Getting started
From Yale HPC Wiki
Logging on
Once you have an account setup, you can access the clusters using ssh/sftp.
Yale HPC machines are only accessible from the Yale network. Anyone wishing to access the cluster from outside the Yale network will have to log onto another machine within Yale then hop from there onto the cluster. The Pantheon student login hosts can be used if you don't have a desktop machine with SSH.
You can also connect to to the clusters directly if you're connected to Yale's VPN service.
Laptop users registered with Yale NetReg (ie. connected to Yale Wireless) can SSH login to HPC clusters.
How a cluster works from 10,000 feet
When you login to the cluster, say bulldogk.wss.yale.edu, you're logging in to what's called the login node. This machine is for development, compiling, and staging your data on the cluster.
Once you have everything ready to do an analysis, you'll want to make a PBS Script to actually run your compute job. Lets call this script test.sh. Using the command qsub, you tell the cluster to run test.sh when the requested compute resources are available. Your job is added to a "queue". Once it reaches head of the queue it will be scheduled to run by the scheduling software
When the cluster is ready, your job will run on any one of the free compute nodes in the cluster. Users can submit any number of test.sh scripts to run as soon as possible.
You can use the command qstat to monitor your compute job.
You can also run an interactive job which will give you a UNIX terminal on your requested compute node.
Available Software
Most of our clusters have a variety of software available for users. You can always find it in /usr/local/cluster. Another great tool for discovering what software is available is module. You can run "module avail" to discover what's available. If you need something that is not available, you can email us. Sometimes scientific software is extremely complex or incompatible with a cluster environment. In those cases, the user is responsible for installing their own software.
