/tag/programming
Python and UVA HPC
Overview Python is an integrated technical computing environment that combines sophisticated computation, advanced graphics and visualization, and a high-level programming language.
Learning Python Research Computing offers an online “Introduction to Programming in Python” course. Click here to start learning Python.
Python on the HPC System The default Python is required for system purposes and is generally too old for applications. We offer Python through the Miniforge distribution.
View our Miniforge on the HPC System documentation for details.
Perl and UVA HPC
Overview Perl is a general-purpose interpreted programming language, originally developed for text manipulation and now used for a wide range of tasks including system administration, web development, network programming, GUI development, and bioinformatics.
Available Versions The default Perl is required for system purposes and is generally too old for applications. We offer more recent versions of Perl as modules. To find the available versions and learn how to load them, run:
module spider perl The output of the command shows the available Perl
module versions.
For detailed information about a particular Perl
module, including how to load the module, run the module spider command with the module’s full version label.
Nvidia Clara Parabricks and UVA HPC
Overview Nvidia Clara Parabricks is a GPU-accelerated software suite for performing secondary analysis of next generation sequencing (NGS) DNA and RNA data. It contains GPU-enabled versions of popular bioinformatics tools such as the aligners BWA-Mem and STAR.
Loading the container On the HPC system, Clara Parabricks is available as an Apptainer container. To load the clara-parabricks container module, you can type:
module load apptainer clara-parabricks The load command will load a default version of Clara Parabricks, unless another version is specified. To see the available versions, type:
module spider clara-parabricks Running Clara Parabricks tools The Clara Parabricks container on the HPC system includes many bioinformatics tools for genomics and transcriptomics.
R and RStudio and UVA HPC
Overview R is a programming language that often is used for data analytics, statistical programming, and graphical visualization.
Loading the R module On the UVA HPC system, R is available through our module system. For example, to load R, you can type:
module load goolf R Notice that we included goolf in the load command. There are two reasons why including goolf is important:
R was built with a compiler, an interface to OpenMPI, and other utilities. The goolf module will ensure that each of these items is loaded.
R has many computationally-intensive packages that are built with C, C++, or Fortran.
Workshops
UVA Research Computing provides training opportunities covering a variety of data analysis, basic programming and computational topics. All of the classes listed below are taught by experts and are freely available to UVa faculty, staff and students.
New to High-Performance Computing? We offer orientation sessions to introduce you to the Afton & Rivanna HPC systems on Wednesdays (appointment required).
– Wednesdays 3:00-4:00pm Sign up for an “Intro to HPC” session Upcoming Workshops DATE WORKSHOP INSTRUCTOR There are currently no training events scheduled. Please check back soon! Research Computing is partnering with the Research Library and the Health Sciences Library to deliver workshops covering a variety of research computing topics.
education,
workshops
bioinformatics,
containers,
HPC,
image processing,
Ivy,
Matlab,
programming,
Python,
R,
Rivanna,
Shiny
Code Debugging and UVA HPC
TotalView TotalView is a full-featured, source-level, graphical debugger for applications written in C, C++, Fortran (77 and 90/95/2003), assembler, and mixed source/assembler codes. It is a multiprocess, multithread debugger that supports multiple parallel programming paradigms including MP and OpenMP. The University has a near-site license (256 tokens) for Totalview on all versions of Linux. Visit the TotalView website for detailed documentation.
Available Versions To find the available versions and learn how to load them, run:
module spider totalview The output of the command shows the available TotalView
module versions.
For detailed information about a particular TotalView
module, including how to load the module, run the module spider command with the module’s full version label.
Matlab and UVA HPC
MATLAB is an integrated technical computing environment from the MathWorks that combines array-based numeric computation, advanced graphics and visualization, and a high-level programming language. Separately licensed toolboxes provide additional domain-specific functionality.
Mathworks provides MATLAB examples and tutorials for all experience levels here.
Available Versions To find the available versions and learn how to load them, run:
module spider matlab The output of the command shows the available MATLAB
module versions. To load the most recent version of MATLAB
, at the terminal window prompt run:
module load matlab For detailed information about a particular MATLAB
module, including how to load the module, run the module spider command with the module’s full version label.
Julia and UVA HPC
Description Julia is a high-level programming language designed for high-performance numerical analysis and computational science. Distinctive aspects of Julia’s design include a type system with parametric polymorphism and types in a fully dynamic programming language and multiple dispatch as its core programming paradigm. It allows concurrent, parallel and distributed computing, and direct calling of C and Fortran libraries without glue code. A just-in-time compiler that is referred to as “just-ahead-of-time” in the Julia community is used. [Ref: Wikipedia](https://en.wikipedia.org/wiki/
Software Category: lang
For detailed information, visit the julia
website.
Available Versions To find the available versions and learn how to load them, run:
