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howto:namd

NAMD

You need to ensure that the relevant NAMD files are in the directory were you wish to submit your job from. Run qnamd_2.11 in order to generate a PBS script and submit a job to the cluster. Examples of the script are provided below:

Examples of input required for these scripts are provided below.

                  EXAMPLE1
Enter project name/shortname
CHEM0100
Enter input file (with .conf extension)
test.conf
Enter number of nodes on which to run job
1
Enter total walltime (hour:minute)
2:00
Enter email address
testing@gmail.com
Generated pbs file for test
Do you wish to submit job to cluster (y/n)
y
  EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES]
Enter project name/shortname
CHEM0100
Enter input file (with .conf extension)
test.conf
Enter number of nodes on which to run job

Enter total walltime (hour:minute)

Enter email address
testing@gmail.com
Generated pbs file for test
Do you wish to submit job to cluster (y/n)
y

NAMD on GPU

Please note that you need to first be added to the gpu_1 queue before you can submit jobs to the GPU cluster

Execute qnamd_2.13_gpu on login node and follow the prompts. Examples of script execution are provided below.

                  EXAMPLE1
Enter research programme name
CHEM0100
Enter default filename for all file options (with .conf extension)
test.conf
Enter total walltime (hour:minute)
2:00
Enter email address
testing@gmail.com
Generated pbs file for test
Do you wish to submit job to cluster (y/n)
y
 
  EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES]
Enter research programme name
CHEM0100
Enter default filename for all file options (with .conf extension)
test.conf
Enter total walltime (hour:minute)

Enter email address
testing@gmail.com
Generated pbs file for test
Do you wish to submit job to cluster (y/n)
y
/var/www/wiki/data/pages/howto/namd.txt · Last modified: 2018/09/13 15:35 by kgovender