Dexter is a cluster of fifty-two dual-processor eight core Intel E5-2670 (Sandy Bridge) based servers. Each machine has sixteen cores and 32Gb of RAM. They all run Linux.
Dexter can only be accessed by sshing into the head node, whose external name is dexter.ch.cam.ac.uk. All work is done from there; there is no need to log into compute nodes. Dexter uses the local Admitto service, so you log in with the same password as on the workstations.
Homespace is on a disk array attached to the head node. The /home filesystem is 1Tb in size and has user quotas which are currently set to 20Gb soft limit with a hard limit of 25Gb. It is backed up regularly. The backups are available under /rsnapshots on the head node.
/home is shared to all nodes on the cluster's internal network, so your job sees the same home directory wherever it is on the machine. It's important to remember that from a compute job's point of view accessing this directory is extremely slow, especially if all the nodes are trying at once. Compute jobs should always write data to a local disk if possible, and copy it back to /home at the end.
There is also a shared scratch filesystem /sharedscratch in which you will have a directory. These are not backed up. They have a quota restriction of 250Gb soft limit and 300Gb hard limit, but it is expected that most people will stay well within that amount. They have the same speed issue as /home. The Frenkel group have an additional scratch filesystem documented elsewhere.
Each node also has a local /scratch filesystem on which the queueing system will create you a directory when you use the node. These filesystems are about 1.8Tb in size with no quota restriction and are the most appropriate place for your jobs to write temporary files during a run. They are local to each node and so considerably faster than the NFS-mounted /home and /sharedscratch. Please clean up files on /scratch when you are done with them; see the queueing documentation for how to find out which node's /scratch to look at. All of the node /scratch directories are accessible under /nodescratch on the head node. The system uses an automounter so the directories only appear when you try to access them. For example to see the /scratch from node node013 you need to type something like 'ls /nodescratch/node013' .
A variety of compilers and libraries are installed. Like most local Linux machines dexter has the modules environment to allow you to switch between different compilers and libraries. The default environment is set up with all the available 64-bit compilers and Intel MPI. If you need to change this then use the module avail command to see what the other options are, and edit the version you want into your ~/.bashrc file.
All compute jobs should be run through the queueing system. The queueing system will run each job on a set of free compute nodes, copying the output back to a user-specified file at the end of the job. The queueing system is Torque/Maui; this will be familiar to users of the other theory sector clusters, but please note that the available queues are not the same on every machine. Read the generic instructions for instructions on how to use Torque and Dexter's queueing setup for details of the queue setup if you already know Torque. The queueing configuration is always provisional and suggestions for improvements are warmly welcomed. To run parallel jobs you will need to use the appropriate job launcher; see Dexter's queue and parallel documentation for details.