The AVIDD-B Cluster

Available Software

Note: Software requests for AVIDD are no longer being accepted due to AVIDD's impending retirement.

The following table contains most of the application software and tools available on the AVIDD-B cluster.

A list of installed Perl modules is also available.

Software packages listed below with an entry in the "Softenv Keywords" column may be added to your environment with the following command:

soft add <keyword>

Alternatively, you may add <keyword> to your ~/.soft file and run resoft. Note that several applications list multiple Softenv keywords, for example, GCC version 3.4.3 can be added to your environment with either +gcc or +gcc-3.4.3. Some applications are available in different compiled forms, differentiated by suffix (e.g. -intel or -gcc). The various keywords should indicate which compiler was used. In addition to keywords, which begin with the '+' symbol, an application may list a Softenv macro (beginning with the '@' symbol). This macro will contain the keyword as well, so either the keyword or the macro will suffice to add the application to your environment.

The default ~/.soft file for AVIDD users contains the @avidd macro; if a package listed below includes @avidd in its softenv keywords, it's already in your environment (assuming you haven't removed @avidd from your ~/.soft file).

Any Softenv keywords listed in parentheses are prerequisites for the application keyword. For more information about Softenv, please see the Softenv section of the Getting Started page.

Software Version Description Keywords Documentation Categories
Acrobat Reader 7.0.0 PDF viewer +acrobat
@avidd		 $ acroread --help
FAQ		 Viewers
AIR 5.2.5 Automatic Image Registration +air Online Docs Viz
AMBER 8 Assisted Model Building with Energy Refinement +amber
+amber-mpich		   Biology
Physics
Chemistry
Ant 1.6.2 Java-based build tool +ant Manual Devel
ATLAS 3.4.1 Automatically Tuned Linear Algebra Software +atlas
+atlas-3.4.1		 Online Docs HPC
ATLAS 3.7.3 Automatically Tuned Linear Algebra Software +atlas-3.7.3 Online Docs HPC
ATLAS 3.7.10 Automatically Tuned Linear Algebra Software +atlas-3.7.10 Online Docs HPC
autoconf 2.57 m4 macros for autoconfiguration   $ man autoconf
Manual 		Devel
automake 1.6.3 Makefile.in generator   $ info automake
HTML Manual
PDF Manual 		Devel
Bash 2.05b Bourne-Again shell   $ man bash
Reference Manual		 Shells
GNU
bc 1.06 Numeric processing language   $ man bc
Manual 		Misc
GNU
binutils 2.14.90 Binary tools (ld, ar, nm, etc)   $ man ar
$ man ld		 Devel
GNU
bison 1.875c Parser generator (yacc replacement)   $ man bison
Manual 		Devel
GNU
BLASTZ 7 Sequence Alignment +blast
@bio		   Biology
blcr 0.4.0 Berkeley Linux Checkpoint/Restart +blcr $ man cr_checkpoint
$ man cr_restart
$ man cr_run
 Job Tools
boost 1.32 C++ Libraries +boost_1_32_0-gcc32
+boost_1_32_0-gcc33
+boost_1_32_0-gcc34
+boost_1_32_0-gcc40
+boost_1_32_0-intel81 		Online Docs Devel
boxshade 3.3.1 Print multiple alignment output (e.g. from ClustalW) +boxshade   Biology
CERNLIB 2004 CERN Program Library +cern CERNLIB Documentation Physics
HPC
ClustalW 1.83 Sequence Alignment +clustalw   Biology
ClustalX 1.83 X-enabled ClustalW +clustalx   Biology
CVS 1.11.2 Concurrent Versions System   $ man cvs
Manual 		Devel
GNU
diffutils 2.8.1 File comparison utilities (diff, cmp, diff3, sdiff)   $ man diff MISC
drseed   Random Seed Generator +drseed $ man drseed Misc
Emacs 21.3.1 Editor, and so much more   $ man emacs
Manuals		 Editors
GNU
FASTA 3.4 Protein and nucleotide similarity searching +batch
@avidd		 $ man fastajob
Online docs		 Biology
HPC
FFTW 3.0.1 Fastest Fourier Transform in the West +fftw
+fftw-3.0.1-float-intel
+fftw-3.0.1-intel		 fftw.org HPC
findutils 4.1.7 Find utilities (find, xargs)   $ man find
$ man xargs		 Misc
GNU
flex 2.5.4 Fast lexical analyzer generator   $ man flex
Manual 		Devel
GNU
Fluent 6.2.16 Computational Fluid Dynamics +fluent   Engineering
gawk 3.1.1 Pattern scanning and processing language (aka awk)   $ man gawk
Manual 		Misc
GNU
GCC 3.2.3 GNU Compilers   $ man gcc
Manual		 Compilers
GNU
GCC 3.3-1 GNU Compilers +gcc-3.3-1 $ man gcc
Manual		 Compilers
GNU
GCC 3.4.3 GNU Compilers +gcc
+gcc-3.4.3		 $ man gcc
Manual		 Compilers
GNU
GCC 4.0 GNU Compilers +gcc-4.0
+gcc-4.0-20050402		 $ man gcc
Manual		 Compilers
GNU
gdb 6.3.0 GNU debugger   $ man gdb Devel
GNU
Ghostscript 7.05 PostScript document viewer   $ man gs Viewers
Globus 2.4.3 Globus Toolkit +globus   Grid
GNU Scientific Library 1.6 Numerical computing routines +gsl
+gsl-1.6-intel
+gsl-1.6-gcc		 $ man gsl
Manual 		Devel
HPC
GNU
gnuplot 3.7.3 Interactive plotter   $ man gnuplot
$ info gnuplot
Online Docs 		Viz
GPT 3.1.1b5 Globus Packaging Toolkit +gpt   Grid
GPT Wizard 0.7.6 GPT Wizard +gpt-wizard   Grid
GridFTP 3.9.5 Globus Grid-enabled FTP +gridftp $ globus-url-copy -help Grid
groff 1.18.1 document formatting system   $ man groff Misc
GNU
Gromacs 3.2.1 Molecular Dynamics Simulation +gromacs Online Docs Chemistry
HPC
gzip 1.3.3 File compression utility (gzip, gunzip, zcat)   $ man gzip Manual Misc
GNU
HSI 2.8 Hierarchical Storage Interface +hpss
@avidd		 $ hsi --help Misc
Intel Compilers 8.1 C/C++ and Fortran compilers (icc, icpc, ifort) +intel-compilers
@avidd		 $ man icc
$ man ifort
icc User's Guide
ifort User's Guide, Quick Reference 		Compilers
Java 1.4.2 IBM Java Developer Kit and Runtime Environment +java Manual Devel
LAM 7.1.1 Local Area Multicomputer MPI +lam-gm-gcc
+lam-gm-intel		 $ man lam
User's Guide 		MPI
less 378 File viewing utility   $ man less Viewers
GNU
m4 1.4.1 Macro processor   $ m4 --help
Manual 		Devel
GNU
make 3.79.1 Program maintenance utility   $ man make
Manual 		Devel
GNU
MATLAB 7 Numeric Calculations & Graphics     Devel
Maui 3.2.6 Batch job scheduling system (showq, checkjob, showres, etc) +maui
@avidd		 $ showq --help
$ checkjob --help
User's Manual 		Job Tools
Mktemp 1.5 Safe creation and use of /tmp files   $ man mktemp Misc
MPICH-G2 1.2.6 Grid-enabled MPI +mpich-g2
(+globus)		 $ man MPI
$ man mpicc
Online Docs 		MPI
HPC
MPICH-GM 1.2.6..14a MPI over Myricom's GM protocol +mpich-gm-intel
+mpich-gm-gcc		 $ man MPI
$ man mpicc 		MPI
HPC
MPICH-P4 1.2.6 MPI over TCP/IP +mpich-p4-gcc $ man MPI
$ man mpicc 		MPI
HPC
mpiexec 0.78 PBS-aware mpirun replacement +mpiexec $ man mpiexec
OSC Website 		MPI
HPC
MULTICLUSTAL 1.1 Sequence Alignment +multiclustal $ man multiclustaljob
Online Docs 		Biology
HPC
nedit 5.3-4.1 GUI text editor   $ man nedit Editors
OpenSSH 3.6.1p2 Secure Shell (ssh, scp, sftp, etc)   $ man ssh Misc
PAML 3.14b Phylogenetic Analysis by Maxiumum Likelihood +paml
@bio		   Biology
HPC
Perl 5.8.0 Practical Extraction and Report Language   $ man perl Misc
Devel
PGI Compilers 6.0-1 Portland Group C and Fortan Compilers (pgcc, pgCC, pgf77, pgf90) +pgi $ man pgcc
$ man pgf77
 Compilers
Python 2.2.3 OO Programming Language   $ man python Devel
R 2.0.1 Statistical Computing and Graphics language/environment +R $ man R
 Viz
RCS 5.7 Revision Control System   $ man rcsintro Devel
GNU
rsync 2.5.7 Remote file synchronization   $ man rsync
Manual 		Misc
root 4.04.02 CERN Object-Oriented Data Analysis Framework +root User's Guide HPC
sharutils 4.2.1 Shar archive utilities (shar, uuencode, etc)   $ man shar
$ man uuencode		 Misc
GNU
subversion 1.1.3 Version Control System   $ man svn Version Control with Subversion Devel
tar 1.13.25 Tape/disk archive   $ man tar Misc
GNU
Tcl 8.3.5 Tool Command Language   $ man tclsh Devel
tcsh 6.12 C shell, only better   $ man tcsh Shells
vim (vi) 6.3 VIsual editor iMproved   $ man vi Editors
wget 1.9 File retrieving utility   $ man wget
Manual 		Misc
GNU
xCAT 1.2.0 IBM eXtreme Cluster Administration Toolkit   $ man psh
$ man prcp
(etc...) 		Misc
xpdf 2.02 X Windows PDF viewer   $ man xpdf Viewers