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--- howto:gromacs [2013/11/22 16:34]
swyngaard [Example Job Submission Script]
+++ howto:gromacs [2024/08/12 13:29] (current)
alopis
@@ Line 1: / Line 1: @@
 ====== Gromacs ======
-===== Initial Setup =====
+The available **Easy Scripts** (cpu and gpu versions) for Gromacs are:
-In order to use Gromacs append the following lines to your .profile file:
-<code bash>
-export MODULEPATH=/opt/gridware/applications/gromacs/modules:$MODULEPATH
-module add gromacs/4.6.1 mpich2/1.5
-</code>
-To complete the setup log out of the cluster and back in again (or just ''source'' your .profile file) to update your environment variables.
+**qgromacs_2024-1,  qgromacs_2023-1, qgromacs_2022-4, qgromacs_2020-1,qgromacs_2019-4, qgromacs_2018-6, qgromacs_2018-2 and qgromacs_2018 **
-===== Example Job Submission Script =====
+**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**
-The following file is a Gromacs template job submission script that can used as a starting point for creating your own scripts:
-<file bash gromacs.job>
-#This job tests GROMACS, it requires the input file min.steep0.tpr to be in the working directory.
-#MSUB -l nodes=2:ppn=12
-#MSUB -l feature=dell
-#MSUB -l walltime=24:00:00
-#MSUB -j oe
-#MSUB -o out.log
-#MSUB -d /export/home/username/scratch5/gromacs
-#MSUB -V
-NP=`cat $PBS_NODEFILE | wc -l`
+Execute any of these **Easy Scripts** on the login node (on a lustre subdirectory) and follow the prompts.
-BIN=mdrun_mpi
+This script handles PBS setup and submission.
-ARGS="-s min.steep0.tpr -deffnm min.steep0 -npme 4"
+Sets up the mpi environment variables allowing you to run over multiple processors and nodes.
+Examples of script execution are provided below.
-mpirun -np $NP -machinefile $PBS_NODEFILE $BIN $ARGS
-</file>
-This job submission script requires that the file ''{{howto:min.steep0.tpr}}'' be in the working directory specified above.
+**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:
-**NOTE:** Please ensure that all file I/O associated with your job only occurs in a sub-directory of your ''scratch5'' partition.
+  module load chpc/easy_scripts
-===== Job Submission =====
-Submit the job using the following command:
-<code bash>
-msub gromacs.job
-</code>
-===== Example Expected Output =====
+                    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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