Attention
The ShARC HPC cluster was decommissioned on the 30th of November 2023 at 17:00. It is no longer possible for users to access that cluster.
Cryo-EM Facility nodes (School of Biosciences)
The School of Biosciences’ Cryo-Electron Microscopy Facility has purchased 3 nodes in ShARC.
that each have more than the standard number of cores for ShARC nodes (16).
Specifications
Three nodes (sharc-node135
, sharc-node136
, sharc-node138
) each have:
Processors |
2x Intel Xeon E5-2640 v4 processors (2.40 GHz, 10 cores per processor i.e. 20 total) |
RAM |
256 GB RAM (12.8 GB / CPU core) |
NUMA nodes |
2x |
Networking |
100 Gbps Omni-Path |
Local storage |
839 GB under |
Requesting Access
Access to the node is managed by Svet Tzokov (s.b.tzokov@sheffield.ac.uk
; Electron Microscopy Facility Manager).
To use the nodes you must:
Be made a member of the
cryoem
Grid Engine (scheduler) Access Control List (ACL i.e. user group) by Svet Tzokov;Submit jobs using the
cryoem
Grid Engine Project;Start interactive jobs and batch jobs in
cryoem.q
Grid Engine Cluster Queue;
Running an interactive session
Once you have obtained permission to use the nodes you can request an interactive session on one of the nodes using:
qrshx -P cryoem -q cryoem.q
Here -P cryoem
specifies that you want to use the cryoem
project for your session,
which gives you access to these big memory nodes and
ensures that your interactive session can run in the cryoem.q
job queue
(as can be seen if you subsequently run qstat -u $USER
from within your session).
The cryoem.q
job queue has a maximum job runtime (h_rt
) of 96 hours for interactive sessions (and batch jobs),
which is much greater than is standard for interactive jobs on SHARC.
Submitting batch jobs
Jobs can be submitted to the nodes by adding the -P cryoem
and -q cryoem.q
parameters.
For example, create a job script named my_job_script.sh
with the contents:
#!/bin/bash
#$ -P cryoem
#$ -q cryoem.q
echo "Hello world"
You can of course add more options to the script such as a request for additional RAM
(e.g. $# -l rmem=10G
).
Run your script with the qsub
command:
qsub my_job_script.sh
You can use the qstat
command to check the status of your current job.
An output file is created in your home directory that captures your script’s outputs.
See Batch Jobs for more information on job submission and the Sun Grid Engine scheduler.