TOMAS setup guide

This page describes how to acquire the latest source code, data, and libraries required to build and run GEOS-Chem with TOMAS aerosol 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. However, the 'bleeding edge' code has many recent developments in GEOS-Chem/TOMAS that are not included in the public release, including parallel computing.

Getting Set Up

Code

You can grab the absolute latest code from my source directory on glooscap:

cp -r /home/sfarina/source/GC_Bleeding_Edge/ ~

or, (safer) you can grab my latest "snapshot"

cp /home/sfarina/source/GC_BE_snapshot-latest.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 extract it directly to your home directory:

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

This will extract the libraries folder to your home directory.

Environment

In order to get the compiler to run and recognize the libraries described above, some environment variables must be set. Below is an excerpt from my .bashrc.

ROOT_LIBRARY_DIR="/home/sfarina/geos-chem-libraries-intel11"
GC_BIN=$ROOT_LIBRARY_DIR/bin
GC_INCLUDE=$ROOT_LIBRARY_DIR/include
GC_LIB=$ROOT_LIBRARY_DIR/lib
export GC_BIN
export GC_INCLUDE
export GC_LIB

export FC="ifort"

export LD_LIBRARY_PATH="/home/sfarina/geos-chem-libraries-intel11/lib"
export PATH="/home/sfarina/geos-chem-libraries-intel11/Compiler/11.1/080/bin/intel64:/home/sfarina/opt/bin:$PATH"
export LD_LIBRARY_PATH="/usr/local/gnu/lib64:/usr/local/gnu/lib:/home/sfarina/geos-chem-libraries-intel11/lib:/home/sfarina/geos-chem-libraries-intel11/Compiler/11.1/080/lib/intel64/:/home/sfarina/geos-chem-libraries-intel11/Compiler/11.1/080/idb/lib/intel64"
export INTEL_LICENSE_FILE="/home/sfarina/geos-chem-libraries-intel11/software/intel/Compiler/11.1/080/Licenses"
source /home/sfarina/geos-chem-libraries-intel11/Compiler/11.1/080/bin/ifortvars.sh intel64

ulimit -S -s unlimited

If you are using bash, you can copy/paste this to your .bashrc. Once the compiler and libraries are installed in ~/geos-chem-libraries-intel11 change instances of sfarina to your username.

source ~/.bashrc
ifort --version

If ifort returns

ifort (IFORT) 11.1 20101201

you should be all set to start compiling

Data

To set up the necessary data for GEOS-Chem, simply

cd ~
ln -s /home/sfarina/data .

This will allow you to link to my data directory, which is mostly a collection of links to the data at /home/rmartin/group/ctm/ with some changes due to recent GC development. DO NOT copy this directory, as it is many many many gigabytes, and is probably beyond your disk quota on glooscap.

Building GEOS-Chem/TOMAS

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. Installation is described above in the libraries section.

Make

Glooscap allows you to use multicore interactive shells to do heavy processing. I invoke a 16 core shell to build geoschem. put this in your .bashrc

alias pshell16="qrsh -V -cwd -l h_rt=08:00:00 -l h_vmem=2.0G -l h_stack=12.5G -N IA_16 -pe openmp 16 bash"
alias pshell8="qrsh -V -cwd -l h_rt=08:00:00 -l h_vmem=2.0G -l h_stack=12.5G -N IA_8 -pe openmp 8 bash"

Then you can do

cd YOUR_CODE_DIR/GC_Bleeding_Edge/GeosCore
pshell16
make -j16 tomas40

This will build GEOS-Chem with 40 bin TOMAS using 16 processors at a time. As an added bonus, this will not choke up the rest of the users on glooscap.

The available target names are:

tomas                 <--TOMAS 30
tomas12
tomas15
tomas40

Important!

When changing tomas versions, always always always do

make realclean

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/

Copy the tarballs (named 40.tgz, 30.tgz, etc.) to a standard location. You can then do

tar zxvf YOUR_STANDARD_LOCATION/40.tgz

to extract the appropriate run directory to your current working directory. The folder will be named run.TOMASXX, where XX is 12, 15,30, or 40 depending on the version you would like to run.

Once you have the appropriate version of geostomas compiled and your run directory extracted, copy the executable to your run directory.

input.geos

The input.geos file is where most of the runtime options for geoschem are configured. There are currently no TOMAS specific entries in the input.geos file, save for diagnostic output quantities. Please see the Users' Guide for more information.

Submitting Jobs to the Parallel Queue

In each folder is a file called parallel.sh. Below is a description of some of the parameters:

#!/bin/bash
# $ -S /bin/bash
./etc/profile
#$ -o job_output
#$ -l h_rt=100:00:00                            #wall clock time requested from grid engine. Lower request times will have higher priority in the queue
#$ -l h_vmem=2.0G                               #vmem requested from grid engine. 2.0 is sufficient for all versions at 4x5 and TOMAS15 at 2x2.5 on 16 cores
#$ -l h_stack=12.5G                             #stack memory requested from grid engine
#$ -N RUN_NAM                                   #a name for your run
#$ -pe openmp 16                                #number of cores you are requesting from grid engine
#$ -cwd                                         #inherit properties from your current shell
export OMP_NUM_THREADS=16                       #number of openMP threads
export KMP_STACKSIZE=500000000                  #stacksize memory limit for each thread

ulimit -t unlimited              # cputime
ulimit -f unlimited              # filesize
ulimit -c unlimited              # coredumpsize
ulimit -m unlimited              # memoryuse
ulimit -l unlimited              # memorylocked

cd YOUR_RUN DIRECTORY
./geostomas > log

You'll need to edit it slightly (run name and working directory), then run:

qsub parallel.sh

You can check on the status in the queue with

qstat

You can watch the logfile output of your simulation with

tail -f log

With some minimal editing, you can find some summary information from your runs using the script here

/net/samqfs/pierce/sfarina/testruns/informed/hourstat.sh

Developing

Writing for GEOS_Chem is pretty straightforward. Please try to follow the style guide as much as possible. Most of TOMAS is contained within tomas_mod.F90, and you should be able to find what you need with a little work and a few invocations of grep. If you can't find what you need, ask.

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.

Setup

I have a copy of git installed at

/home/sfarina/opt/bin

You can either use this executable or build it yourself from source. To use this executable, add the following to your .bashrc

export PATH="/home/sfarina/opt/bin:$PATH"

Branching and Commits

Once you have git installed, 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
vi fictional_example_mod.F90
git status
git add fictional_example_mod.F90
git commit

Patching

If I make some new changes to my branch of code, you will need to do a patch and merge. My current branch in git is called tomasmerge. If I provide you with update.patch, this should do the trick:

git checkout tomasmerge
git apply update.patch
git checkout MY_BRANCH
git merge tomasmerge

Reference

There are many useful resources for git on the web. Here are some I found useful:

• Branching and Merging
• Creating and Applying Patches
• Understanding git through gitk

Debugging

There are two major ways of debugging: inserting massive amounts of print statements, or using a debugger. Both are useful.

ifort comes with a debugger similar to gdb: iidb.

geos-chem-libraries-intel11/Compiler/11.1/080/bin/intel64/iidb

In order to use it, you must compile geostomas as follows

make realclean
make DEBUG=yes tomas

Apart from the debugger and normal print statements, TOMAS has a very useful builtin called DEBUGPRINT, that prints the values of the TOMAS size bins in a big table.

Post Processing

Now that you've successfully run the model, there are a few more hurdles to inspect your data.

Installing IDL

Copy the IDL / gamap scripts from my home directory.

cp -r ~sfarina/IDL ~

Edit the following as needed, and add it to your .bashrc

IDL_STARTUP="/home/sfarina/IDL/idl_startup/idl_startup.pro"
IDL_DIR="/usr/local/itt/idl/idl80/"
IDL_PATH="$IDL_DIR:/home/sfarina/IDL"
module load idl/8.0

Processing

GEOS-Chem currently outputs all data in the form of a binary punch file (.bpch). These files must be handled using IDL. The process is outlined below:

Copy

Copy the relevant files to your postprocessing directory for a given run

ctm.bpch
diaginfo.dat
tracerinfo.dat
proc_one.pro
averageCNCCN_XX.py             <-- XX is TOMAS version
plotCNCCN.py

Split

Use the script Bpch_Sep_Sal interactively from within the IDL environment to ctm.bpch into separate months For example, to extract august, 2005 from ctm.bpch

idl
> Bpch_Sep_Sal,'ctm.bpch','ctm.08.bpch',Tau0=nymd2tau(20050801) 
> exit

Create netcdf output

Using the IDL script proc_one.pro, we extract information from the monthly .bpch files and save it to the standard netCDF Edit proc_one.pro to use the correct infile/outfiles Execute proc_one from your shell:

idl proc_one.pro

Counting CN and CCN

Run averageCNCCN_XX.py, where XX is the model version For example, to bin and average the August results from TOMAS15:

./averageCNCCN_15.py 08

Plotting the Results

Edit your directory name to be of the format YYY_run.TOMASXX, where YYY is a run number, and XX is the TOMAS version. plotCNCCN.py will automatically detect the model version and customize map names. To plot the surface and zonal average concentrations of CN3, CN10, CN40, and CN80 for august:

./plotCNCCN.py 08

Once you have completed this process, you will have a zonal and surface level map of CN3, CN10, CN40 and CN80 predicted by the model.

NCview

You can also use ncview on the file ctm.nc to view individual species concentrations or nucleation rates.

ncview ctm.nc
ncview ctm_nuc.nc

Other Advice / Issues

• If you have followed these instructions and geoschem crashes without any output, try (un)commenting the "welcome to geoschem" and the following call flush lines from main.F
• I use the GNU Bourne Again SHell (bash). I suggest you do the same. The csh is fine, but I have written all of my scripts using bash. Your life will probably be easier if you use bash.
• It is a good idea to TAKE NOTES on the details of your simulations.
• Making a backup of your code and any important files is a good idea. Making two backups is a better idea.
• if you have any questions or you are running into trouble, please ask either myself, Sajeev, or Jeff for help. I am usually able to respond to emails within a day, and am willing to use gchat or skype if need be.

--Salvatore Farina 17:28, 25 July 2013 (EDT)