Software on nyx

The following list of software is available on the nyx cluster. To access any of these packages, use the module load modulename command; for more information on the module command see this page.

Many of these packages have multiple versions, to see available versions, type module avail.

Module Name Versions Description Additional Information
R 2.2.1-gcc
2.4.1-gcc
2.6.1-gcc
2.7.0-gcc
R is a software environment for statistical computing CAC Documentation
Vendor Website
abaqus 6.5.4
6.6
6.7
abaqus is set of general purpose nonlinear finite element analysis (FEA) tools CAEN Documentation
Vendor Website
acml 3.0.0-pgi
3.5.0-gnu
3.5.0-pgi
3.5.0-pgi-mp
4.0.0-pgi
4.0.0-pgi-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
amber 8-intel
8-pgi
Amber a set of molecular mechanical force fields for the simulation of biomolecules. You must possess a license to use this software, see the Vendor Website or contact cac-support@umich.edu for more information. CAC Documentation
Vendor Website
ampl 2006 AMPL is a comprehensive, powerful and flexible algebraic modeling language CAEN Documentation
Vendor Website
ansys 10.0 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 CAEN Documentation
Vendor Website
arpack 96-pgi7.0 ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. It is most appropriate for large sparse or structured matrices Vendor Website
autodock 4.0.1 AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Vendor Website
blat 34 Blat is a tool which performs rapid mRNA/DNA and cross-species protein alignments. Vendor Website
blcr 0.7.1 loads the blcr kernel modules Vendor Website
charmm c32b2 CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations. You must possess a license to use this software. CAC Documentation
Vendor Website
comsol 3.2b
3.3a
3.4
COMSOL Multiphysics is a modeling package for the simulation of any physical process you can describe with partial differential equations CAEN Documentation
Vendor Website
cplex 10.0
10.1
10.2
11.0
CPLEX is a high-performance optimizer for linear programming CAC Documentation
CAEN Documentation
Vendor Website
cplex-threaded 10.2
11.0
CPLEX is a high-performance optimizer for linear programming CAC Documentation
CAEN Documentation
Vendor Website
cuda 1.1 CUDA is the development environment for using nVidia's graphics cards for processing Vendor Website
ddt 1.10
2.0
2.1.3
2.2.1
ddt is a parallel debugger CAC Documentation
Vendor Website
eel 1.1 Enhancer Element Locator, or EEL, is a tool for locating distal gene enhancer elements in mammalian genomes by comparative genomics. Vendor Website
espresso 3.1
3.1.1
3.2
Espresso: Electronic Structure Computation Software Vendor Website
fftw 2.1.5-gcc
2.1.5-pgi
2.1.5-pgi-6.2
2.1.5-pgi-7.0
3.1.1-gcc
3.1.1-pgi
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions Vendor Website
flomerics flotherm Flotherm is Vendor Website
fluent 6.2
6.3
fluent - a comprehensive CFD (computational fluid dynamics) analysis tool. The FLUENT solver can be used to model turbulence, combustion, and multiphase applications. CAC Documentation
CAEN Documentation
Vendor Website
gadget2 2.0.3 Gadget2 (GAlaxies with Dark matter and GasintEracT) is a code for collisionless and gasdynamical cosmological simulations Vendor Website
gaussian 03-32bit
03-64bit
03-64bit-linda
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. CAC Documentation
CAEN Documentation
Vendor Website
goto 1.16-pgi The GotoBLAS codes are currently the fastest implementations of the Basic Linear Algebra Subroutines Vendor Website
gromacs 3.3.1 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. CAC Documentation
Vendor Website
gti 6.2 GT-SUITE offers the only true virtual engine/powertrain tool, capable of integrated simulations of the total engine and powertrain system Vendor Website
hdf5 1.6.5-gcc
1.6.5-pgi
HDF5 is a general purpose library and file format for storing scientific data. Vendor Website
hfss 10.1 loads the hfss environment for Full-Wave Sprice extraction and electromagnetic field simulation Vendor Website
hspice 2006.09-sp1 HSPICE is used for circuit simulation Vendor Website
ibmdsa   loads the IBM DSA diagnostic tool environment
idl 6.3 IDL is software for data analysis, visualization, and cross-platform application development CAEN Documentation
Vendor Website
intel-comp all
c-10.0.025
c-9.1.043
fortran-10.0.025
fortran-9.1.037
The Intel Fortran Compiler produces highly optimized code for the Intel CPUs Vendor Website
ioapi 3.0 IO/API provides the environmental model developer with an easy-to-learn, easy-to-use programming library for data storage and access, available from both Fortran and C. Vendor Website
java 1.5.0_06 loads the Java development and runtime environment Vendor Website
lam 7.0.6-gcc
7.0.6-pgi
7.0.6-pgi52
7.1.2-gcc
7.1.2-pgi
loads the deprecated LAM-MPI compiler environment; you should use OpenMPI if possible Vendor Website
lammps 1Apr08
8Nov07
loads the LAMMPS MD environment Vendor Website
lsdyna 970-5434a
970-6763-usermat
971-41097-usermat
971-7600
LS-DYNA is a general purpose transient dynamic finite element program; we support a parallel version Vendor Website
marc 2007r1 MARC is a non-linear FEA program CAEN Documentation
Vendor Website
mathematica 5.2
6.0
Mathematica is a compuer algebra system CAC Documentation
CAEN Documentation
Vendor Website
matlab 2006a
2006b
2007a
7.1
Matlab is interactive package for numerical analysis, matrix computation, control system design, and linear system analysis and design CAC Documentation
CAEN Documentation
Vendor Website
mcnp5 1.4 loads the mcnp5 environment Vendor Website
memtester memtester use: memtester memory_in_mb number_of_iterations
metis 4.0-gcc
4.0-pgi
METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes developed in our lab. Vendor Website
moabscripts   showprivatepreemptjobs: Show currently running preemptable jobs on private standing reservations (root only)
modules   loads the modules environment for software selection and version management CAC Documentation
Vendor Website
mpe 1.0.3p1-gcc
1.0.3p1-pgi
MPE performance libarary environment for MPI Vendor Website
mpiblast 1.4 loads the mpiblast and NCBI/Blast environment Vendor Website
mpich 1.2.7-nag MPICH is an MPI environment supporting the NAG compilers and libraries Vendor Website
mrbayes 3.1.2-pgi MrBayes is a program for the Bayesian estimation of phylogeny Vendor Website
msmodel 4.0
4.1
msmodel provides Castep, Dmol VAMP CAC Documentation
CAEN Documentation
Vendor Website
nag 5-32b
5-64b
5.1-64b
7
nag is set of routines for the solution of numerical and statistical problems CAC Documentation
CAEN Documentation
Vendor Website
naglib 7.0-gcc
7.0-pgi
7.0-pgi-mp
NAG has over 1,450 tried and tested routines that are both flexible and portable Vendor Website
namd 2.6
2.6b1
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Vendor Website
nastran 2006r1 Nastran is a powerful general purpose finite element analysis solution for small to complex assemblies CAC Documentation
CAEN Documentation
Vendor Website
ncbi 200506 Provides Blast. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. Vendor Website
nco 3.9.1-gcc
3.9.1-pgi
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
netcdf 3.6.1-gcc
3.6.1-pgi
NetCDF (network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data. Vendor Website
numpy   Numpy is the fundamental package needed for scientific computing with Python Vendor Website
ocean 5.114-32bit
5.114-64bit
loads the Open Command Environment OCEAN part of Cadence IC Vendor Website
octave 2.1.57 GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language. Vendor Website
oommf 1.1b2 OOMMF is a portable, extensible public domain micromagnetic program and associated tools. Vendor Website
openmpi 1.0.2-gcc
1.0.2-nag
1.0.2-pgi
1.0.3a1-pgi
1.1.0-pgi
1.1.0-pgi616
1.1.2-intel
1.1.2-pgi
1.1.4-pgi62
1.1a8-nag
1.1a9-pgi
1.2-pgi
1.2.3-gcc
1.2.3-pgi
1.2.6-intel
loads the OpenMPI/GCC compiler environment Vendor Website
opt 1.3.1 opt is a parallel profiler/optimizer Vendor Website
optistruct 7.0 Optistruct finite element based software program for both structural analysis and design optimisation. OptiStruct is used to design, evaluate and improve performance of mechanical structures. CAC Documentation
CAEN Documentation
Vendor Website
paml 3.15-gcc
3.15-pgi
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Vendor Website
parmetis   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
perlmodules   CPAN : Statistics-Descriptive: http://search.cpan.org/~colink/Statistics-Descriptive-2.6/Descriptive.pm
petsc 2.3.1-pgi
2.3.1p14-pgi-opt
2.3.3p1-pgi
2.3.3p1-pgi-opt
PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Vendor Website
pgi 5.2
6.0
6.1
6.1-6
6.2
7.0
7.2
loads the PGI compiler environment CAC Documentation
Vendor Website
python 2.5.1
2.5.2
This is not the provided python compiler from RedHat Vendor Website
scalapack 1.8.0-ompi Distributed Memory solvers for: Dense and band matrix Ax=B Vendor Website
sentaurus 2007.03 Loads the Synopsys TCAD programs Vendor Website
siesta 2.0-acml
2.0-acml-noopt
SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Vendor Website
simpson 1.1.1-gcc
1.1.1-pgi
solid-state NMR simulation software Vendor Webiste
snow 0.2-2
0.2-2-R241
0.2-9
SNOW is an R module for parallel computing (Simple Network of Workstations) CAC Documentation
Vendor Website
spm 2 SPM is statistical parametric mapping software designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. Vendor Website
stata 10
9.2
Stata is a complete, integrated statistical package that provides everything you need for data analysis, data management, and graphics. CAC Documentation
Vendor Website
subversion 1.4.5
1.4.6
loads the subversion source code managment system Vendor Website
torque   loads the Torque and Maui batch computing environment CAC Documentation
Vendor Website
udunits 1.12.4-gcc
1.12.4-pgi
The UDUNITS package supports conversion between string and binary representations of units, arithmetic manipulation of units, and conversion of numeric values between compatible units. This module sets PATH, UDU_LINK and UDU_INC Vendor Website
valgrind 3.2.3 Valgrind is a suite of memory and performance checking tools Vendor Website
vasp 4.6 VASP is a licensed package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set; you must own a license to use this. CAC Documentation
Vendor Website
verilog 5.8 loads the Verilog part of Cadence IC Vendor Website
xpressmp 2007a Xpress-MP is a suite of mathematical modeling and optimization tools used to solve linear, integer, quadratic, non-linear, and stochastic programming problems. Vendor Website
Automatically generated at Fri Jul 4 04:02:29 2008.