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howto:gromacs [2013/11/22 16:34]
swyngaard [Example Job Submission Script]
howto:gromacs [2020/04/17 11:33] (current)
kgovender
Line 1: Line 1:
 ====== Gromacs ====== ====== Gromacs ======
  
-===== Initial Setup ===== +Execute **qgromacs_2018**,​ **qgromacs_2018-2**,​**qgromacs_2019-4** or **qgromacs_2020-1** on login node and follow the prompts. 
-In order to use Gromacs append ​the following lines to your .profile file: +This script handles PBS setup and submission. 
-<code bash> +Sets up the mpi environment variables allowing you to run over multiple processors and nodes
-export MODULEPATH=/​opt/​gridware/​applications/​gromacs/​modules:​$MODULEPATH +Examples of script execution are provided below.
-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 ​fileto update your environment variables. ​+                    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 
 +  1 
 +  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 
 +   
 +  ​
  
-===== Example Job Submission Script ===== +    EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES] 
-The following ​file is a Gromacs template ​job submission script that can used as a starting point for creating your own scripts+  Enter project name/​shortname 
-<file bash gromacs.job> +  CHEM0100 
-#This job tests GROMACS, it requires the input file min.steep0.tpr ​to be in the working directory.+  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
  
-#MSUB -l nodes=2:ppn=12 +====== Gromacs on GPU ======
-#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` +** //Please note that you need to first be added to the gpu_1 queue before you can submit jobs to the GPU cluster// **
-BIN=mdrun_mpi +
-ARGS="​-s min.steep0.tpr -deffnm min.steep0 -npme 4"+
  
-mpirun ​-np $NP -machinefile $PBS_NODEFILE $BIN $ARGS +Execute **qgromacs_2018-2_gpu**, **qgromacs_2018-6_gpu**, **qgromacs_2019-4_gpu** or **qgromacs_2020-1_gpu** on login node and follow the prompts. 
-</​file>​+Examples of script execution are provided below.
  
-This job submission script requires that the file ''​{{howto:​min.steep0.tpr}}''​ be in the working directory specified above. +                    EXAMPLE1 
- +  Enter research programme name 
-**NOTE:** Please ensure that all file I/O associated with your job only occurs on a sub-directory of your ''​scratch5''​ partition. +  ​CHEM0100 
- +  Enter default filename for all file options (without any extension to the file) 
-===== Job Submission ===== +  test 
-Submit the job using the following command+  Enter total walltime (hour:​minute) 
-<code bash> +  2:00 
-msub gromacs.job +  Enter email address 
-</code> +  ​testing@gmail.com 
- +  Generated pbs file for test 
-===== Example Expected Output =====+  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
  
/var/www/wiki/data/attic/howto/gromacs.1385130849.txt.gz · Last modified: 2013/11/22 16:34 by swyngaard