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--- howto:gromacs [2013/11/14 16:08]
dane
+++ howto:gromacs [2024/08/12 13:29] (current)
alopis
@@ Line 1: / Line 1: @@
-Before running your scripts remember to run((Note: Make sure the line:<code bash>export MODULEPATH=/opt/gridware/bioinformatics/modules:$MODULEPATH</code>exists in your //~/.profile// file)):<code bash>user@login01:~ $ module add gromacs/4.6.3</code>
+====== Gromacs ======
-Then your job script called //my_job.msub// will look something like this:
-<file bash>
-#/bin/sh
-#MSUB -l procs=64
-#MSUB -l feature=dell
-#MSUB -l walltime=10:00:00
-#MSUB -m be
-#MSUB -V
-#MSUB -o ${HOME}/scratch5/GROMACS/stdout.txt
-#MSUB -e ${HOME}/scratch5/GROMACS/stderr.txt
-#MSUB -d ${HOME}/scratch5/GROMACS/
-#MSUB -N MyGromacsJob
-#MSUB -mb
-NP=`cat ${PBS_NODEFILE} | wc -l`
+The available **Easy Scripts** (cpu and gpu versions) for Gromacs are:
-EXE=mdrun
+**qgromacs_2024-1,  qgromacs_2023-1, qgromacs_2022-4, qgromacs_2020-1,qgromacs_2019-4, qgromacs_2018-6, qgromacs_2018-2 and qgromacs_2018 **
-ARGS="-s input.tpr -deffnm input.tpr"
-mpirun -np ${NP} -machinefile ${PBS_NODEFILE} ${EXE} ${ARGS}
+**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**
-</file>
+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
-Finally submit your job using:<code bash>user@login01:~ $ msub my_job.msub</code>

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