On July 12th, 2016 OSC migrated its old GPFS and Lustre filesystems to new Project and Scratch services, respectively. We've moved 1.22 PB of data, and the new capacities are 3.4 PB for Project, and 1.1 PB for Scratch. If you store data on these services, there are a few important details to note.
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB.
OnDemand provides two related job managment tools, one which allows you to create and submit jobs via your web browser, and the other allows you to monitor your queued and running jobs.
OnDemand provides a web-based FTP client that can be used to upload and download files to your OSC home directory or project directory, and move, delete, rename, modify permissions, and even edit files.
OnDemand is our "one stop shop" for access to our High Performance Computing resources. With OnDemand, you can upload and download files, create, edit, submit, and monitor jobs, run GUI applications, and connect via SSH, all via a web broswer, with no client software to install and configure.
Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language.
Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, integrating ordinary functions, manipulating polynomials, and integrating ordinary differential and differential-algebraic equations. It is easily extensible and customizable via user-defined functions written in Octave's own language, or using dynamically loaded modules written in C++, C, Fortran, or other languages.
While our python installations come with many popular packages installed, you may come upon a case where you need an addiditonal package that is not installed. If the specific package you are looking for is available from Anaconda.org (formerlly binstar.org) you can easily install it and required dependencies by using the Conda package manager.
To be able to install a package using the conda package manager:
While we provide a number of Python modules, you may need a module we do not provide. If it is a commonly used module, or one that is particularly difficult to compile, you can contact OSC Help for assistance, but we have provided an example below showing how to build and install your own Python modules, and make them available inside of Python.
OSC provides Allinea Performance Reports and Allinea MAP to all OSC users.
- Allinea Performance Reports: very simple tool to generate one single-page HTML report that presents overall performance characteristics of HPC applications
- Allinea MAP: HPC application profiler with easy-to-use GUI environment.
The following versions of Allinea are available on OSC clusters:
Sometimes the best way to get access to a piece of software on the HPC systems is to install it yourself as a "local install". This document will walk you through the OSC-recommended procedure for maintaining local installs in your home directory or project space.