Part 5 - Job submission: GROMACS from outside NGS
Posted June 30, 2010 - 12:43pm
We have beening using NGS hosts so far with both AMBER and NAMD. And we're going to try the last exercise from a local Linux machine that's not an NGS node but has GT4 installed.
Let's close the connection to LEEDS in the lower window:
[ngs0208@ngs ~]$ logout
Now connect to the NeSC training cluster. Select menu File -> New Connection, fill Hostname with tc03.nesc.ed.ac.uk, keep port as 2222, select publickey, and press Connect.
Once we're in there, we can grab the example data files from RAL and modify them locally. We have previously used gsiscp to copy files. While it is easy to use, it may be unstable dealing with large files. So let's use the GridFTP tool globus-url-copy this time. (Find out your home directory with pwd command and replace user00 with it in the following command.)
-bash-2.05b$ globus-url-copy gsiftp://ngs.rl.ac.uk/apps/Gromacs/examples/* file:///home/user00/
All the files are silently transferred to your home directory.
-bash-2.05b$ ls -l total 84 -rw-r--r-- 1 ngs0208 ngspool 29266 Nov 13 15:46 conf.gro -rw-r--r-- 1 ngs0208 ngspool 8029 Nov 13 15:46 grompp.mdp -rw-r--r-- 1 ngs0208 ngspool 1102 Nov 13 15:46 index.ndx -rw-r--r-- 1 ngs0208 ngspool 43420 Nov 13 15:46 spc216.pdb -rw-r--r-- 1 ngs0208 ngspool 87 Nov 13 15:46 topol.top
Suppose that we modify these files and change file name conf.gro to myconf.gro.
-bash-2.05$ mv conf.gro myconf.gro
And then upload these files to our working directory on RAL for use by GROMACS. Let's create a subdirectory gromacs on RAL in the upper window.
-bash-3.00$ mkdir ~/gromacs
And copy these files to that directory using globus-url-copy again, from our local host.
-bash-2.05$ globus-url-copy file:///home/user00/* gsiftp://ngs.rl.ac.uk/home/ngs0383/gromacs/
Now we can submit our job to work on those data files and get some result. We use argument '-c myconf.gro' to give our version of the conf file, and we expect the output file is output.tpr.
-bash-2.05$ globus-job-submit ngs.rl.ac.uk/jobmanager-lsf -d /home/ngs0383/gromacs -x '&(jobtype=single)' /usr/ngs/GROMACS_3_3_1 grompp_d -np 8 -shuffle -sort -f grompp.mdp -p topol.top -c myconf.gro -o output.tpr https://ngs.rl.ac.uk:64106/16053/1226595307/
Now let's check the running status.
-bash-2.05$ globus-job-status https://ngs.rl.ac.uk:64106/16053/1226595307/ DONE
Since the job is finished, we can get the result now. Again, we use globus-url-copy to copy the output file to our local machine.
-bash-2.05$ globus-url-copy gsiftp://ngs.rl.ac.uk/home/ngs0383/gromacs/output.tpr file:///home/user00/
Congratulations for reaching this far!
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