Part 4 - Job submission: NAMD
Posted June 30, 2010 - 12:43pm
In previous exercise, we have seen submitting a job directly on the RAL host. This time we're going to do remote submission. Let's take RAL for our local host and submit our NAMD job to LEEDS host, and we also need to stage input files over beforehand.
Make sure we're connected to RAL in the upper window, create a subdirectory namd under our home directory, and copy over the example files required by the NAMD application.
-bash-3.00$ mkdir ~/namd
-bash-3.00$ cd ~/namd
-bash-3.00$ cp /apps/namd/examples/* .
-bash-3.00$ ls -l
total 48
-rw-r--r-- 1 ngs0383 ngs0383 464 Nov 13 11:19 alanin
-rw-r--r-- 1 ngs0383 ngs0383 17389 Nov 13 11:19 alanin.params
-rw-r--r-- 1 ngs0383 ngs0383 5616 Nov 13 11:19 alanin.pdb
-rw-r--r-- 1 ngs0383 ngs0383 12953 Nov 13 11:19 alanin.psf
-bash-3.00$ cd ~/namd
-bash-3.00$ cp /apps/namd/examples/* .
-bash-3.00$ ls -l
total 48
-rw-r--r-- 1 ngs0383 ngs0383 464 Nov 13 11:19 alanin
-rw-r--r-- 1 ngs0383 ngs0383 17389 Nov 13 11:19 alanin.params
-rw-r--r-- 1 ngs0383 ngs0383 5616 Nov 13 11:19 alanin.pdb
-rw-r--r-- 1 ngs0383 ngs0383 12953 Nov 13 11:19 alanin.psf
Focus on the lower window, and make sure it is connected to Leeds host. Because we're going to submit the job to this host, we need to copy the data files to the home directory. Let's find out what our home directory is like:
[ngs0208@ngs ~]$ pwd
/home/ngs0208
/home/ngs0208
Let's go back to RAL and issue a remote copy command using gsiscp. ( the argument -P is in uppercase).
-bash-3.00$ gsiscp -P 2222 -r ~/namd ngs.leeds.ac.uk:/home/ngs0208
alanin 100% 464 0.5KB/s 00:00
alanin.params 100% 17KB 17.0KB/s 00:00
alanin.pdb 100% 5616 5.5KB/s 00:00
alanin.psf 100% 13KB 12.7KB/s 00:00
alanin 100% 464 0.5KB/s 00:00
alanin.params 100% 17KB 17.0KB/s 00:00
alanin.pdb 100% 5616 5.5KB/s 00:00
alanin.psf 100% 13KB 12.7KB/s 00:00
Then, let's submit our job NAMD to the Leeds host. The executable is /usr/ngs/NAMD_2_6, and we need to specify the working directory as namd under our home directory with argument (-d), and also the job type as mpi. The output is redirected to the file result.out(-stdout) and the number of processing elements is 6 (-np). There're two arguments following the NAMD executable, namd2 specifies the operation we want, and the path of alanin tells the application how to find the required input files.
-bash-3.00$ globus-job-submit ngs.leeds.ac.uk/jobmanager-pbs -np 6 -d /home/ngs0208/namd -stdout result.out -x '(jobtype=mpi)' /usr/ngs/NAMD_2_6 namd2 /home/ngs0208/namd/alanin
https://ngs.leeds.ac.uk:64015/12333/1226579444/
https://ngs.leeds.ac.uk:64015/12333/1226579444/
We can then query the job status using the URI:
-bash-3.00$ globus-job-status https://ngs.leeds.ac.uk:64015/12333/1226579444/
DONE
DONE
The NAMD application will save the standard output into file result.out and some other related output files in the namd subdirectory.
[ngs0208@ngs namd]$ ls -l
total 68
-rw-r--r-- 1 ngs0208 ngspool 464 Nov 13 11:23 alanin
-rw-r--r-- 1 ngs0208 ngspool 17389 Nov 13 11:23 alanin.params
-rw-r--r-- 1 ngs0208 ngspool 5616 Nov 13 11:23 alanin.pdb
-rw-r--r-- 1 ngs0208 ngspool 12953 Nov 13 11:23 alanin.psf
-rw------- 1 ngs0208 ngspool 1588 Nov 13 12:34 output.coor
-rw------- 1 ngs0208 ngspool 1588 Nov 13 12:34 output.vel
-rw------- 1 ngs0208 ngspool 83 Nov 13 12:34 output.xsc
-rw------- 1 ngs0208 ngspool 6994 Nov 13 12:34 result.out
total 68
-rw-r--r-- 1 ngs0208 ngspool 464 Nov 13 11:23 alanin
-rw-r--r-- 1 ngs0208 ngspool 17389 Nov 13 11:23 alanin.params
-rw-r--r-- 1 ngs0208 ngspool 5616 Nov 13 11:23 alanin.pdb
-rw-r--r-- 1 ngs0208 ngspool 12953 Nov 13 11:23 alanin.psf
-rw------- 1 ngs0208 ngspool 1588 Nov 13 12:34 output.coor
-rw------- 1 ngs0208 ngspool 1588 Nov 13 12:34 output.vel
-rw------- 1 ngs0208 ngspool 83 Nov 13 12:34 output.xsc
-rw------- 1 ngs0208 ngspool 6994 Nov 13 12:34 result.out
Hopefully, we have got what we want, the file 'result.out', in the file list.
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