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howto:gromacs [2018/09/10 11:34]
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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 ====== Gromacs on GPU ====== ====== Gromacs on GPU ======
  
-Execute **qgromacs_2018-2_gpu** on login node and follow the prompts.+** //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. Examples of script execution are provided below.
  
                     EXAMPLE1                     EXAMPLE1
-  Enter project name/shortname+  Enter research programme name
   CHEM0100   CHEM0100
   Enter default filename for all file options (without any extension to the file)   Enter default filename for all file options (without any extension to the file)
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     EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES]     EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES]
-  Enter project name/shortname+  Enter research programme name
   CHEM0100   CHEM0100
   Enter default filename for all file options (without any extension to the file)   Enter default filename for all file options (without any extension to the file)
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