Welcome to the CQLS HPC Documentation Website¶
The Center for Quantitative Life Sciences (CQLS) has established a new
high-performance computing (HPC) infrastructure (hpc.cqls.oregonstate.edu,
aka the 'Wildwood' HPC Cluster) that is connected to, but distinct from, the
'old' computing infrastructure (shell.cqls.oregonstate.edu).
Connecting to the Wildwood HPC cluster¶
Note
Instead of using your old cqls password, you will be using your ONID password for validating your account.
The default port 22 is sufficient to connect to the Wildwood HPC. An alternatively defined port is uneccesary on the command-line.
If you are hard-wired on campus and attempting to connect, or logged in to the campus VPN, you can directly connect to
the Wildwood HPC cluster through ssh:
Warning
If you attempt to connect directly from an off-campus location, your connection will fail!
For more information, see the Connecting page.
Accessing the newly installed software¶
More information can be found in the Configuration section.
To get up and running straight away, run this tool:
This will modify your dotfiles so that the latest installations are preferred over the legacy software. New software is
installed in /local/cqls/software/$ARCH where $ARCH depends on the cpu architecture of the machine you are logged
into. You can find more information in the Software section.
Running jobs on the cluster¶
We are using
Slurm
for submitting jobs on the infrastructure. If you are familiar with SGE_Batch
or SGE_Array, or more recently, hqsub
(more information here),
you can continue using hqsub for submitting jobs on the cluster. See the documentation, or run hqsub --help from the
command-line to get a run-down of how to use the software.
hqsub is built to use SGE or Slurm, and will use Slurm by default on the Wildwood HPC.
Interactive jobs¶
Using SGE, one could check out an interactive session on a compute node using the qrsh command. The replacement for
this command in Slurm is the salloc command. See here for more information.
Finding compute resources¶
You can use the hqavail command to see what servers you have available to submit jobs to. You can use the
hqsub -q $QUEUENAME option to send jobs to a specific queue.
Monitoring jobs¶
Use the hqstat command to see what jobs are running at the current moment. Run scontrol show job $JOBID to get more
information about your jobs that are currently running.
Terminating jobs¶
Use the scancel JOBID command to terminate a single job. To kill all of your pending or running jobs use
scancel --me -t pending or scancel --me -t running, respectively.
Account request¶
See our old account request form to request an account. An updated form is in the works.
Support request¶
See our old support request form to request support or software installs. An updated form is in the works.