Poseidon Linux 3.2

Custom Linux distributions that tailor the operating system to the needs of a specific set of users are one of the joys of open source development. Classrooms, audio production and recording studios, and high-performance computing (HPC) clusters — all have individual requirements that diverge from the standard server or office-oriented desktop distribution. Poseidon Linux is a perfect example, a specialty distribution created for scientists. The core maintainers are oceanographers at Brazil's Universidade Federal do Rio Grande, but Poseidon has grown in popularity enough that releases are now made to support English, German, and Spanish in addition to Portuguese.

Poseidon Linux dates back to 2004, and was originally built on top of the Kurumin live CD distribution, a now-defunct Portuguese version of Debian running KDE. With 2008's 3.0 release, however, Poseidon migrated to Ubuntu as its base distribution and GNOME as its desktop environment. The project's site describes the latest version as 3.2, released in May 2010, but so far 3.2 only appears to be available on one of the mirror sites in Germany, although it is not a German localization. In addition, only the 32-bit version of 3.2 has been made publicly available (previous releases have always included both 32-bit and 64-bit builds).

The ISO image requires DVD media, weighing in at 2.4GB, and is provided as a direct HTTP download only. Poseidon can be run as a live DVD, or installed on the hard drive. Other than the cosmetic changes (which are a nice touch), Poseidon deviates from its Ubuntu parent base by stripping down the installed set of general-purpose applications, and packaging in a long list of scientific applications, libraries, and development tools.

Some of these applications are available in upstream Ubuntu and Debian, such as the GNU Octave computation system, GRASS geographic information system (GIS), or IBM's data visualization package OpenDX. Others are not, such as the Terraview and SPRING GIS programs. The support tools include Python and C libraries for numerical computation, the G77 FORTRAN compiler, and modules for using GIS data with PostgreSQL. It is also nice that the distribution includes a wide variety of R statistical packages that users would otherwise have to seek out and download individually.

The bulk of the specialty packages involve either mapping and GIS, or statistics and data modeling, which reflects the creators' field of study. There are physics, astronomy, math, chemistry, and biology packages in the default install, too, however. TeX is represented by the GUI editors LyX and Kile, and by the BibTeX bibliographic editor JabRef. The 3-D modeler Blender is included as well, and its placement as a computer-aided design (CAD) tool points to the lack of a high-quality open source 3-D CAD program.

I tested the 32-bit 3.2 release, from the mirror site mentioned above, in live DVD mode, with only a few hiccups along the way (not counting the lack of a Bittorrent release for the ISO image, which is its own, practical, issue). A few of the packages were (quite puzzlingly) not as up-to-date as upstream Ubuntu repositories, notably the R-Commander GUI interface to R, which reported a version conflict with the installed R package. In addition, only the German keyboard layout was functional, even after I added the appropriate US keyboard layout. These are minor difficulties that may get ironed out as the work on 3.2 continues — hopefully 64-bit ISOs and other updates are still to come.

Usage, applications, and updates

Poseidon aims for the full-featured desktop Linux model, not a stripped-down environment with a minimalist window manager. As such, it feels exactly like a standard GNOME or Ubuntu desktop, and the traditional packages that Poseidon omits from the default installation can be installed through Apt as usual. The project provides package updates to the scientific applications through its own repository. Full releases of Poseidon Linux have been irregular; 3.0 and 3.1 both occurred within 2008, but it was more than a year between 3.1 and 3.2. Judging by the change log, however, this appears to have more to do with updates to the core scientific software applications than with any effort to align with Ubuntu's six-month release cycle.

Several of the add-on scientific packages are not likely to gain official Debian or Ubuntu maintainers thanks to their niche userbase (or, in some cases, outdated toolkit dependencies). MB-System, for example, is a sonar processing and display tool clearly of importance to oceanographers, and perhaps to others who live or work by the ocean, but requires such domain-specific knowledge that it is unlikely to get packaged by a typical distribution. The tide predictor XTide, on the other hand, is still packaged for Ubuntu, but is one of the few such applications using the X Athena Widgets toolkit (Xaw). Most other Xaw programs (xclock, xload, xbiff, etc.) have been supplanted by GTK+ and Qt replacements, but there is no alternative for XTide.

Many of the applications are produced by small teams (at least, compared to the organizations that work on Firefox or other widely-deployed programs) scratching their own research itch, often in an academic or institutional setting. That makes them afterthoughts to modern distributions focusing on the desktop, which in turn can mean that they are harder to install and keep up-to-date. In those cases, using a targeted distribution like Poseidon will undoubtedly save time and frustration, particularly if one has to maintain a laboratory's worth of computers.

The same is also true of the computational programming libraries, R packages, and other add-ons. Poseidon ships with Emacs support for Prolog and GRI, two languages with small user bases outside of their particular fields. While an individual user might have no problem checking for updates and installing the Lisp packages by hand, having to keep an entire team up-to-date simultaneously is more difficult.

There are at least a few other "scientific"-targeted Linux distributions under active development. Fermilab and CERN both originally maintained their own distributions that were source-compatible with Red Hat Enterprise Linux (RHEL), but combined forces to work on Scientific Linux (SL). Like Poseidon, SL includes scientific applications and libraries, but SL also incorporates several important system-level tweaks, such as including support for the distributed Andrew File System (AFS). Quantian is a Knoppix-based live DVD distribution that focuses exclusively on numerical and quantitative analysis, such as the ability to quickly set up an OpenMosix cluster of nodes running Quantian.

Setting sail

If there is one area in which Poseidon falls short, it is the lack of community tools. The Poseidon site does not maintain a mailing list or discussion forum, although searching on the web indicates that it is used at several other institutions that do oceanographic research, and that it has a following among GIS and mapping enthusiasts as well. The project site ostensibly has an RSS news feed, but it is a full release cycle out of date. There is one contact email address, and a list of requested packages to be considered for future versions, but otherwise development is a black box.

Perhaps this is attributable to Poseidon's creators' full-time jobs in oceanographic research; that is an acceptable excuse, but it would still be nice to see the team open up some form of public discussion outlet, if not a full issue tracker and other large-distribution paraphernalia. They are doing good work in bringing useful applications and libraries to scientific users in a turn-key distribution — reaching out to the community is simply the next step, for the feedback, additional volunteer-hours, and increased exposure overall.

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