computing molecular dynamics skills

Setting up a GROMACS cluster

1. Install Ubuntu

Untangling ethernet cables can be surprisingly tricky

On the Apple Xserves, the only way I have found of doing this is via CD or USB stick. Because they are EFI-boot machines I cannot get PXE booting to work and therefore I’ve never been able to get ROCKS or OSCAR working. Since I am sitting in a cold and noisy machine room, I had hoped to install say four nodes at once using four CDs, however, I’ve found that if you swap the monitor from one machine to another (by unplugging the mini DisplayPort-to-VGA adaptor from the back of the machine), it won’t work when you reconnect later to see how the install is going. Since I only have two monitors, that limits me to two installations at a time. Installation time from CD was 18 minutes, from USB stick around 14 minutes. I used Ubuntu 14.04.4 Server.

Since I am setting up the cluster just for me to begin with, I setup the same user with the same password on each machine – this user is given a UID and GID of 1000 by default. During the process you have to make various decisions. For the record I chose a guided partition of the whole disc using LVM, to automatically install security updates and to install the open-ssl and mail servers. The latter to be configured as a local mail server using the hostname. As we are talking about hostnames, this is what I chose for the private network.

hostname Private IP

Update the packages on each machine,

$ sudo apt-get update -y && sudo apt-get upgrade -y

There are also some common packages each machine will need

$ sudo apt-get install environment-modules htop slurm-llnl

Finally, each machine will need a mount point for the NFS software share

$ sudo mkdir /opt/software

By Philip Fowler

Philip W Fowler is a computational biophysicist studying antimicrobial resistance working at the John Radcliffe Hospital in Oxford.

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