Instructors:
Jason Macklin, Aaron McDivitt, Matt Bradley
Helpers:
Sue McClatchy
General Information
This workshop introduces high performance computing using
the Jackson Laboratory’s computing cluster. The goal
is to teach novice programmers to use powerful tools and
computing resources, and to engage in best practices
for using these resources. The emphasis of this workshop
is to give attendees a strong foundation in the fundamentals
of the bash shell and to teach best practices for
scientific computing in high performance computing environments.
By the end of this workshop, participants will be able to:
Use the UNIX command line to operate a computer, connect to a cluster, and write simple shell scripts
Submit and manage jobs on a cluster using a scheduler, transfer files, and use software through environment modules
Find, create and manage containers with Singularity
Who:
The course is aimed at graduate students and other researchers at the Jackson Laboratory.
For IT security reasons, external participants will not be admitted.
You can attend in classrooms in Bar Harbor or Farmington, however, remote participation from desks,
home, or away will not be supported.
You don't need to have any previous knowledge of the tools
that will be presented at the workshop.
Where:
Holt Conference Room, 10 Discovery Dr, Farmington CT | Bioinformatics Training Room, 600 Main St, Bar Harbor ME.
Get directions with
OpenStreetMap
or
Google Maps.
Requirements: Participants must bring a laptop with a
Mac or Windows operating system (not a tablet, Chromebook, etc.). Windows users should have specific software installed (listed below).
Accessibility: We are committed to making this workshop
accessible to everybody.
The workshop organizers have checked that:
The room is wheelchair / scooter accessible.
Accessible restrooms are available.
Materials will be provided in advance of the workshop and
large-print handouts are available if needed by notifying the
organizers in advance. If we can help making learning easier for
you (e.g. sign-language interpreters, lactation facilities) please
get in touch (using contact details below) and we will
attempt to provide them.
To participate in a
Software Carpentry
workshop,
you will need access to the software described below.
In addition, you will need an up-to-date web browser.
If your "HOME" environment variable is not set (or you don't know what this is):
Open command prompt (Open Start Menu then type cmd and press [Enter])
Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
Press [Enter], you should see SUCCESS: Specified value was saved.
Quit command prompt by typing exit then pressing [Enter]
The default shell in some versions of macOS is Bash, and
Bash is available in all versions, so no need to install anything.
You access Bash from the Terminal (found in
/Applications/Utilities).
See the Git installation video tutorial
for an example on how to open the Terminal.
You may want to keep Terminal in your dock for this workshop.
To see if your default shell is Bash type echo $SHELL in
Terminal and press the enter/return key. If the message printed does
not end with '/bash' then your default is something else and you can run
Bash by typing bash.
The default shell is usually Bash and there is usually no need to
install anything.
To see if your default shell is Bash type echo $SHELL in
a terminal and press the enter/return key. If the message printed does
not end with '/bash' then your default is something else and you can run
Bash by typing bash.