Installed Software

The following software is available on theECCO cluster at Scripps Institution ofOceanography (Ice, Fjord, Ring, Mist etc.). Please note that some softwarerequires additional setup of each user (e.g. StarOffice) or additions tothe searchpath. Notes on installation and use are given below. If problemsoccur please contact the responsible persons for the specific package).

General comments for users:

To access smaller software software packages the path has to be expanded, e.g. by:

set path=(/net/ice/ecco/bin $path) in your ~/.cshrc

For all path extensions it is usefull thatthe direcories are called before the origional path. This mnakes sure that no (older) versions of the software are found at IGPP
To access the manpages include:

set MANPATH=(/net/ice/ecco/man:$MANPATH) inyour ~/.cshrc

General comments for installer of new software:

I recommend to put single or few binaries in the general directory /net/ice/ecco/bin. This makes sure that the path does not get too long. They are reached very easiliy if the path is extended (see above).
Please make subdirectories for all bigger software packages. In that case it is sometimes usefull to use links tothis subdirecory in the standard directory, e.g.: netscape --> ../netscape/netscape
When manpages of new software should be available,please install those in /net/ice/ecco/man and do a

catman -M /net/ice/ecco/man -wto update the index. These manpages then can very easily accessed by extendingthe variable $MANPATH (see above)


Text Processing	Visualization	Libraries

Netscape Communicator ( ArneBiastoch)

web browser
actual version is 4.76 (128bit encryption, copied from Netscape, 10/25/2000)

start by: /net/ice/ecco/netscape/netscape

there is also the new version, Netscape 6 (copied from Sun, 1/31/2001), available. This can be used parallel to the older version (uses ~/mozilla and not ~/.netscape)

start by: /net/ice/ecco/netscape6/netscape
please note that I am currently testing this version. Right now, I do not know how stable it is....

XEmacs ( ArneBiastoch)

editor
actual version is 21.1.3 (precompiled version,solaris 2.6, copied fromXEmacs Homepage )
additional packages/settings:

tex-toolbar: Buttons for LaTeX commands
Ispell is available from Xemacs by pressing button "Spell"
other special adaptations for this site arein site-start.el

to use add /net/ice/ecco/bin/sparc-sun-solaris2.6toyour path , e.g. (in csh)

set path=(/net/ice/ecco/teTeX-1.0/bin/sparc-solaris $path)

StarOffice (Arne Biastoch)

office package (textprocessing and co.)
actual version is 5.1 (precompiled version, copied from Sun)
this version is installed as a net version. To initialize every user has to run /net/ice/ecco/Office51/bin/setup
after installation of only a few necessary files StarOffice integrates into CDE workspace
new version 5.2 is also installed, but doesnot work with the "older" machines (e.g. ice, ring) because of a missing patch. Installation similar to 5.1., but /net/ice/ecco/Office52/bin/setup. This version can be installed parallel to version 5.1!

Adobe Acrobat Reader ( ArneBiastoch)

viewer for pdf files
actual version is 4.0 (precompiled version, solaris, copied from Adobe)
start by /net/ice/ecco/Acrobat4/bin/acroread
Modifications are done to Netscape to useAcrocread inside of Netscape (script Browsers/netscape)

LaTeX ( ArneBiastoch)

text typesetting system
actual distribution is teTeX 1.0 (precompiled version, solaris 2.4 or later)
copied from Wuarchive(see teTeX Homepage for an overviewof binaries), automatic installation script
special notes for installation:

after installing new components run texhashto rebuild the search tree
to set up (e.g. printer) call texonfig

to use add /net/ice/ecco/teTeX/bin/sparc-solaristoyour path
Documentation
To use manpages: setenvMANPATH /net/ice/ecco/teTeX/man:$MANPATH
extra installed packages:

AGUstyle files (Jan 7, 2000, copied from ftp://kosmos.agu.org/agutex)
WO

latex2html ( ArneBiastoch)

converts latex files to html
actual version is 98.1p1
use by l2h <texfile>
also installed is the Netpbm package (in binand man ) which provides the conversion tools for graphics

Ispell ( ArneBiastoch)

(english) dictonary
actual version is 3.1.20 (precompiled versioncopied from Vector)
to use add /net/ice/ecco/bintoyour path
use by: ispell-d/net/ice/ecco/lib/americanmed+ <filename>

--> how can thisbe made system default?

PSUtils ( ArneBiastoch)

tools for changing postscript files
copied from http://www.dcs.ed.ac.uk/home/ajcd/psutils/ and compiled (corrected Makefile)
to use add /net/ice/ecco/bintoyour path
the following utils are available:

psresize -- Alters document paper size
psselect -- Selects pages andpage ranges
pstops -- Performs general pagerearrangement and selection
psnup --Prints multiple documentpages per physical sheet of paper
psbook -- Rearranges pages into"signatures"
epsffit -- Fits an EPSF fileto a given bounding box

Ferret ( ArneBiastoch)

plot software
actual version is 5.22 (precompiled version, solaris, copied on 8/28/2000 from FERRETHomepage)
initialize with: source/net/ice/ecco/ferret/ferret_paths
start by: ferret orferret -gui (latter for graphical user interface)
note: the old version 5.0 is still available: initialize with: source /net/ice/ecco/ferret50/ferret_paths
Documentationand ReleaseNotes

GrADs ( KyozoUeyoshi)

plot software
actual version is 1.7
/net/ice/ecco/GrADs
Documentation

NCAR Graphics ( KyozoUeyoshi)

actual version is 4.1.1.
initialization:

set environment variable NCARG_ROOTto /net/ice/ecco/ncarg
include /net/ice/ecco/ncarg/bin in your path
ncargversion should give the correct versionnumber

NCAR Graphics documentation
output:

on the screen: idtgmeta
color hard copy: clickon "dsc" or "dsb" in the box print
postscript file: clickon "postscript" (file named "gm.ps" in your working directory)
You can test this withan example gmeta file /net/ice/ecco/ncarg/lib/ncarg/test_gm/gmet

MATLAB ( ArneBiastoch)

MATLAB is installed systemwide by IGPP. However there are two points that might be of importance:

The documentation is not installed by IGPP.However the files are on ice. To use the documentation copy the file /net/ice/ecco/MATLAB/docopt.minto your personal MATLAB directory (usually ~/matlab). This contains thecorrect path.

To use the documentation type " doc"in MATLAB
Here is the directlink for your browser.

Toolboxes

The M_Map toolbox was installed in /net/ice/ecco/MATLAB/m_mapand can be used by adding this directory to your MATLABPATH. Documentation.
The MexCDF and NetCDF toolboxes (downloaded from http://crusty.er.usgs.gov/mexcdf.html) were installed in /net/ice/ecco/MATLAB/toolbox (Users Guide)

To use add the following lines to your MATLAB startup file:

addpath('/net/ice/ecco/MATLAB/toolbox/netcdf');

addpath('/net/ice/ecco/MATLAB/toolbox/netcdf/ncfiles');

addpath('/net/ice/ecco/MATLAB/toolbox/netcdf/nctype');

addpath('/net/ice/ecco/MATLAB/toolbox/netcdf/ncutility');

works with MATLAB6

mpeg_encode ( ArneBiastoch)

movie encoder, converts single pictures (e.g.JPEG) in mpeg format
actual version is 1.5 (binary obtained fromBerkeley )
/net/ice/ecco/bin/mpeg_encode

XFig ( ArneBiastoch)

Xfig is an interactive drawing tool
actual version is 3.2.3b, copied from ftp://www-epb.lbl.gov/xfig, compiled (Imakefile, Makefile)and installed in /net/ice/ecco/xfig (7/21/2000)
before starting include the application defaultsinto your .Xdefaults by

xrdb -merge /net/ice/ecco/lib/X11/app-defaults/Fig
xrdb -merge /net/ice/ecco/lib/X11/app-defaults/Fig-color

start by typing xfig(make sure /net/ice/ecco/bin is included at the beginning of your paths)
Documentation
additional installed libraries/programs:

transfig package (3.2.3b from ftp://www-epb.lbl.gov/xfig)
XPM3 package (xpm 3.4k from ftp://ftp.x.org/contrib/libraries/)
JPEG library (v6b from ftp://ftp.uu.net/graphics/jpeg/)

Ncview ( ArneBiastoch)

Ncview is a viewer for NetCDF files
actual version is 1.90b, compiled by Rolf Käse
before starting include the application defaultsinto your .Xdefaults by

xrdb -merge /net/ice/ecco/lib/ncview/Ncview

start by typing ncview<filename> (make sure /net/ice/ecco/bin is included at the beginning of your paths)

NetCDF Library ( ArneBiastoch)

library for manipulation of netcdf files
actual version is 3.5 beta2 (source code obtainedfrom Unidata)
installation notes:

installed without c++ because of compiling problems (both with c++ and g++ for this an older versions of netcdf)
used environment:

CC=/opt/SUNWspro/bin/c89
CPPFLAGS=-DNDEBUG
CFLAGS=-O
FPP=fpp
FPPFLAGS=-D__SUNPRO_F90
COMPILE_F=
FC=/opt/SUNWspro/bin/f90
FFLAGS=-O -w
CXX=/opt/SUNWspro/bin/CC

installed files:

ncgen and ncdump (binaries in /net/ice/ecco/bin for conversion between CDF and text)
/net/ice/ecco/lib/libnetcdf.a (library)
netcdf.inc and netcdf.h (include files in/net/ice/ecco/include; necessary for compiling programs that read/write NetCDF)

Numerical Recipes ( KyozoUeyoshi)

routines for scientific computing
/net/ice/ecco/recipes
contains FORTRAN, FORTRAN90 and C source codeas well as library (in ./lib)
FORTRAN90 --> please read noteby Kyozo on testing the routimes

NAG Math Library ( KyozoUeyoshi)

routines for scientific computing
actual version is Mark 19
FORTRAN source code
/net/ice/ecco/naglib/flsol19da
the object library is/net/ice/ecco/naglib/flsol19da/libnag-spl.so.19
Documentation can befound in /net/ice/ecco/naglib/flsol19da/doc/in.html and /net/ice/ecco/naglib/flsol19da/doc/un.html.
the library was testedwith the examples supplied with it. All example programs in sec 4.2 of./doc/in.html run ok. (please see ./scripts/my_nagexample .)

Install Tools and Misc(Arne Biastoch, prepared by RalfGiering)

The following tools/programs are installed in the standard directories (bin, lib, ...) under /net/ice/ecco. To use them these directories have to be in the path. All installationare made by "./configure --prefix=/net/ice/ecco;make;make install". Afterwards links are made that point to the actual versions of wish and tclsh.

autoconf 2.13
automake 1.4
m4 1.4
Tcl 8.3.2
Tk 8.3.2 (note: forcompiling Tk Tcl has to compiled in a parallel directory)

CVS (Patrick Heimbach)

Concurrent Versions System (CVS) 1.11
To use:

add /net/ice/ecco/bin to your path
add the following linesto your .cshrc:

setenv CVSROOT :ext:@bronte.lcs.mit.edu:/u/gcmpack
setenv CVS_RSH ssh

Patrick has set up someguidelinesfor using CVS

Kerberos ( ArneBiastoch)

Kerberos authentification software for NAVOcomputers
copied from ftp://ftp.cmf.nrl.navy.mil/pub/kerberos5 (11/13/2000)
to use include /net/ice/ecco/bin into yourpaths and place

setenv KRB5_CONFIG /net/ice/ecco/etc/krb5.conf in your .cshrc

first access by: kpasswd username@NAVO.HPC.MIL

--> old passwd (from letter)

--> passcode (currently on RSA SecurId)

--> new PIN (4-6 digits)

--> new PIN

--> new password (your choice)

--> new password

initialization for 10 hours: kinit username@NAVO.HPC.MIL

--> password

--> PIN (give PIN into RSA SecurId andget 6 digit number)

use krtelnet or krlogin (or kerberized versionof ssh)

This page is maintained by ArneBiastoch, September 26, 2000