Submit MD++ Jobs to a Cluster

Submit MD++ to a cluster

Besides running MD++ on your own computers, we can also submit MD++ job to clusters. Here take cluster mc2 as an example. Make a sub-directory Codes in the home directory, and extract the downloaded MD++ files there.

$ mkdir Codes 
$ cd Codes 
$ tar -zxvf md++-2015-01-14.tar.gz

Then we compile the potential energy we need, for example, 'ljbond', for Python files

$ cd MD++
$ make ljbond build=R SYS=mc2 PY=yes

Now we want to submit a job 'scripts/ex_polymer/polymer_expansion.py' with the potential energy 'ljbond_mc2' to the mc2 cluster. We need to prepare the following .pbs file.

1. !/bin/bash
2. PBS -N polymer_equil
3. PBS -j oe
4. PBS -l nodes=1:ppn=24,walltime=96:00:00
5. PBS -V
   1. 1. ---------------------------------------
      2. BEGINNING OF EXECUTION
      3. ---------------------------------------

echo The master node of this job is `hostname` echo The working directory is `echo $PBS_O_WORKDIR` echo This job runs on the following nodes: echo `cat $PBS_NODEFILE` ncpu=`cat $PBS_NODEFILE | wc -w` echo "Number of processors = $ncpu "

1. 1. 1. end of information preamble

cd $PBS_O_WORKDIR echo $PWD sleep 2 py_bin/ljbond_mc2 scripts/ex_polymer/polymer_expansion_press.py & wait

Suggestions

1. Add searching function in the manual website. 2. Add a comment to clear the variable input.