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howto:gromacs [2016/04/04 09:57]
kgovender 		howto:gromacs [2024/08/12 13:29] (current)
alopis
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 ====== Gromacs ====== ====== Gromacs ======
  
-Execute **qgromacs_5.1.2** on login node and follow the prompts.+The available **Easy Scripts** (cpu and gpu versions) for Gromacs are:  
 + 
 +**qgromacs_2024-1,  qgromacs_2023-1, qgromacs_2022-4, qgromacs_2020-1,qgromacs_2019-4, qgromacs_2018-6, qgromacs_2018-2 and qgromacs_2018 ** 
 + 
 +**qgromacs_2024-1_gpu,  qgromacs_2023-1_gpu, qgromacs_2021-1_gpu, qgromacs_2020-1_gpu, qgromacs_2019-4_gpu and qgromacs_2018-6_gpu** 
 + 
 + 
 +Execute any of these **Easy Scripts** on the login node (on a lustre subdirectory) and follow the prompts.
 This script handles PBS setup and submission. This script handles PBS setup and submission.
 Sets up the mpi environment variables allowing you to run over multiple processors and nodes. Sets up the mpi environment variables allowing you to run over multiple processors and nodes.
 Examples of script execution are provided below. Examples of script execution are provided below.
 +
 +
 +**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
 +
  
                     EXAMPLE1                     EXAMPLE1
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   Enter number of nodes on which to run job   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**, **qgromacs_2020-1_gpu** or **qgromacs_2021-1** on the 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 total walltime (hour:minute)
      
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