Ascend

Linaro DDT

Linaro DDT is a graphical debugger for HPC applications. It supports pthreads, OpenMP, or MPI code on CPU, GPU, and MIC based architectures.

Availability & Restrictions

Versions

The Linaro DDT versions currently available at OSC are:

Apptainer/Singularity

Apptainer/Singularity is a container system designed for use on High Performance Computing (HPC) systems. It allows users to run both Docker and Singularity containers.

From the Docker website: "A container image is a lightweight, stand-alone, executable package of a piece of software that includes everything needed to run it: code, runtime, system tools, system libraries, settings."

RELION

RELION (REgularised LIkelihood OptimisatioN) is a stand-alone computer program for the refinement of 3D reconstructions or 2D class averages in electron cryo-microscopy. 

We have identified some issues with the RELION installations. For more details, please refere the "Known Issues" section below.

To address the issues, we have decided to deprecate affected versions, including: relion/3.1, relion/3.1-gpu, relion/3.1.3, relion/4.0.0, and relion/4.0b on both Owens and Pitzer. Additionally, we will deprecate other versions that are rarely used to improve maintenance. These versions include relion2/2.0 and relion/3.0.4.

The deprecation action was done on January 23, 2024. To migrate your jobs, please refer to the "Versions" table below for available versions. If you require any assistance, please contact OSC help.

Overview of File Systems

OSC has several different file systems where you can create files and directories. The characteristics of those systems and the policies associated with them determine their suitability for any particular purpose. This section describes the characteristics and policies that you should take into consideration in selecting a file system to use.

The various file systems are described in subsequent sections.

HOWTO: Reduce Disk Space Usage

This HOWTO will demonstrate how to lower ones' disk space usage. The following procedures can be applied to all of OSC's file systems.

We recommend users regularly check their data usage and clean out old data that is no longer needed.

Users who need assistance lowering their data usage can contact OSC Help.

R and Rstudio

R is a language and environment for statistical computing and graphics. It is an integrated suite of software facilities for data manipulation, calculation, and graphical display. It includes

  • an effective data handling and storage facility,
  • a suite of operators for calculations on arrays, in particular matrices,
  • a large, coherent, integrated collection of intermediate tools for data analysis,
  • graphical facilities for data analysis and display either on-screen or on hardcopy, and
  • a well-developed, simple and effective programming language which includes conditionals, loops, user-defined recursive functions and input, and output facilities

More information can be found here.

HOWTO: Create and Manage Python Environments

While our Python installations come with many popular packages installed, you may come upon a case in which you need an additional package that is not installed. If the specific package you are looking for is available from anaconda.org (formerly binstar.org), you can easily install it and required dependencies by using the conda package manager.

Procedure

The following steps are an example of how to set up a Python environment and install packages to a local directory using conda. We use the name  local for the environment, but you may use any other name.

Pages