Software in /net/aps

Software available to staff members at the Faculteit der Letteren, on Linux (LWP).

Available software

/net/aps/haytabo: The newest software, compiled on the machine haytabo, running Ubuntu 16.04.3 LTS, Xenial.
/net/aps/64: Software old and new, the newest compiled on machine zardoz, running Ubuntu 14.04.5 LTS, Trusty.
/net/aps/32: Very old software, compiled on a 32 bits machine.
/net/aps/common: Material not dependent on a particular platform version.

Example `.bashrc` for LWP users

if [ `hostname -s` = lwp-ssh ]
then
    exit
fi

alias ..='cd ..'
alias ll='ls -Fla'
alias acroread=evince

source /usr/share/mc/bin/mc.sh

export COLUMNS
export LINES
export EDITOR=nano

umask 002

case `hostname -s` in

    haytabo)
        PATH=$PATH:/net/aps/haytabo/bin
        source /net/aps/haytabo/etc/alias.sh
        ulimit -v 264137760 # 50%
        ;;

    *)
        if grep -q -E 'Ubuntu (1[6-9]|[2-9][0-9])' /etc/issue   # Ubuntu 16 or above
        then
            PATH=$PATH:/net/aps/haytabo/bin
            source /net/aps/haytabo/etc/alias.sh
        else
            PATH=$PATH:/net/aps/64/bin:/net/aps/32/bin
        fi
        ;;

esac

PATH=$HOME/bin:$PATH:/net/aps/common/bin

source /net/aps/common/etc/alias.sh

Overview

The workhorse haytabo is the replacement for the workhorse zardoz. At the moment, there is considerable less software installed in /net/aps/haytabo than in /net/aps/64 (compiled on zardoz).

One reason is that some software in /net/aps/64 is now mature enough to be part of Ubuntu. Another reason is that some software in /net/aps/64 is no longer used because there are better alternatives available.

Software from /net/aps/64 that is now also installed in /net/aps/haytabo was compiled from recent sources, as much as possible.

Activation of packages

Most of the software on /net/aps/64 is executable from /net/aps/64/bin. That are a lot of programs. Putting everything in one bin directory has some disadvantages, so a different approach was chosen for /net/aps/haytabo.

There are still many programs in /net/aps/haytabo/bin, but some large packages, primarily those for specific domains and with lots of binaries, are not directly executable. To use such a package, you first activate it by running an activate alias, which prepares your environment and puts the binaries in the front of your PATH. These aliases are defined if you source the file /net/aps/haytabo/etc/alias.sh (or /net/aps/haytabo/etc/alias.csh for users of csh).

alpino-activate

activate-alpino

Alpino — A dependency parser for Dutch.

anaconda3-activate

activate-anaconda3

Anaconda — The Python Data Science Platform, including:

Conda — Package, dependency and environment management for any language: Python, R, Ruby, Lua, Scala, Java, JavaScript, C/C++, FORTRAN
Glue — Multidimensional data exploration
Jupyter Notebook — With support for Julia, Matlab, Octave, Python 3, and R — See examples
Orange — Open source machine learning and data visualization for novice and expert
RStudio — Makes R easier to use, with a code editor, debugging & visualization tools
Spyder — The Scientific PYthon Development EnviRonment
Visual Studio Code — Code editing, Redefined

fsa-activate

activate-fsa

fsa — Programs for constructing finite state automata.

L04-activate

activate-L04

RuG/L04 — Software for dialectometrics and cartography.

lamachine-activate

activate-lamachine

LaMachine — Natural Language Processing software, with Timbl, Frog, Mbt, FoLiA-tools, and much more.

moses-activate

activate-moses

Moses — A statistical machine translation system, with mosesdecoder, GIZA++, irstlm, mgiza, srilm.

python-xml-activate

activate-python-xml

For running old Python 2 scripts that still use libxml2 or libxslt. When writing new scripts, don't use libxml2 or libxslt, but use lxml instead.

stanford-activate

activate-stanford

The Stanford Parser — A statistical parser.

treex-activate

activate-treex

Treex — Highly Modular NLP Framework.

treex-devel-activate

activate-treex-devel

Like treex-activate, but with many more modules that are not mature enough for distribution on CPAN.

Go

Some packages require special environment variables. You can set these by running go via envgo, for example:

envgo -a2 go build hello.go

Run envgo without arguments to get a list of options.

Don't mix arguments with conflicting software versions.

LaTeX & Co

For all LWP machines, there is a complete distribution of Tex Live 2017 available, as well as some packages specific for the Faculteit der Letteren. This is not available by default. Read this.

18 February 2023
p.c.j.kleiweg