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howto:amber

Amber jobs on non-GPU nodes

When running jobs for either AMBER12 or AMBER14 use the easy setup and submission scripts provided on the login node. Just execute qamber_12, qamber_14 or qamber_18. Examples of what the scripts look like are provided below.

         EXAMPLE1
Enter project name/shortname
CHEM0100
Enter input file (with .in extension)
test.in
Enter parameter and topology file
prmtop
Enter coordinate file
inpcrd
What do you wish to run SANDER, PMEMD or MDGX
SANDER
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 (TAKE NOTE OF THE EMPTY SPACES)
Enter project name/shortname
CHEM0100
Enter input file (with .in extension)
test.in
Enter parameter and topology file

Enter coordinate file

What do you wish to run SANDER, PMEMD or MDGX

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

AMBER18 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 qamber_18_gpu on login node and follow the prompts. Examples of script execution are provided below.

                  EXAMPLE1
Enter research programme name
CHEM01
Enter input file (with .in extension)
test.in
Enter parameter and topology file
prmtop
Enter coordinate file
inpcrd
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
CHEM01
Enter input file (with .in extension)
test.in
Enter parameter and topology file

Enter coordinate file

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/amber.txt · Last modified: 2018/09/13 15:38 by kgovender