Software

This page lists the software provided by ARC as part of the Flux environment. The lists are broken into three sections: The first section lists compilers, libraries, and debuggers that are available as separate packages; the second section lists open-source software; the third lists software that has been licensed to run on Flux.

In addition to the software provided by ARC, several units also contribute software to Flux. You can find information about those by looking at the software categories on the CAC website.

You should assume that software is for non-profit, academic research only, and that it is not to be used for consulting, product development, or for any service for which a fee is charged. Some software may be available only for certain labs or research groups.

Please contact hpc-support@umich.edu with any questions.

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Compilers, libraries, debuggers
Open source software
Licensed software
Privately licensed software

Flux software

Compilers, libraries, and debuggers

Module Name Versions Description Documentation
acml 5.1.0-gcc
5.1.0-gcc_mp
ACML is the AMD Core Math Library, which contains functions from BLAS and LAPACK, among other things, optimized for the AMD CPUs Vendor Website
Manual
boost 1.50.0-gcc
1.50.0-intel
1.54.0-gcc
1.54.0-intel
Boost provides free peer-reviewed portable C++ source libraries. Vendor Website
Manual
cmake 2.8.8 CMake is a family of tools designed to build, test and package software. Vendor Website
Manual
ddt 4.0 Distributed Debugging Tool is a comprehensive graphical debugger designed for the complex task of debugging parallel code. Flux Documentation
Vendor Website
Manual
epd 7.3-2 The Enthought Python Distribution provides scientists with a comprehensive set of tools to perform rigorous data analysis and visualization. Python, distinguished by its flexibility, coherence, and ease-of-use, is rapidly becoming the programming language of choice for researchers worldwide. EPD extends this capacity with a powerful collection of Python libraries to enable interactive technical computing and cross-platform rapid application development. This module also includes pymc. Vendor Website
fftw 3.3.2 FFTW is a C/Fortran subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions Vendor Website
Manual
flexlm 11.7.0.0 The Flexlm is a common floating license manager commonly used by applications Vendor Website
g95 0.94 Users should use gfortran rather than G95. G95 is a stable, production Fortran 95 compiler available for multiple cpu architectures and operating systems. Innovations and optimizations continue to be worked on. Parts of the F2003 and F2008 standards have been implemented in g95 Vendor Website
gcc 4.4.6
4.6.3
4.7.0
4.8.0
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada Vendor Website
Manual
gsl 1.14
1.15
The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite Vendor Website
Manual
h5py 2.1.0 HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data. Vendor Website
Manual
hdf5 1.8.5-p1
1.8.9
HDF5 is a set of file formats and libraries designed to store and organize large amounts of numerical data. Vendor Website
Manual
hwloc 1.5.1 The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, …) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. Vendor Website
Manual
imsl fnl
intel-comp 11.1
12.1
13.0
13.0.1
13.1
This loads both the Intel C and Fortran compilers Vendor Website
java 1.6.0 Java is a general-purpose, concurrent, class-based, object-oriented language that is specifically designed to have as few implementation dependencies as possible. Vendor Website
matplotlib 1.1.1 matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms Vendor Website
Manual
mkl 10.3.7
11.0
11.1
This loads the Intel Math Kernel Library (MKL) runtime. Flux Documentation
Vendor Website
Manual
mpi4py mpi-1.6.0 MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. Vendor Website
Manual
nag 5.1
5.2
NAGWARE – f95/f90 fortran compiler Flux Documentation
Vendor Website
Manual
naglib 23 NAG has over 1,450 tried and tested routines that are both flexible and portable Vendor Website
Manual
netcdf 4.2.0 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 Vendor Website
Manual
numpy 1.6.2
1.6.2-3k
Numpy is provided by the scipy module, please run `module load scipy` NumPy is the fundamental package for scientific computing with Python. It contains a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities Vendor Website
Manual
openmpi 1.4.5
1.6.0
1.6.1
1.6.2
1.6.3
1.6.4
loads the OpenMPI libraries for particular compiler environments. Please use the
$ module available openmpi
command on Flux to see which compiler/version combinations are installed.
Vendor Website
Manual
perfexpert 2.1.2 PerfExpert automatically analyzes the performance of programs and suggests optimizations to alleviate the identified bottlenecks. It is intended to make performance assessment easy while providing accurate diagnoses of core, chip, and node-level performance bottlenecks. Because of this focus, it suffices (and is recommended) to use scaled-down data sets and resource configurations to obtain accurate analyses. Vendor Website
Manual
petsc 3.3-p6
3.3.0-p2
PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for parallelism. Flux Documentation
Vendor Website
Manual
pgi 10.5
11.8
12.10
12.3
12.9
13.5
Loads the PGI compiler environment Flux Documentation
Vendor Website
Manual
python 2.6.6
2.7.3
2.7.5
3.2.3
Loads the python development and runtime environment This is not the provided python compiler from RedHat. Scipy 0.10.1 and Numpy 1.6.2 are also loaded. Vendor Website
scipy 0.10.1
0.10.1-3k
Scipy is open-source software for mathematics, science, and engineering. Vendor Website
Manual

Open source software

Module Name Versions Description Documentation
R 2.15.0
2.15.1
3.0.0-mkl
3.0.1
R is a software environment for statistical computing Flux Documentation
Vendor Website
Manual
RHadoop 2.15.1
3.0.1
RHadoop is a part of Hadoop, an open source data processing framework. Vendor Website
Manual
abinit 6.12.3-intel
7.0.3-intel
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 basis. Vendor Website
Manual
adina 8.8.3
8.9.2
8.9.3
ADINA System for the analysis of solids, structures, fluids and fluid flow with structural interactions. Vendor Website
ase 3.6.0.2515 The Atomic Simulation Environment (ASE) is the common part of the simulation tools developed at CAMd. ASE provides Python modules for manipulating atoms, analyzing simulations, visualization etc. Vendor Website
Manual
cfour v1 CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum mechanical calculations on atoms and molecules. Vendor Website
Manual
chombo 3.1 Chombo provides a set of tools for implementing finite difference methods for the solution of partial differential equations on block-structured adaptively refined rectangular grids. Both elliptic and time-dependent modules are included. Chombo supports calculations in complex geometries with both embedded boundaries and mapped grids, and Chombo also supports particle methods. Most parallel platforms are supported, and cross-platform self-describing file formats are included. Vendor Website
cuda 4.2
5.5
CUDA is the development environment for using nVidia’s graphics cards for processing Flux Documentation
Vendor Website
Manual
dakota 5.2 Dakota — A Multilevel Parallel Object-Oriented Framework for design optimi Vendor Website
Manual
emacs 24.3 GNU Emacs is an extensible, customizable text editor Vendor Website
Manual
espresso 5.0.1
5.0.2
Espresso: Electronic Structure Computation Software Flux Documentation
Vendor Website
Manual
flux Adds the Flux software repository to the modules system
freesurfer 5.2.0 Program to overlay fMRI data onto reconstructed cortical surfaces. Vendor website
fsl 5.0.2.2 FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. Vendor Website
License information
git 1.8.1 Git is a distributed version control system designed to handle everything from small to very large projects with speed and efficiency. Vendor Website
Manual
globus 5.2.1 Globus provides the GSI/MyProxy in addition to GridFTP cli tools Vendor Website
gnuplot 4.2.6
4.6.0
Gnuplot is a portable command-line driven graphing utility for linux. Gnuplot supports many types of plots in either 2D and 3D. It can draw using lines, points, boxes, contours, vector fields, surfaces, and various associated text. It also supports various specialized plot types. Vendor Website
Manual
gromacs 4.5.5 GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. Flux Documentation
Vendor Website
Manual
gti 7.x GT-SUITE offers the only true virtual engine/powertrain tool, capable of integrated simulations of the total engine and powertrain system Vendor Website
h5utils 1.12.1 H5utils is a set of utilities for visualization and conversion of scientific data in the free, portable HDF5 format. tBesides providing a simple tool for batch visualization as PNG images, h5utils also includes programs to convert HDF5 datasets into the formats required by other free visualization software (e.g. plain text, Vis5d, and VTK Vendor Website
hadoop 1.1.0
1.1.2
Hadoop is an open source data processing framework. Vendor Website
Manual
hbase 0.94.7 Hive is a part of Hadoop, an open source data processing framework. Vendor Website
Manual
hive 0.9.0 Hive is a part of Hadoop, an open source data processing framework. Vendor Website
Manual
hpctoolkit 5.3.2 HPCToolkit is an integrated suite of tools for measurement and analysis of program performance on computers ranging from multicore desktop systems to the nation’s largest supercomputers. By using statistical sampling of timers and hardware performance counters, HPCToolkit collects accurate measurements of a program’s work, resource consumption, and inefficiency and attributes them to the full calling context in which they occur. Vendor Website
Manual
hypre 2.8.0b Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. Flux Documentation
Vendor Website
Manual
jmol 13.2.3 Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. Vendor Website
Manual
julia 0.2 Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments. Vendor Website
Manual
lammps 4Jul12
8Oct12
A classical molecular dynamics code LAMMPS, which stands for Large-scale Atomic/Molecular Massively Parallel Simulator Flux Documentation
Vendor Website
Manual
meep 1.2.1 Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems, along with our MPB eigenmode package. Vendor Website
Manual
mercurial 1.4
2.3
Mercurial is a free, distributed source control management tool. It offers you the power to efficiently handle projects of any size while using an intuitive interface. It is easy to use and hard to break, making it ideal for anyone working with versioned files. Vendor Website
Manual
metis 5.0.2 METIS – Serial Graph Partitioning and Fill-reducing Matrix Ordering Vendor Website
moab loads the Moab scheduling command environment Vendor Website
Manual
mongodb 2.4.2
mpb 1.4.2 This program computes definite-frequency eigenstates (harmonic modes) of Maxwell’s equations in periodic dielectric structures for arbitrary wavevectors, using fully-vectorial and three-dimensional methods. It is especially designed for the study of photonic crystals (a.k.a. photonic band-gap materials), but is also applicable to many other problems in optics, such as waveguides and resonator systems. (For example, it can solve for the modes of waveguides with arbitrary cross-sections.) Vendor Website
Manual
mpcci 4.2.1 Multiphysics Code Coupling Interface Vendor Website
ncl 6.1.0-beta NCL is an interpreted language designed specifically for scientific data analysis and visualization. Supports netCDF3 and 4, GRIP1 and 2 HDF-SDS, HDF4-EOS, binary, shapefiles, and ascii files. Vendor Website
Manual
nco 4.2.0 The netCDF Operators, or NCO, are a suite of programs known as operators. Each operator is a standalone, command line program which is executed at the UNIX shell-level like, e.g., ls or mkdir. The operators take netCDF files as input, then perform a set of operations (e.g., deriving new data, averaging, hyperslabbing, or metadata manipulation) and produce a netCDF file as output. Vendor Website
Manual
nwchem 6.1.1
6.3
NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. Vendor Website
Manual
octopus 4.0.1 Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation. Vendor Website
Manual
openfoam 1.6-ext-07122012
1.7.x-07142011
2.1.x-06062012
2.2.x-03182013
OpenFOAM CFD Toolbox Vendor Website
Manual
paraview 4.1.0 ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities. Vendor Website
Manual
parmetis 4.0.2 ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. Vendor Website
pbzip 1.1.6 tPBZIP2/MPIBZIP2 is a parallel implementation of the bzip2 block-sorting file compressor that uses pthreads(pbzip2) or MPI (mpibzip2) and achieves near-linear speedup on SMP machines or clusters. Anything compressed with pbzip2/mpibzip2 can be decompressed with bzip2 Vendor Website
pcp 1.1 tPCP: a parallel copy directory copy program for Lustre (/scratch /nobackup) Vendor Website
pig 0.11.1 Pig is an open source data processing tool. Vendor Website
Manual
pigz 2.3 Pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. It does not decompress in parallel. Vendor Website
povray 3.6.1 loads povray a high-quality raytracer for 3D Graphics Vendor Website
Manual
sage 5.12 Sage is a free open-source mathematics software system licensed under the GPL. It combines the power of many existing open-source packages into a common Python-based interface. Vendor Website
Manual
sqoop 1.4.3 Sqoop is a part of Hadoop, an open source data processing framework. Vendor Website
Manual
subversion 1.6.11 Vendor Website
Manual
tct 5.2.1 Teragrid/Xsede Client Toolkit for connecting with your Teragrid/Xsede portal password to Xsede/Teragrid resources using gsissh myproxy-login and globus-url-copy. Flux Documentation
Vendor Website
torque Loads the Torque batch computing environment Flux Documentation
Vendor Website
Manual
visit 2.5.1
2.6.2
loads the Visit serial and parallel engine for visualization of large data Flux Documentation
Vendor Website
Manual
vmd 1.9 VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Vendor Website
Manual
wannier90 1.2
2.0
Maximally-localised Wannier functions (MLWFs) and Wannier90, the computer program that calculates them. Both wannier90.x (the program) and libwannier.a (the library) are built and available. Vendor Website
Manual
wrf 3.4.1
3.5.1
The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. It features multiple dynamical cores, a 3-dimensional variational (3DVAR) data assimilation system, and a software architecture allowing for computational parallelism and system extensibility. Vendor Website
Manual
xsede 5.2.1 Xsede Client Toolkit for connecting with your Xsede portal password to Xsede resources using gsissh myproxy-login and globus-url-copy. Flux Documentation
Vendor Website

Licensed software

Module Name Versions Description Documentation
abaqus 6.11
6.12
6.12-3
abaqus is set of general purpose nonlinear finite element analysis (FEA) tools Flux Documentation
Vendor Website
Manual
ampl 12.2
20130903
AMPL is a comprehensive, powerful and flexible algebraic modeling language for the linear, nonlinear and integer programming problems often encountered in optimization.
ansys 14.0
14.5
15.0
ANSYS, produced by ANSYS, Inc., is a finite element simulation tool that incorporates multiphysics to simulate real world conditions. This allows users to analyze parts for behavior under multiple physical forces simultaneously Vendor Website
cfx 14.0
14.5
ANSYS CFX is a high-performance, general purpose CFD program that has been applied to solve wide-ranging fluid flow problems. Vendor Website
chemkin 10112 Loads the CHEMKIN runtime environment CHEMKIN software enables the simulation of complex chemical reactions Vendor Website
Manual
comsol 3.5a
4.3
Comsol is no longer available due to licensing issues.
cplex 12.4 CPLEX is a high-performance optimizer for linear programming Flux Documentation
Vendor Website
Manual
cubit 13.2 loads the CUBIT Mesh Generation Kit Vendor Website
Manual
dytran 2012 Dytran is an explicit finite element analysis (FEA) solution for analyzing complex nonlinear behavior involving permanent deformation of material properties, or the interaction of fluids and structures. Flux Documentation
Vendor Website
Manual
fluent 14.0
14.5
fluent – a comprehensive CFD (computational fluid dynamics) analysis tool. The FLUENT solver can be used to model turbulence, combustion, and multiphase applications. Flux Documentation
Vendor Website
gambit 2.4 gambit – GAMBIT is the preprocessor supplied with Fluent’s computational fluid dynamics (CFD) software. Vendor Website
gaussian 09-revc Gaussian is an electronic structure program that predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. Flux Documentation
Vendor Website
Manual
Gurobi 5.6.3 The Gurobi Optimizer is a solver for mathematical programming. Flux Documentation
Vendor Website
Gurobi documentation
hfss 13.0
14.0
15.0
loads the hfss environment for Full-Wave Sprice extraction and electromagnetic field simulation Flux Documentation
Vendor Website
idl 8.2 IDL is software for data analysis, visualization, and cross-platform application development Vendor Website
lsdyna 971-R5.1.1
971-R610
LS-DYNA is a general purpose transient dynamic finite element program; we support a parallel version Vendor Website
Manual
maple 16
17
Maple is a mathematical computing engine Vendor Website
Manual
marc 2012 MARC is a non-linear FEA program Vendor Website
mathematica 7.0
8.0
9.0
9.0.1
Mathematica is a compuer algebra system Flux Documentation
Vendor Website
Manual
matlab 2010b
2012a
2012b
2013a
Matlab is interactive package for numerical analysis, matrix computation, control system design, and linear system analysis and design Flux Documentation
Vendor Website
Manual
msmodel 5.5
6.0
6.1
Material Studio — a software environment that brings the world’s most advanced and validated materials simulation technology to the CAC Flux Documentation
Vendor Website
nastran 2012 Nastran is a powerful general purpose finite element analysis solution for small to complex assemblies Flux Documentation
Vendor Website
sas 9.3 SAS is a complete, general-purpose statistical analysis system. Flux Documentation
Vendor Website
starccm 7.02
7.04
7.06
8.04
Star-ccm+ is a CFD application that supports parallel processing Vendor Website
stata 12
13
Stata is a complete, integrated statistical package that provides everything you need for data analysis, data management, and graphics. Flux Documentation
Vendor Website
Manual
stata-mp 12
13
Stata is a complete, integrated statistical package that provides everything you need for data analysis, data management, and graphics. Flux Documentation
Vendor Website
Manual
tecplot 2012 Plotting and visualization software that gives full control over 2-D and 3-D plot parameters. Includes Tecplot 360 & Tecplot Focus Vendor Website

Privately licensed software

Module Name Versions Description Documentation
converge 2.0.0_020713
2.0.0_090612
2.1.0_083013
Computational fluid dynamics software for complex geometries with moving boundaries. Licensing: This software is licensed for academic, noncommercial use at the University of Michigan Vendor Website
helios 1.10 HELIOS Generalized Geometry Lattice Analysis package. Includes Casmo and Simulate from the Studsvik suite. Vendor Website
kintecus 4.40 Kintecus is chemical modeling software for simulation of combustion, nuclear, biological, enzyme, atmospheric and many other chemical kinetic and equilibrium processes. Kintecus is licensed only for use by specific classes. If you are not in one of those classes, you will not be able to run it. Flux documentation
Vendor website
lahey 6.2
8.1
loads the Fujitsu Lahey LF95 environment Vendor Website
mcnp5 1.6 loads the mcnp5 environment Vendor Website
mcnpx 2.7.0 loads the mcnpx environment Vendor Website
molpro 2010.1
2010.1-mrcc
Molpro is a complete system of ab initio programs for molecular electronic structure calculations Vendor Website
Manual
synopsys 2009.06-SP2
2012.06
Synopsys Synthesis environment Vendor Website
vasp 4.6.36Feb09
5.2.12.11Nov2011
5.3.2.13Sep2012
5.3.3.18Dec2012
VASP is a licensed package for performing ab-initio quantum-mechanical molecular dynamics (MD) Flux Documentation
Vendor Website
Manual