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--- howto:gromacs [2016/04/04 09:55]
kgovender
+++ howto:gromacs [2024/08/12 13:29] (current)
alopis
@@ Line 1: / Line 1: @@
 ====== Gromacs ======
+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.
+Sets up the mpi environment variables allowing you to run over multiple processors and nodes.
+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
+  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)
+: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**, **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)
+: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

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