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howto:gromacs [2016/04/04 09:55]
kgovender
howto:gromacs [2020/04/17 11:33] (current)
kgovender
Line 1: Line 1:
 ====== Gromacs ====== ====== Gromacs ======
  
 +Execute **qgromacs_2018**,​ **qgromacs_2018-2**,​**qgromacs_2019-4** or **qgromacs_2020-1** on login node and follow the prompts.
 +This script handles PBS setup and submission.
 +Sets up the mpi environment variables allowing you to run over multiple processors and nodes.
 +Examples of script execution are provided below.
  
 +                    EXAMPLE1
 +  Enter project name/​shortname
 +  CHEM0100
 +  Enter default filename for all file options (without any extension to the file)
 +  test
 +  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 default filename for all file options (without any extension to the file)
 +  test
 +  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
 +
 +====== Gromacs 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 **qgromacs_2018-2_gpu**,​ **qgromacs_2018-6_gpu**,​ **qgromacs_2019-4_gpu** or **qgromacs_2020-1_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 (without any extension to the file)
 +  test
 +  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 (without any extension to the file)
 +  test
 +  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/attic/howto/gromacs.1459756557.txt.gz · Last modified: 2016/04/04 09:55 by kgovender