User talk:Salvatore Farina

This page describes how to acquire the latest source code, data, and libraries required to build and run GEOS-Chem with TOMAS microphysics on the ace-net glooscap cluster.

Overview

The latest public release of GEOS-Chem with TOMAS does not include many of the recent developments in aerosol science. It also cannot take advantage of parallel computing technologies. Lately I've been working on the "Bleeding Edge" code to address these issues. Here's a guide that should help you get started if you're using the glooscap cluster.

Getting Set Up

Code

You can grab the code from my source directory on glooscap: /home/sfarina/source/GC_BE_snapshot_7-13-13.tgz

Libraries

geos-chem-libraries-intel11 is a bundle of software required to build and run the latest version of GEOS-Chem. Included in this package:

• Intel Ifort Fortran compiler - v11.1 - required to build geoschem
• NetCDF - Network Common Data Format libraries - required to read and write certain datasets
• HDF5 - Hierarchical Data Format - required to read and write certain datasets
• other dependencies - required for netcdf and hdf5

You can copy this folder as a tarball from /home/sfarina/gclibs.tgz or simply:

cd ~
tar zxvf /home/sfarina/gclibs.tgz

This will extract the libraries folder to your home directory.

Environment

As for environment variables, take a look at the first few lines of my .bashrc. The crucial part there is the LD_LIBRARY_PATH and license file stuff.

Data

I have my data directory set up slightly differently than the last versions of geoschem to fix some of the issues that popped up as they added datasets, etc. you can probably just link to it.

Compiling

Compiler

Please note that the ONLY VERSION of the intel compiler which reliably compiles a working executable of geos-chem with TOMAS is version 11.1, described above in the libraries section.

Make

cd GeosCore and do make tomas40

and always do make realclean when changing tomas versions.

Running GEOS-Chem with TOMAS

Run Directories

There are run directories for each of the tomas versions at: /net/samqfs/pierce/sfarina/standard_run_directories/ either copy the tarballs named 40.tgz, etc (recommended) or copy the folders they're based on (run.TOMAS40, etc).

Submitting Jobs to the Parallel Queue

In each folder is a file called parallel.sh. you'll need to edit it slightly (run name and working directory), then run qsub parallel.sh and it should go if it's set up / compiled right.

I forgot where I got them, but there's a folder you'll need called geos-chem-libraries-intel11 that you'll need to build geoschem. Sajeev can help you with this if it's not on the wiki,oryou can copy mine (I think).

Developing

Version Control

Git! You should definitely use git to track your changes. I have a copy built/installed at /home/sfarina/opt/bin/git that you can probably either copy or just use. make a separate branch for yourself as soon as you make a copy of the code, this way we can easily trade/track updates / advances / bugfixes. git checkout -b my_new_branch

Other Advice

if you have any questions or you are running into trouble, please ask. I am usually able to respond to emails within a day, and am willing to use gchat or skype if need be.

--Salvatore Farina 14:51, 25 July 2013 (EDT)