Overview

CP2K is an open source program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. It provides a general framework for different methods such as e.g., density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) and classical pair and many-body potentials.

Quick steps to run CP2K

$ tutorial cp2k                 # Copies input and script files to the directory "tutorial-cp2k".
$ cd tutorial-cp2k              # Takes you to the directory "tutorial-cp2k".
$ condor_submit cp2k.submit # Submits the condor job script file "cp2k_run.submit".

After few minutes, CP2K outputs are generated in the directory tutorial-cp2k. In the following sections, we will discuss the details of preparing the input and job script files to run the CP2K simulations.

CP2K tutorial files

In the command prompt, type

$ tutorial cp2k # Copies the input and script files to the directory tutorial-cp2k.

This will create a directory tutorial-cp2k. Inside the directory, you will see the following files

cp2k.submit               # Condor job submission script file.
cp2k.sh                   # Job execution script file.
cs_cell_opt_direct_lbfgs.inp  # Input configuration file  for running the cp2k simulation.

Here, cp2k_run.submit and cp2k_run.sh are the script files related to job submission and the file cs_cell_opt_direct_lbfgs.inp is the input file for the CP2K simulation. The details regarding the preparation of the input file for CP2K are available at the CP2K website.

Job execution and submission files

The file cp2k.submit is the condor description file. Please refer to the Quickstart tutorial to learn about the key words in the script file. Here, we will discuss the condor file transfer mechanism. The option transfer_input_files specifies what input files are transferred from the login machine (where you log in and submit the jobs) to the remote worker machine (where the jobs are being executed). In the cp2k.submit file, the option

transfer_input_files = cs_cell_opt_direct_lbfgs.inp # Name of the input file transferred to the worker machine.

means that the listed file cs_cell_opt_direct_lbfgs.inp is transferred from the login machine to the worker machine. Similarly, we can specify the output files from the worker machine to Midway by adding the following lines in the condor job submission script file - cp2k.submit.

transfer_output_files = file1.out, file2.out, file3.out ... etc # List of output files separated by commas.
should_transfer_files=Yes          # Key word to activate the file transfer
when_to_transfer_output = ON_EXIT  # After the job execution is finished

For vanilla universe jobs, all the output files are transferred automatically (the current example runs the job in the vanilla universe). In other universe types, for example grid universe, the user needs to specify the list of output files.

The script file cp2k.sh includes information about loading the module and the job execution commands:

#!/bin/bash
source /cvmfs/oasis.opensciencegrid.org/osg/modules/lmod/5.6.2/init/bash # Reads and executes the bash file located in the init directory.
module load cp2k  # Sets up cp2k module
cp2k.x cs_cell_opt_direct_lbfgs.inp > cs_cell_opt_direct_lbfgs.out   # Runs the CP2K program

Running the simulation

To run the simulation, type

$ condor_submit cp2k.submit # Submit the condor job script "cp2k_run.submit"

Now you have submitted the CP2K simulation on the open science grid. The present job should be finished quickly (in less than an hour). You can check the status of the submitted job by typing

$ condor_q username # The status of the job is printed on the screen. Here, username is your login name.

After the simulation is completed, you will see the output files from CP2K including the main output file, trajectory files and restart files in your work directory.

Getting Help

For assistance or questions, please email the OSG User Support team at user-support@opensciencegrid.org or visit the help desk and community forums.

 

This page was updated on Dec 19, 2018 at 08:02 from tutorials/tutorial-cp2k/README.md.