' with one of the [[#Fortran resources|supported Fortran compilers]].  The compilation is managed by the [[#GNU Make|GNU Make]] utility,  which reads the various [[GEOS-Chem Makefile Structure|GEOS-Chem makefiles]] to produce the executable with the desired options.
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For more information and detailed downloading instructions, please see our ''[[Downloading GEOS-Chem source code]]'' wiki page.
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--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 13:56, 12 June 2019 (UTC)
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== The GEOS-Chem shared data directories ==
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For more information, please see our ''[[Downloading GEOS-Chem data directories]]'' wiki page.
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:15, 14 June 2019 (UTC)
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== Restart files ==
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This content has been migrated to the [https://geos-chem.readthedocs.io/en/latest/gcc-guide/04-data/restart-files.html '''Restart files''' chapter of <tt>geos-chem.readthedocs.io</tt>].
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== Visualization packages ==
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Please see our ''[[Guide to visualization and analysis tools for GEOS-Chem]]'' for information about software packages that you can use to analyze or plot GEOS-Chem output.
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:59, 14 June 2019 (UTC)
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== The GEOS-Chem wiki ==
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The GEOS-Chem wiki (i.e. this wiki) is located at: [http://wiki.geos-chem.org '''wiki.geos-chem.org'''].
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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 [[Main Page]] of the wiki contains links to several commonly-read pages.  If you can't find your desired topic, the best way to search for information on the wiki is by using the Search Box located in the upper right corner of each wiki page.
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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.
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In particular, the [[GEOS-Chem Support Team]] has begun an 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.
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=== Logistics ===
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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).
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The best way to find information on the GEOS-Chem wiki is to use the Search Box located in the upper right corner of each wiki page.  You can also 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]].
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 22:08, 11 January 2019 (UTC)
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== GEOS-Chem tutorials ==
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Please see the following GEOS-Chem tutorials:
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*[http://youtube.geos-chem.org GEOS-Chem video tutorials ('''youtube.geos-chem.org''')]
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*[http://cloud.geos-chem.org Using GEOS-Chem on the Amazon Web Services Cloud computing environment ('''cloud.geos-chem.org''')]
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*[https://github.com/geoschem/GEOSChem-python-tutorial GEOS-Chem Python Tutorial]
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*IGC9 model clinics:
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**[http://acmg.seas.harvard.edu/presentations/IGC9/talks/MonD_Clinics_yantosca_bob_1_pc.pdf Working with GEOS-Chem]
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**[http://acmg.seas.harvard.edu/presentations/IGC9/talks/MonD_Clinics_lundgren_lizzie_2_mac.pptx High-performance GEOS-Chem (GCHP)]
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**[http://acmg.seas.harvard.edu/presentations/IGC9/talks/MonD_Clinics_lin_haipeng_1_pc.pdf WRF-GC: GEOS-Chem in WRF]
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**[http://acmg.seas.harvard.edu/presentations/IGC9/talks/ThuB_Clinics_zhuang_jiawei_1_mac.pdf GEOS-Chem on the AWS Cloud]
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**[http://acmg.seas.harvard.edu/presentations/IGC9/talks/ThuB_Clinics_keller_christoph_1_mac.pdf GEOS-Chem in Earth System Models]
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**[http://acmg.seas.harvard.edu/presentations/IGC9/talks/ThuB_Clinics_wang_yuxuan_1_mac.pdf GEOS-Chem nested model]
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**[https://prezi.com/iut9jtq9muas/?utm_campaign=share&utm_medium=copy&rc=ex0share GEOS-Chem adjoint model]; [http://acmg.seas.harvard.edu/presentations/IGC9/talks/ThuB_Clinics_GCAdjoint_Handout.pdf Handout]
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--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 14:12, 12 June 2019 (UTC)
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== For more information ==
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You can find much more information about GEOS-Chem on our website and wiki.  We invite you to consult the following resources:
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*[https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/related-docs.html GEOS-Chem user manuals]
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*[[GEOS-Chem overview#GEOS-Chem Guides|GEOS-Chem Guides]]
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*[[Frequently asked questions about GEOS-Chem]]
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*[[Guide to GEOS-Chem error messages|What should I do if my GEOS-Chem simulation dies with an error?]]
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*[https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/debug-guide.html Debug GEOS-Chem and HEMCO errors]
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*[[Submitting GEOS-Chem support requests|How can I contact the GEOS-Chem Support Team for assistance?  What should I include in my request?]]
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Revision as of 22:12, 9 August 2022

This content has been migrated to geos-chem.readthedocs.io