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.
OSC Classroom Support
CLASSROOM RESOURCES FOR DISTANCE LEARNING
If your class has lost or limited access to computer labs, the Ohio Supercomputer Center might be able to help by providing no-cost access to cloud computing resources. Classes and workloads of any size can gain access. OSC's web-browser interface to its substantial Linux computer systems provides novice users with virtual desktops preloaded with applications, such as MATLAB, RStudio, or Jupyter Notebook.
As an example, an OSU undergrad statistics class recently used iPads to remotely access RStudio on OSC systems.
Gaussian
Gaussian is a very popular general purpose electronic structure program. Recent versions can perform density functional theory, Hartree-Fock, Möller-Plesset, coupled-cluster, and configuration interaction calculations among others. Geometry optimizations, vibrational frequencies, magnetic properties, and solution modeling are available. It performs well as black-box software on closed-shell ground state systems.
PyTorch
PyTorch is an open source machine learning framework with GPU acceleration and deep neural networks that is based on the automatic differentiation in the Torch library of tensors.
CMake
CMake is a family of compilation tools that can be used to build, test and package software.
Availability and Restrictions
Versions
The current versions of CMake 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."
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.
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.
OpenMPI
MPI is a standard library for performing parallel processing using a distributed memory model. The Ruby, Owens, and Pitzer clusters at OSC can use the OpenMPI implementation of the Message Passing Interface (MPI).
GNU Compilers
Fortran, C and C++ compilers produced by the GNU Project.
Availability and Restrictions
Versions
GNU compilers are available on all our clusters. These are the versions currently available: