Introduction

This tutorial aims to show how to run coupled Gromacs/Dalton multiscale simulation on production e-Infrastructure using QosCosGrid services and tools. The presented work was a join effort of the MAPPER and ScalaLife EU projects. At first please familiarize yourself with these introductory presentations:

• Hybrid QM/MD simulations of molecular properties in complex systems
• How to Turn an Application into Multiscale and Run it with QosCosGrid?

The PL-Grid e-infrastructure

The PL-Grid e-infrastructure is a federation of resources provided by 5 leading HPC centers in Poland. In this tutorial we will use one of the six clusters that are available via QosCosGrid services.

UI (User Interface) machine

We will use UI machine located in Wroclaw Networking and Supercomputing Center. At first we must copy the keystore file that we have generated in the PL-Grid portal.

scp plgmamonski.p12 plgmamonski@ui.plgrid.wcss.wroc.pl:~/

and convert it:

$ssh plgmamonski@ui.plgrid.wcss.wroc.pl

[plgmamonski@ui ~]$qcg_set_env plgmamonski.p12
[plgmamonski@ui ~]$exit #we must logout and login again
$ssh plgmamonski@ui.plgrid.wcss.wroc.pl

Now check if you can run qcg-list command:

$qcg-list
https://qcg-broker.man.poznan.pl:8443/qcg/services/
/C=PL/O=GRID/O=PSNC/CN=qcg-broker/qcg-broker.man.poznan.pl
UserDN = /C=PL/O=GRID/O=PSNC/CN=Mariusz Mamonski
ProxyLifetime = 23 Days 18 Hours 57 Minutes 45 Seconds
NO TASKS

Downloading input files

For your convinience all needed files can be downloaded as a single package:

$wget http://fury.man.poznan.pl/~mmamonski/MAPPER/mapper-scalalife-tutorial.tar.gz

$tar -xzf mapper-scalalife-tutorial.tar.gz

$cd tutorial/

XMPP Notifications

For the jabber notifications to work with GTalk you need to add qcg-notification@plgrid.pl address to your contacts (howto). If you do not have a jabber/gtalk account skip this step, its optional.

Submitting Gromacs Job

Submit Gromacs job using the qcg-sub command:

$cd gromacs/

$vim gromacs.qcg #EDIT #QCG notify directive

$qcg-sub gromacs.qcg 
...
gromacs.qcg 0 jobId = J1370130391659__1480

You can list all your active jobs with the qcg-list command:

$qcg-list
JOB IDENTIFIER          NOTE                  SUBMISSION TIME  START TIME       FINISH TIME      STATUS            HOSTNAME  FLAGS  STATUS DESCRIPTION    

When job is in the running state you can view it standard output with the qcg-peek command: