Pitzer
HMMER
HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMS). HMMER is designed to detect remote homologs as sensitively as possible, relying on the strength of its underlying probability models.
Availability and Restrictions
Versions
HMMER is available on the OSC clusters. These are the versions currently available:
AlphaFold 2.0.0 available on Pitzer
Date:
Friday, August 20, 2021 - 4:30pm
System(s):
AlphaFold version 2.0.0 is now available on Pitzer cluster; usage via module load alphafold.
AlphaFold
AlphaFold is a software package that provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and pusblished in Nature.
Rolling reboots on owens and pitzer starting 18 Aug 2021
We will have rolling reboots of Owens and Pitzer cluster, including login and compute nodes, starting from 9am on August 18, 2021. The rolling reboot is for urgent security updates. The rolling reboots won't affect any running jobs, but users may experience longer queue wait time than usual on the cluster. User will also expect about a 10 minute outage of login nodes during the reboot of login nodes. If there are interactive jobs started from a login node and that login node is rebooted, then the job will be killed.
Jupyter security issue Aug. 13, 2021
Please do not run any Jupyter applications at OSC until further notice due to a security vulnerability. OSC will update JupyterLab and Jupyter Notebook applications to rectify this as soon as possible.
See the Jupyter known issue for details:
https://www.osc.edu/resources/technical_support/known_issues/jupyter_security_issue_aug_13_2021
Backup failures on ess filesystem
The backups on the /fs/ess filesystem are having issues running. There has not been a successful backup of this filesystem since Sunday, 08 August 2021.
OSC is working with the vendor to resolve this issue as soon as Possible.
JupyterLab 3.0 available on Owens and Pitzer
JupterLab 3.0 is now available on Owens and Pitzer through OnDemand Jupyter app.
HOWTO: Use a Conda/Virtual Environment With Jupyter
The IPython kernel for a Conda/virtual environment must be installed on Jupyter prior to use. This tutorial will walk you though the installation and setup procedure.
Enable JupyterLab extensions
Extension feature is now enabled for JupyterLab 2.1 and 3.0. See HOWTO: Use Extensions with JupyterLab for more detail.
