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First time GEOS-Chem users

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First time GEOS-Chem users - AtmosWiki
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First time GEOS-Chem users
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Here is a brief rundown of what you have to do to run GEOS-Chem for the first time. The best resource for this is
the GEOS-Chem Users Manual, found at GEOS-Chem website (http://www.geos-chem.org), under Manuals &
Documents. It goes through the installation and run setup step by step. Definitely check it out.
Follow these steps to install GEOS-Chem:
1. Get the source code. You can get it from Harvard using git:
git clone git://git.as.harvard.edu/bmy/GEOS-Chem/ my_code
This gets the most up-to-date version of the code and puts it in a directory called my_code
2. Get a run directory. You can get run directories from Harvard using git, but it is probably easier to ask a fellow
group member for one, as they'll have an input.geos file with the correct paths (this will mean something to you
later). Make sure the run directory has a restart file with the correct met fields and resolutions.
2b. As a pointer, most people set their directories up so there's a directory called Code or GEOS-Chem that has both
the run directory and the my_code directory in it. Not necessary, but its convenient.
3. Now, there are really only two files that you need to look at to get started. 3a. In your code directory,
Headers/define.h has the switches that tell GEOS-Chem what type of met fields you want to use, and what
resolution you'd like to run at. Scroll to this section:
!----- Model types ----!#define GCAP
'GCAP'
!#define GEOS_3
'GEOS_3'
!#define GEOS_4
'GEOS_4'
#define GEOS_5
'GEOS_5'
!#define MERRA
'MERRA'
!----- Grid sizes ----!#define NESTED_CH
'NESTED_CH'
!#define NESTED_NA
'NESTED_NA'
!#define NESTED_EU
'NESTED_EU'
!#define GRID05x0666 'GRID05x0666'
!#define GRID1x1
'GRID1x1'
!#define GRID1x125
'GRID1x125'
#define GRID2x25
'GRID2x25'
!#define GRID4x5
'GRID4x5'
#define GRIDREDUCED 'GRIDREDUCED'
and set the comments (marked by !) to your desired settings. In this case, running at 2x2.5 resolution using GEOS-5
met fields.
3b. In your run directory, input.geos has all the input options for your simulation. Here's where you set the dates
you want to simulate, the emissions you want to use, and what you want to output. It's too much info to put here, so
I recommend looking at the Users Manual section on input.geos, Chapter 5.2.1. The manual goes through what
each line of this file means, and should be able to walk you through it.
4. Compile the code. This takes all the individual pieces of the code and turns them into an executable that you can
run. From the code directory, enter
make all
. The code will compile, and place an executable called
bin/geos
. Then make a copy of/link to the executable into your run directory.
5. Lastly, some quick settings needed to run on stetson. From your run directory, enter these lines:
export KMP_STACKSIZE=2097152000
ulimit -s 2097152
export OMP_NUM_THREADS=16
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First time GEOS-Chem users - AtmosWiki
http://fizz.phys.dal.ca/~atmos/wiki/index.php?title...
The first two lines are memory settings that are needed to keep your simulation from crashing. The third will set
your simulation to run on all 16 cores of whatever node you're on. Note that this will pretty much take up a whole
node, so if stetson is busier than usual, consider setting it to run on just 4 or 8.
6. Now you're ready to go. To run the model in the background, type
nohup ./geos > log &
. You should now be up and running.
Of course, it's often the case that there are little things that go wrong or are not set up properly. It almost always
happens the first time you run the model. If that happens, ask a fellow group member who will gladly help!
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