What can I run ?

In order to execute applications, they need to be on the remote execution environment. One of the most popular ways of delivering applications is via CVMFS.

Straight from our Jenkins to you

Our build system performs continuous integration on applications which are supported by the infrastructure, as well as user-proposed applications. Below you can find the overview of the status of these. These are executable in local-only or under the sagrid.ac.za VO.

Name Versions Status Repo Description Published
GMP 6.1.0

GNU Multiprecision library

MPFR 3.1.2 3.1.5

GNU MPFR is a C library for multiple-precision floating-point computations with correct rounding.

MPC 1.0.1 1.0.3

Gnu MPC is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result

GCC 4.9.4 5.4.0 6.3.0

The GNU Compiler Collection

CMake 3.4.0

Cross-platform build tools

LLVM 3.7.0

The LLVM Project is a collection of modular and reusable compiler and toolchain technologies.

Name Versions Status Repo Description Published
argtable 2.13

No description

OpenMPI 1.10.2 1.8.8 1.8.1

Message Passing Interface


Message Passing Interface

zlib 1.2.11

Free Compression Library

bzip2 1.0.6

Free Compression Library

libxml2 2.9.3

XML library

openssl 1.1.0c 1.0.2j

Open SSL cryptographic libraries and tools

LUA 5.3.2

A powerful, fast, lightweight, embeddable scripting language.

ncurses 6.0

The Ncurses library is a free software emulation of curses in System V Release 4.0, and more.

readline 6.3 7.0

A utility which aids in the consistency of user interface across discrete programs

BOOST C++ 1.62

Boost provides free peer-reviewed portable C++ source libraries.

LAPACK 3.6.0 3.7.0

Linear Algorithm packages for HPC

ScaLAPACK 2.0.2

Scalable, parallel Linear Algebra Libraries

ATLAS 3.10.2

Automatically-Tuned Linear Algebra Software

GSL 1.16 2.1 2.3

GNU Science Libraries

HDF5 (with OpenMPI) 1.8.15 1.8.16

HDF5 is a data model, library, and file format for storing and managing data.

HDF5 (with MPICH) 1.8.14 1.8.15

HDF5 is a data model, library, and file format for storing and managing data.

NetCDF 4.3.3 4.4.1

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

FFTW3 3.3.4

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).

SparseHash 2.0.3

Google's SparseHash library

gnuplot 4.6.7 5.0.3 5.0.5 5.0.6

GNU Plotting Library

proj 4.9.2

Cartographic Projections Library

Java OpenJDK 7u80 8u66

Java platform libraries and tools

JasPer 1.900.1

open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard (i.e., ISO/IEC 15444-1).

FreeType 2.6.1 2.7.1

a free, high-quality and portable Font engine.


Cross-platform C library that implements a self-contained, embeddable, zero-configuration SQL database engine.

SuiteSparse 4.4.6

A suite of sparse matrix algorithms.

Tcl/Tk 8.6.6

scripting language

MatPlotLib 4.8.4 4.9.2

Plotting functions for python


Class Library for High-Energy Physics

Name Versions Status Repo Description Published

Symbolic Python

ROOT v6.06.02

Object-Oriented Data Analysis Toolkit

HEAsoft 6.21

A Unified Release of the FTOOLS and XANADU Software Packages

Name Versions Status Repo Description Published
Python 2.7.13 3.6.0

Python is a programming language that lets you work quickly and integrate systems more effectively.

SciPy 0.5.1

Scientific Python

NumPy 1.9.1

Numerical Python

MatPlotLib 4.8.4 4.9.2

Plotting functions for python

Pandas 0.20.2

pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming


Symbolic Python

Name Versions Repo Description Published
Quantum Espresso 5.1.3

Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

Abinit 7.10.5

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.


A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids

Motheur 6.2

No description

Name Versions Repo Description Published
HTK 3.4.1 3.5.beta-1

Hidden Markov Model Toolkit (HTK)

LibSVM 3.14 3.21

General purpose library for Support-Vector Machine learning.

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Name Versions Repo Description Published
FastQC 0.11.4

A quality control application for high throughput sequence data

PRINSEQ 0.20.4 Proposed Proposed

PReprocessing and INformation of SEQuence data

SolexaQA 3.1.4 Proposed

SolexaQA calculates sequence quality statistics and creates visual representations of data quality for second-generation sequencing data

Trimmomatic 0.35 0.36 Proposed Proposed

A flexible read trimming tool for Illumina NGS data

Fluent No versions</td> Proposed Proposed

No description

OpenFoam 3.0.1

Computational Fluid Dynamics

Dlpoly Proposed Proposed

No description

Cosmo MC / CAMB No versions</td> Proposed

MCMC parameter sampling for cosmology

WRF 3.3 3.5 Proposed Proposed

No description

Ferret 7.1.0 Proposed Proposed

No description

Amber 12 Proposed Proposed

No description

Vasp 5.2 Proposed Proposed

No description

Emboss 6.5.7 Proposed Proposed

No description

Clustal Omega 1.2.4 Proposed Proposed

No description


PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale nalyses in a computationally efficient manner.

Published in CVMFS `apprepo` and modulefile available. Used at production sites and your milage wil be good :smile:
Published in CVMFS `devrepo` - modulefile not guaranteed to be available, used for integration testing and early adopters. YMMV :smirk:
Not published anywhere yet.

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