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Configure GEOS-Chem Run

Updating paths for HPC

• I have downloaded GEOS-Chem inputs: /scratch/lfs/groups/henderson/geos-chem/

• Your simulation will need to point to my input folder




Test configuration

Exercise 1: Update configuration

1. Revert to a v9-01-03-Release (`git checkout tags/v9-01-03-Release`)

2. Change paths for simulation

3. Change dates for simulation

4. Change dates for output

5. Should look like input.geos listing below. (... indicates part of file not shown) (i.e. find the locations of input.geos seen below and update it to match)

6. Disable KPP


Listing 1: input.geos (... indicates part of the file is not shown)

GEOS-CHEM SIMULATION v9-01-03: GEOS-5 NOx-Ox-HC-Aerosol simulation (53 tracers)
Start YYYYMMDD, HHMMSS  : 20040101 000000
End   YYYYMMDD, HHMMSS  : 20040107 000000
Run directory           : ./
Input restart file      : restart.4x5.geos5.YYYYMMDDhh
Make new restart file?  : T
Output restart file(s)  : restart.4x5.geos5.YYYYMMDDhh
Root data directory     : /scratch/lfs/groups/henderson/geos-chem/
Dir w/ 1x1 emissions etc: /scratch/lfs/groups/henderson/geos-chem/
Turn on Chemistry?      : T
Use linear. strat. chem?: T
 => Use Linoz for O3?   : T
Chemistry Timestep [min]: 60
Read and save CSPEC_FULL: F
USE solver coded by KPP : F
%%% OUTPUT MENU %%%     : 123456789.123456789.123456789.1--1=ZERO+2=BPCH 
Schedule output for JAN : 3000003000000000000000000000000
Dir w/ archived OH files: /scratch/lfs/groups/henderson/geos-chem/
%%% O3 P/L MENU %%%     :
Dir w/ O3 P/L rate files: /scratch/lfs/groups/henderson/geos-chem/
END OF FILE             :


Test run script

• HPC uses torque to manage job load

– Each job is configured to request resources

– The resources used and assetts of the user determine when the job actually gets run

• Options/Resources can be defined in a run script

– any option in man qsub

– `#PBL -flag option` where flag is a flag and option is a string specified as valid for that flag

– the -l flag and -W are specieal and can be used with subsequent keywords separated by :

• Special commands

– `-W group_list=`: group is the group whose resources you are using

– `-l nodes=` where is the number of computers you want

– `-l ppn=` where is the number of processes per node

• Each job starts its own environment

Exercise 2: Create a run script

1. Open putty and connect to HPC

2. `cd /lfs/scratch/username/geos-chem/simulations/4x5/geos5/standard/`

3. Use `man qsub` to research and document the first 7 lines of the code below (listing 5: Enter answer in letters a-f below.

(a) ___________________________________

(b) ___________________________________

(c) ___________________________________

(d) ___________________________________

(e) ___________________________________

(f) ___________________________________

4. What does line 9 do?

5. Why do you think I put lines 10-13?

6. What do you think line 14 does?

7. Create a copy of the in your `standard` folder


Listing 2:

#PBS -W group_list=henderson
#PBS -l walltime=04:00:00
#PBS -m be
#PBS -q default
#PBS -l nodes=1:ppn=2
#PBS -l mem=4gb
#PBS -l pmem=2gb

export KMP_STACKSIZE=4294967296
ulimit -s 4294967

module purge
module load intel/2012
module load hdf5/1.8.9
module load netcdf/4.2
./geos > geos.$(date +"%FT%T").log