The following is a generic example of how to get an application up and running on the NYSgrid. This a by no means and eloquent example, basically brute-force. Assume you have a machine connected to nysgrid and a valid proxy.
1. Set up directory
On a machine connected to the nysgrid, we put all required files together:
/san/user/jbednasz/u2/NAMD_GRID
Contents of /san/user/jbednasz/u2/NAMD_GRID:
tar ball from PI:
-rw-r--r-- 1 jbednasz ccrstaff 39475200 Aug 4 11:36 namd.tar
Contents of tar ball:
-rw-r--r-- 1 jbednasz ccrstaff 1730 Jun 30 15:26 fep.tcl -rw-r--r-- 1 jbednasz ccrstaff 190613 Jun 30 15:30 par_all27_prot_lipid_111808A.inp -rw-r--r-- 1 jbednasz ccrstaff 25584392 Jun 30 15:31 alc_eval5_autopsf.psf -rw-r--r-- 1 jbednasz ccrstaff 13686212 Jun 30 15:32 eval5_autopsf.fep -rw-r--r-- 1 jbednasz ccrstaff 39475200 Aug 4 11:36 namd.tar -rw------- 1 jbednasz ccrstaff 13686237 Aug 4 11:36 eval5_con10.pdb -rw-r--r-- 1 jbednasz ccrstaff 3794 Aug 11 07:58 eval9.conf
grid scripts:
-rwxr-xr-x 1 jbednasz ccrstaff 2065 Aug 11 07:59 run_grid_job.sh -rw-r--r-- 1 jbednasz ccrstaff 530 Aug 4 11:53 grid.sh
pbs script to run NAMD
-rw-r--r-- 1 jbednasz ccrstaff 706 Aug 4 11:37 pbsNAMD
2. Scripts defined
run_grid_job.sh - The script you will execute on your machine. It take the machine you want to run on and the "experiment" you are running as command line options. The "experiment" is used to help you organize your runs.
grid.sh - The script that gets executed once your grid job makes it out to the machine it will run on.
pbsNAMD - A sample script of how NAMD is run on the grid machine it we were going to run thru local batch system.
3. Sample Run
cd /san/user/jbednasz/u2/NAMD_GRID ./run_grid_job.sh u2-grid.ccr.buffalo.edu bednasz_cuny (I want to run on u2-grid.ccr.buffalo.edu and I am calling my experiment "bednasz_cuny") Your identity: /DC=org/DC=doegrids/OU=People/CN=Jon Bednasz 258078 Enter GRID pass phrase for this identity: Creating proxy ........................................ Done Your proxy is valid until: Fri Aug 14 10:00:07 2009 Remote directory: /san/scratch/grid/grid-tmp/grid-data Creating the experiment directories Staging files to the grid Running the job https://u2-grid.ccr.buffalo.edu:18637/6361/1249992199/ Running the job Use globus-job-status <url> to get status of job -bash-3.2$ globus-job-status https://u2-grid.ccr.buffalo.edu:18637/6361/1249992199/ PENDING -bash-3.2$ globus-job-status https://u2-grid.ccr.buffalo.edu:18637/6361/1249992199/ ACTIVE -bash-3.2$ globus-job-status https://u2-grid.ccr.buffalo.edu:18637/6361/1249992199/ COMPLETED
4. What do this scripts do
a. source osg software stack's "setup.sh"
b. setup my proxy
c. discover the run_directory on the host machine
d. create application and experiment directories
e. Staging files to the grid
f. Run the job
g. Return the id of the job.