The AVIDD-O 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-O 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, LAM 7.1.2 can be added to your environment with either +lam-gcc or +lam-gm-7.1.2b18-gcc. Some applications are available in different compiled forms, differentiated by suffix (e.g. -pgi 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-O users contains the @default macro; if a package listed below includes @default in its softenv keywords, it's already in your environment (assuming you haven't removed @default 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 |
|---|---|---|---|---|---|
| AMBER | 8 | Assisted Model Building with Energy Refinement | +amber +amber-8.0-pgi |
Biology Physics Chemistry |
|
| autoconf | 2.59 | m4 macros for autoconfiguration | $ man autoconf Manual |
Devel | |
| automake | 1.9.2 | Makefile.in generator | $ info automake HTML Manual PDF Manual |
Devel | |
| Bash | 3.0-19.2 | Bourne-Again shell | $ man bash Reference Manual |
Shells GNU |
|
| bc | 1.06 | Numeric processing language | $ man bc Manual |
Misc GNU | |
| binutils | 2.15.92 | Binary tools (ld, ar, nm, etc) | $ man ar $ man ld |
Devel GNU | |
| bison | 1.875c | Parser generator (yacc replacement) | $ man bison Manual |
Devel GNU | |
| Delphi | 4.1.1 | 3D PB Equation Solver | +delphi +delphi-4.1.1 |
||
| diffutils | 2.8.1 | File comparison utilities (diff, cmp, diff3, sdiff) | $ man diff | MISC | |
| Emacs | 21.3.19 | Editor, and so much more | $ man emacs Manuals |
Editors GNU |
|
| findutils | 4.1.20 | Find utilities (find, xargs) | $ man find $ man xargs |
Misc GNU | |
| flex | 2.5.4a | Fast lexical analyzer generator | $ man flex Manual |
Devel GNU | |
| gawk | 3.1.3 | Pattern scanning and processing language (aka awk) | $ man gawk Manual |
Misc GNU | |
| GCC | 3.4.4 | GNU Compilers | $ man gcc Manual |
Compilers GNU |
|
| gdb | 6.3.0 | GNU debugger | $ man gdb | Devel GNU | |
| Ghostscript | 7.07 | PostScript document viewer | $ man gs | Viewers | |
| GNU Scientific Library | 1.5.2 | Numerical computing routines | +gsl +gsl-1.6-intel +gsl-1.6-gcc |
$ man gsl Manual |
Devel HPC GNU |
| gnuplot | 4.0.0 | Interactive plotter | $ man gnuplot $ info gnuplot Online Docs |
Viz | |
| groff | 1.18.1 | document formatting system | $ man groff | Misc GNU | |
| gzip | 1.3.3 | File compression utility (gzip, gunzip, zcat) | $ man gzip Manual | Misc GNU | |
| Java | 1.4.2 | IBM Java Developer Kit and Runtime Environment | Manual | Devel | |
| LAM | 7.1.2 | Local Area Multicomputer MPI | +lam-gcc +lam-gm-7.1.2b18-gcc |
$ man lam User's Guide |
MPI |
| less | 382 | File viewing utility | $ man less | Viewers GNU | |
| m4 | 1.4.1 | Macro processor | $ m4 --help Manual |
Devel GNU | |
| make | 3.80 | Program maintenance utility | $ man make Manual |
Devel GNU | |
| Maui | 3.2.6 | Batch job scheduling system (showq, checkjob, showres, etc) | +maui @default |
$ showq --help $ checkjob --help User's Manual |
Job Tools |
| Mktemp | 1.5 | Safe creation and use of /tmp files | $ man mktemp | Misc | |
| MPICH-GM | 1.2.6..14b | MPI over Myricom's GM protocol | +mpich-gm-pgi +mpich-gm-gcc |
$ man MPI $ man mpicc |
MPI HPC |
| nedit | 5.4-3 | GUI text editor | $ man nedit | Editors | |
| OpenSSH | 3.9p1-8 | Secure Shell (ssh, scp, sftp, etc) | $ man ssh | Misc | |
| Perl | 5.8.5 | Practical Extraction and Report Language | $ man perl | Misc Devel | |
| PGI Compilers | 6.0-5 | Portland Group C and Fortan Compilers (pgcc, pgCC, pgf77, pgf90) | +pgi |
$ man pgcc $ man pgf77 |
Compilers |
| Python | 2.3.4 | OO Programming Language | $ man python | Devel | |
| RCS | 5.7-26 | Revision Control System | $ man rcsintro | Devel GNU | |
| rsync | 2.6.3 | Remote file synchronization | $ man rsync Manual |
Misc | |
| sharutils | 4.2.1 | Shar archive utilities (shar, uuencode, etc) | $ man shar $ man uuencode |
Misc GNU | |
| subversion | 1.1.4 | Version Control System | $ man svn Version Control with Subversion | Devel | |
| tar | 1.14-8 | Tape/disk archive | $ man tar | Misc GNU | |
| Tcl | 8.4.7 | Tool Command Language | $ man tclsh | Devel | |
| tcsh | 6.13-9 | C shell, only better | $ man tcsh | Shells | |
| vim (vi) | 6.3 | VIsual editor iMproved | $ man vi | Editors | |
| wget | 1.10.2 | File retrieving utility | $ man wget Manual |
Misc GNU | |
| xCAT | 1.2.0 | IBM eXtreme Cluster Administration Toolkit |
$ man psh $ man prcp (etc...) |
Misc | |
| xpdf | 3.00 | X Windows PDF viewer | $ man xpdf | Viewers |
