User Tools

Site Tools


howto:gromacs

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
howto:gromacs [2014/09/08 09:58]
dane typo
howto:gromacs [2020/04/17 11:33] (current)
kgovender
Line 1: Line 1:
 ====== Gromacs ====== ====== Gromacs ======
  
-This page is out-of-dateFor updated information ​you can look at these two pages[[howto:bioinformatics#​gromacs|sun gromacs]]; [[howto:gpu_gromacs|gpu 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.1410163129.txt.gz · Last modified: 2014/09/08 09:58 by dane