Parallel environments

Introduction

The Grid Engine basically does not distinguish between CPUs or cores or the internal used term slots.

This means: 1 core = 1 CPU = 1 slot

By default the Grid Engine calculates 1 job = 1 core. Some programs need more than 1 core or even more cores than 1 node/host/server has to offer. You enable this by configurable environments inside the Grid Engine which are called parallel environments.

Currently the following parallel environments are used @IMP/IMBA:

Preconditions

That the Grid Engine can start the OpenMPI and Qmake jobs as the submitting user, the ssh host signatures should be know from all used nodes. Otherwise the starting process get stuck at a message similar do you want to add the ssh key for host xxx (yes/no). You won't see this message, since it is not in the redirected output of your program!

So do the following:

 cd ~/.ssh/
 mv known_hosts known_hosts.save
 wget http://aragon/known_hosts
 chmod 644 known_hosts


Or generally disable the checking of host keys by adding the following lines to the local ssh configuration ~/.ssh/config:

 Host *
   StrictHostKeyChecking no