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Software
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HPC Software

Applications Installed on HPC

* = Legend
M = application requires module load

Languages / Compilers / Debuggers

* Name Description Executable
as Assembler /usr/bin/as
cc, CC C, C++ compiler /usr/bin/cc
cvd WorkShop debugger /usr/sbin/cvd
cvperf WorkShop Performance View /usr/sbin/cvperf
dbx source-level debugger /usr/bin/dbx
ddd, xddd Data Display Debugger /usr/local/bin/ddd
gcc, c++, g++ GNU compiler /usr/local/bin/gcc, c++, g++
f77, f90 Fortran compiler /usr/bin/f77, f90
ftnchek Fortran source checker (v.3.1) /usr/local/bin/ftnchek
gdb GNU Debugger /usr/local/bin/gdb
icon Icon compiler /usr/local/icon
java Java compiler /usr/java/bin/java
mpi Message Passing Interface /usr/bin/mpirun
perl script programming language /usr/local/bin/perl
python an interpreted, interactive, object-oriented language /usr/local/bin/python

Editors / Text Formatting Utilities

* Name Description Executable
dvips converts TeX DVI to PostScript /usr/local/bin/dvips
emacs editor with text and windows modes /usr/local/bin/emacs
groff document formatter /usr/local/bin/groff
latex text formatter /usr/local/bin/latex
nedit GUI text editor /usr/local/bin/nedit
pico text editor - with Pine and standalone /usr/local/bin/pico
sed stream editor /usr/bin/sed
vi editor /usr/bin/vi
vim enhanced version of vi for programmers /usr/local/bin/vim

Readers / Viewers

* Name Description Executable
Adobe Acrobat PDF viewer /usr/local/bin/acroread
ghostview views PostScript with gs /usr/local/bin/gv
gs PostScript and PDF previewer /usr/local/bin/gs
less enhanced version of more /usr/local/bin/less
xv image display for X-Windows /usr/local/bin/xv

Biosciences

* Name Description Directory
amber7 molecular dynamics simulator /usr/local/amber7/
artemis DNA-sequence viewer, annotation tool /usr/local/artemis/
bioperl perl modules for bioinformatics /usr/local//bioperl/
blast fast-sequence similarity search tool /usr/local/ncbi/bin
clustalw DNA-, protein-alignment program /usr/local/clustalw/
entrez sequence-search program /usr/local/
fasta sequence database search /usr/local/fasta/
M HDF data format and library /opt/HDF
RasMol molecular visualization /usr/local/rasmol/

Chemistry

* Name Description Directory
amber7 molecular dynamics simulator /usr/local/amber7/
Dalton quantum chemistry /usr/local/dalton/dalton (Quartz)
Dalton manual as PDF
GAMESS quantum chemistry /usr/local/dalton/Gamess (Quartz)
GAMESS documentation at
/usr/local/dalton/Gamess/Doc/
Gaussian chemistry /usr/local/G98
Gaussview Gaussian viewer /usr/local/Gv_2.0/gv
grace 2D plotting /usr/local/grace/
RasMol molecular visualization /usr/local/rasmol/
spartan molecular building and visualization /usr/local/spartan/
(2 versions available)

Math / Science / Engineering Packages

* Name Description Directory
M Abaqus finite element pkg with GUI ability /opt/abaqus
Ansys group access required
(see setup -l for versions)
Dalton quantum chemistry /usr/local/dalton/dalton (Quartz)
Dalton manual as PDF
GAMESS quantum chemistry /usr/local/dalton/Gamess (Quartz)
GAMESS documentation at /usr/local/dalton/Gamess/Doc/
Gaussian chemistry /usr/local/g98/bin
Gaussview Gaussian viewer /usr/local/Gv_2.0/gv
imsl / vni (IMSL now VNI) libraries
compatible with Fortran 90 only
(see setup -l for versions)
Mathematica /usr/local/bin/math/
/usr/local/bin/mathematica/
Matlab /usr/local/matlab/
(see setup -l for versions)
R data analysis /usr/local/lib/R/

Graphics / Plotting / Image

* Name Description Executable
GNUplot interactive plotting program /usr/local/bin/gnuplot
grace plotting tool /usr/local/bin/xmgrace
jpegtran lossless transformer of JPEGs /usr/local/bin/jpegtran
ImageMagick graphics viewer and converter /usr/local/bin/display
NCAR Graphics graphics libraries for Fortran and C (see setup -l for versions)
xfig X-Windows interactive drawing tool /usr/local/bin/xfig
xpm X11 pixmap library /usr/local/bin/sxpm
zlib compression/decompression library -

Scientific Visualization

* Name Description See path
OpenDX visualization package /usr/local/dx2

Networks / Mail / News / Browsers

* Name Description Executable
kermit file transport /usr/local/bin/kermit
lynx non-graphical webpage viewer /usr/local/bin/lynx
mailx email /usr/sbin/mailx
ncftp Internet file transport /usr/local/bin/ncftp
pine email /usr/local/bin/pine
ssh secure replacement for ftp and telnet /usr/local/bin/ssh
zmodem /usr/local/bin/sz,sx,etc.

General Utilities

* Name Description Executable
agrep searches file for pattern /usr/local/bin/agrep
bash scripting language /usr/local/bin/bash
bison /usr/bin/bison
bzip2,bunzip2 block-sorting file compressor/decompressor /usr/local/bin/bzip2, bunzip2
egrep searches file for pattern /usr/bin/egrep
fgrep searches file for pattern /usr/bin/fgrep
flex /usr/bin/flex
grep searches file for pattern /usr/bin/grep
gzip,gunzip file compression/decompression /usr/sbin/gzip,gunzip
lex /usr/bin/lex
make /usr/bin/make
pbs batch-job processing system /usr/pbs/bin/qstat, qsub, xpbs,...
transfig /usr/local/bin/transfig
zip, unzip package & compress files (tar + compress) /usr/local/bin/zip, unzip

Libraries

* Name Description Directory
CERN /usr/local/CERN/
fftw /usr/local/fftw/
M HDF data format and library -
IRAF /usr/local/iraf/
NumRec /usr/local/lib/librecipes_f.a, librecipes_f90.a
S NCAR graphics library (see setup -l for versions)

Miscellaneous

* Name Description Executable
a2ps text and graphics print utility /usr/local/bin/a2ps
enscript text print utility /usr/local/bin/enscript
find recursively searches directory structure for a file /usr/local/bin/find
gawk pattern-scanning, -processing language /usr/local/bin/gawk
ispell interactive spell checker /usr/local/bin/ispell
libwmf /usr/local/bin/xwmf, wmftofig, wmftogif
ncurses /usr/local/lib
/usr/local/share/tabset/
/usr/local/share/terminfo
readline read user input /usr/local/bin/readline
sed stream editor /usr/bin/sed
xdisk temporary user storage allocator/manager /usr/local/bin/xdisk

* = Legend

M = application requires module load

 
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