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howto:amber [2016/03/30 11:28]
kgovender 		howto:amber [2024/10/09 12:42] (current)
alopis
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 ===== Amber jobs on non-GPU nodes ===== ===== 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. +When running jobs for either AMBER14, AMBER18 or AMBER20 use the easy setup and submission scripts provided on the login node.
-Just execute **qamber_12** or **qamber_14**. +
-Examples of what the script looks like is provided below.+
  
-        EXAMPLE1+**Note**, please first include this **module load** - even better if your add this line to your .bashrc, then the Easy Scripts should be visible and available: 
 + 
 +  module load chpc/easy_scripts 
 + 
 + 
 +Just execute **qamber_14** or **qamber_18** or **qamber_20**. 
 +Examples of what the scripts look like are provided below. 
 + 
 +           EXAMPLE1
   Enter project name/shortname   Enter project name/shortname
   CHEM0100   CHEM0100
Line 25: Line 31:
   Do you wish to submit job to cluster (y/n)   Do you wish to submit job to cluster (y/n)
   y   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 and AMBER20 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
 +
/app/dokuwiki/data/attic/howto/amber.1459330114.txt.gz · Last modified: 2021/12/09 16:42 (external edit)

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