zaydh / hummingbird

Modules Related to Using UCSC's Hummingbird Server

Getting Started with Hummingbird

These are notes I found helpful for getting started with the University of California, Santa Cruz (UCSC)'s Hummingbird HPC server. Complete information is available on the official Hummingbird page.

Logging In

From the terminal, enter:

ssh <cruzid>@hb.ucsc.edu

Note: this is your CRUZID, not your SOE id.

Off-Campus Access

If you are using Hummingbird away from campus, you must be logged into UCSC's VPN. For more information, see UCSC's IT page.

Slurm

This is a protocol for running batch jobs. I have included an example in the "examples" folder. You need to modify the parameters in <...> brackets. Pay special care to select the right partition. This is done by removing one of the preceding pound signs ("#").

Harvard compiled a set of useful sbatch commands. Examples of commands I have used include: squeue to check the status of a command, scancel to kill a running job, and scontrol.

Loading Modules

Modules are how you get access to pre-install tools (e.g., python, R, Matlab, etc.). You load modules by entering:

module load <name>

To get the list of available modules, enter:

module spider

To find the list of modules YOU have currently load, enter:

module list

mpi4py and Anaconda

This is a Python module that allows you to communicate with MPI via OpenMPI. mpi4py was recently installed on the server.

If you ever need a custom (or want control of the) Python distributions, install install Anaconda in your user directory. To do this, run the command:

./install_anaconda

You can change the version of Anaconda through the variable VERSION_NUM in the file. After an install, you may need to call source .\bashrc for your bash profile to be updated.

If you are using Anaconda, make sure you slurm file references the absolute path to conda's bin file and does not call the standard python. You may also want to have it activate the conda environment using the command:

source activate <CondaEnvironmentName>