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SUG Conference - October 7, 2021
Agenda
Gateway, Owens, Pitzer
Add to a Classroom Project
We provide the instructor (PI of the classroom project) with information on how to get students added to the classroom project. Usually, invites will be sent to new OSC users; existing OSC users will be automatically added to the project if they have an OSC account which matches the email information provided by the PI.
SUG Conference - April 14, 2021
Agenda
The data transfer speed between OSC and another network can be tested.
Test data transfer speed with iperf3 tool
Connect to a data mover host at osc and note the hostname.
$ ssh sftp.osc.edu # login $ hostname datamover02.hpc.osc.edu # the hostname may also be datamover01.hpc.osc.edu
From there, an iperf3 server process can be started. Note the port used.
Pitzer
Unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurrig due to beam-induced motion. It reads stacks of movies that are stored in MRC/CCP4 format. Unblur generates frame sums that can be used in subsequent image processing steps and optionally applies an exposure-dependent filter to maximize the signal at all resolutions in the frame averages. Movie frame sums can also be calculated using Summovie, which uses the alignment resuls from a prior run of Unblur.
Pitzer
OpenCV is an open-source library that includes several hundreds of computer vision algorithms.
In December 2021 OSC updated its firewall to enhance security. As a result, SSH sessions are being closed more quickly than they used to be. It is very easy to modify your SSH options in the client you use to connect to OSC to keep your connection open.
In ~/.ssh/config (use the command touch ~/.ssh/config to create it if there is no exisitng one), you can set 3 options:
Pitzer
MotionCor2 uses multi-GPU acceleration to correct anisotropic cryo-electron microscopy images at the single pixel level across the whole frame, making it suitable for single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting.
Availability and Restrictions
Versions
The following versions are available on OSC clusters:
Gateway
MyOSC now offers the ability for PIs to view the billing statements of current un-billed usage for their projects.
Login to my.osc.edu and navigate to Project -> Billing Statements.
There are two sections:
Current usage
The current usage section provides information usage charges up to the current day.
Keep protected data in proper locations
Protected data must be stored in predetermined locations. The only locations at OSC to store protected data are
(Only with prior approval from OSC may a protected data service project not have a project prefix of PDE).
/fs/ess/PDEXXXX and /fs/scratch/PDEXXXX directories.(Only with prior approval from OSC may a protected data service project not have a project prefix of PDE).