|
|
|
acml
|
2.7.0
|
AMD
Core Math Library for Linux. A tuned math library designed for
high performance on AMD64 machines. It includes Basic Linear
Algebra (BLAS) routines, Linear Algebra (LAPACK) routines, and Fast
Fourier Transforms (FFTs). |
afni
|
2005_11_18_1920
2006_06_30_1332
|
AFNI
is a set of C programs for
processing, analyzing, and displaying functional MRI (FMRI) data - a
technique for mapping human brain activity.
|
amber
|
6
9
|
Assisted
Model Building with
Energy Refinement (AMBER) - is the collective name for a suite of
programs designed to carry out molecular dynamics simulations,
particularly on biomolecules. |
apprentice2
|
2.5.0
|
Cray
Apprentice2 is a
performance data visualization tool. It is used to visualize
performance data generated by CrayPay experiments.
|
arpack/parpack
|
96
|
ARPACK
is a collection of Fortran77 subroutines designed to solve large scale
eigenvalue problems. This package contains PARPACK (Parallel
ARPACK).
|
atlas
|
3.7.11
|
Automatically
Tuned Linear
Algebra Software. ATLAS's purpose is to provide portably optimal
linear
algebra software. The current version provides a complete BLAS API (for
both C and Fortran77),
and a very small subset of the LAPACK API. |
cpmd
|
3.11.1
|
Car-Parrinello
Molecular
Dynamics. An ab initio Electronic Structure and Molecular Dynamics Program.
|
craypat
|
1.2.0
|
Cray
performance analysis tool.
|
cvs
|
1.11.22
|
Concurrent
Versions System is a version control system for source code files.
|
ddd
|
3.3.11
|
Data
Display Debugger. A
graphical front-end for GDB and other command-line debuggers.
|
eclipse
|
3.1.2
|
Eclipse
SDK. Provides a feature rich development environment that allows
the developer to efficiently create tools that integrate seamlessly
into the Eclipse Platform.
|
emacs
|
21.3
|
Extensible,
customizable,
self-documenting real-time
display editor |
fftw
|
2.1.5
3.0.1
|
Utility
to create FFT wisdom
files.
|
freesurfer
|
|
FreeSurfer
is a set of
semi-automated tools for reconstruction of the brain’s cortical surface
from structural MRI data, and overlay of functional MRI data onto the
reconstructed surface. |
gaussian
|
03-d1
|
Gaussian
predicts the
energies, molecular structures, and
vibrational frequencies of molecular systems, along with numerous
molecular properties derived from these basic computation types. |
gcc
|
4.1.0
|
GNU
Compiler suite.
|
| gmp |
4.2 |
GNU MP is a portable library written in C for arbitrary precision arithmetic on integers, rational numbers, and floating-point numbers. It aims to provide the fastest possible arithmetic for all applications that need higher precision than is directly supported by the basic C types. |
| gnuplot |
4.2.2 |
Command-line driven interactive data and function plotting utility. |
grace
|
5.1.19
|
Grace
is a WYSIWYG tool to make
two-dimensional plots of numerical
data. Its capabilities are roughly similar to GUI-based programs
like Sigmaplot or Microcal Origin plus script-based tools like Gnuplot
or Genplot. Its strength lies in the fact that it combines the
convenience of a graphical user interface with the power of a scripting
language which enables it to do sophisticated calculations or perform
automated tasks.
|
gromacs
|
3.3.1
|
A
molecular dynamics simulation package. |
jdk
|
1.5.0_06
|
Java
Development Kit.
|
libsci
|
1.3
|
LibSci
is a collection of
numerical routines tuned for performance on the Cray XD1 system. |
| mathematica |
6.0 |
Mathematica
is a fully integrated technical computing system, combining
interactive calculation (both numeric and symbolic), visualization tools,
and a complete programming environment. |
matlab
|
7.2.0
|
Matlab
is a high-level technical
computing language and interactive environment for algorithm
development, data visualization,
data analysis, and numeric computation. Using Matlab, you can solve
technical computing problems faster than with traditional
programming languages, such as C, C++, and Fortran. |
mpich
|
1.2.6
|
Portable
implementation of MPI.
|
namd
|
2.6b1
|
A
parallel, object-oriented
molecular dynamics code. Designed for high-performance simulation
of large biomeclar systems.
|
nano
|
1.2.5
|
A
pico-like text editor.
|
netcdf
|
3.6.1
|
Unidata
Network Common Data Form library. 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. |
neuron
|
5.9.39-iv-17
|
NEURON
is a simulation environment for developing and exercising models of
neurons and networks of neurons. |
nusmv
|
2.3.1
2.4.0
|
New
Symbolic Model Verifier. NuSMV is a re-implementation and
extension of SMV, the first model checker based on BDDs. It has been
designed to be an open architecture for model checking, which can be
reliably used for the verification of industrial designs, as a core for
custom verification tools, and as a test-bed for formal verification
techniques.
|
ocaml
|
3.09.1
|
The
Objective Caml system is the
main implementation of the Caml language. It features a powerful module
system and a full-fledged object-oriented layer. It comes with a
native-code compiler that supports numerous architectures, for high
performance; a bytecode compiler, for increased portability; and an
interactive loop, for experimentation and rapid development. |
| OpenBUGS |
2.2.0 |
BUGS (Bayesian inference Using Gibbs Sampling) is a piece of computer software for the Bayesian analysis of complex statistical models using Markov chain Monte Carlo (MCMC) methods. |
papi
|
3.1.0
|
Performance
Application
Programming Interface. Provides machine and operating system
independent access to hardware performance counters found on most
modern processors. Any of over 100 preset events can be counted through
either a simple high level programming interface or a more
complete low level interface from either C or Fortran.
|
perl
|
5.8.3
|
General
purpose programming and
scripting language.
|
petsc
|
2.3.1-p11
2.3.1-p14
|
Portable,
Extensible Toolkit for Scientific Computing is a suite of data
structures and routines that provide the building blocks for the
implementation of large-scale application codes on parallel and serial
computers. It includes a suite of parallel linear, nonlinear
equation solvers and time integrators that can be used with Fortran, C,
and C++.
|
pgi
|
6.0.2
6.1.2
|
Portland
Group compiler suite.
|
pgipp
|
5.2
|
The
Portability Package enables
programming for multiple linux versions using
PGI compilers.
|
python
|
2.3.3
|
An
interpreted, interactive,
object-oriented programming language.
|
R
|
2.2.1
2.3.1
2.4.0
|
A
language for data analysis and
graphics.
|
ruby
|
1.8.1
|
Interpreted
object-oriented scripting language
|
sac
|
100.0
|
SAC
(Seismic Analysis Code) is a general
purpose interactive program designed for the study of sequential
signals, especially timeseries data. |
SAS
|
9.1.3
|
SAS
Business Intelligence
application for analytics, data manipulation, and reporting.
|
subversion
|
1.3.2
|
Version
control system.
|
swig
|
1.3.28
|
Simplified
Wrapper and Interface
Generator (SWIG) is a software development tool that connects programs
written in C and C++ with a variety of high-level programming
languages. |
totalview
|
7.2.0
|
Powerful,
sophisticated, and programmable tool that lets
you debug, analyze, and tune the performance of complex serial,
multiprocessor, and multithreaded programs. |
trilinos
|
6.0.15
|
A
string of packages whose aim
is to develop parallel solver algorithms and libraries for large-scale,
complex scientific applications. |
ufapps
|
1.3.03
|
UFPApps
package consists of
example code, FPGA logic and utilities to work with the FPGA
co-processor on the Cray XD1 system. |
vmd
|
1.8.3
|
Visual
Molecular Dynamics.
A molecular visualization program for displaying, animating, and
analyzing large biomolecular systems using 3-D graphics and built-in
scripting. |
| xemacs |
21.4.19 |
XEmacs is a highly customizable open source text editor and application development system. |
