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Linux facilitates scientific research in the Atlantic Ocean and Antarctica.
by Craig Donlon and James Crawshaw
A cold and windy September afternoon marks the start of the fifth Atlantic Meridional Transect (AMT) experiment aboard the British Antarctic Survey (BAS) research vessel RRS James Clark Ross. Each year the ship sails from the UK to the Falkland Islands in September en route to service the UK Antarctic research bases. Jim (our UNIX support engineer) is busy fastening down his trusty Toshiba laptop (Tecra 730XCDT with 48MB) in his cabin on board James Clark Ross in preparation for the inevitable bad weather. Ahead of us lie six weeks of precision ocean-atmosphere measurements, near real-time data processing, heated debate, troubleshooting and, hopefully, some scientific discovery. Fortunately, we have both chosen one of the most versatile and reliable operating systems at hand to maximize our output during this experiment--Linux. This article discusses the impact of Linux, which is now routinely used at BAS and during the AMT experiments. (See http://www1.npm.ac.uk/amt/ for more information on the AMT project.)
The RRS James Clark Ross (shown in Figure 1) was launched in 1990 and is one of the world's most complex marine research vessels, incorporating over 400 square meters of scientific laboratory space. It was named after the scientist and polar explorer Admiral Sir James Clark Ross, RN (1800-1862), who in February 1842 reached 78.9 degrees S--a record which remarkably stood well into the 20th century.
Figure 2 shows the track taken by the James Clark Ross during the and AMT-5 cruise superimposed on a monthly composite satellite image of Chlorophyll a derived from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) carried on the SeaStar spacecraft. Different types of phytoplankton have characteristically different concentrations of chlorophyll and are, therefore, different in color. By measuring the color of the ocean with the SeaWiFS instrument, estimates of the amount and general type of phytoplankton in specific regions can be made as shown in Figure 2. An extensive web site provides a wealth of information on the SeaWiFS mission at http://seawifs.gsfc.nasa.gov/SEAWIFS.html.
The ocean-atmosphere measurements taken during the AMT cruises are fundamental for the calibration, validation and interpretation of remotely sensed observations, including sea-surface temperature, wind speed, atmospheric water vapour and ocean colour (which can be related to bio-optical processes)--all of which are vital for ongoing climate research. Figure 3 shows the instrument cluster mounted on the forward mast of the James Clark Ross which measures, among other things, sea-surface temperature (using an infrared radiometer), solar radiation, wind speed and direction, air temperature, radar backscatter (a measure of surface roughness) and humidity. All of these measurements are used to investigate the processes, occurring at the air-sea interface, which in many cases define the signal actually measured by the satellite instruments. (See http://www1.npm.ac.uk/amt/ for more information on the AMT project.)
From a system engineer's point of view, the main requirement of an operating system is that it integrate with the existing computing infrastructure available on (in this case) BAS ships and also at Antarctic bases as well as at headquarters. Since the majority of instruments are logged to Sun SPARC workstations, it makes sense to run an OS which allows NFS mounts to the data areas the workstations create. Many users require the ability to perform data processing locally without having to place extra strain on the data-logging workstations. As most of this is undertaken using shell scripts or compiled C source code, it made sense to run a form of UNIX locally. This enables shell scripts to run with no modifications and the C code to easily recompile. Other user-driven considerations included access to backup hardware, hard-copy output, real-time data displays and access to a common library of software packages.
Upon considering these requirements, our choice was made simple: it had to be Red Hat Linux. For our purpose, Linux provides an extremely versatile operating system with the ability to effortlessly and seamlessly integrate itself efficiently into any existing network system. The immense amount of supported hardware made installation on Jim's laptop and on our desktop machines a painless exercise, and we were delighted with the way that even a default installation gave us exactly what we wanted. It is this kind of hardware support and user-friendly installation interface which caught our eye in the first place when considering various UNIX systems for Intel processors.
After unpacking our brand new PC (Intel DX 120; 32MB RAM) and removing the pre-installed OS (we did ask for Linux), the whole installation took less than an afternoon. We now had a fully working UNIX workstation configured within the James Clark Ross NIS domain, auto-mounting file systems whenever required. Jim went even further with his laptop. Using Caldera Wabi 2.0, he had the ability to run the BAS standard word processor and e-mail packages (which are MS Windows-based). Being able to do all this using free or inexpensive software proves what a professional product Linux is. Gone are the days when Linux was considered a ``toy UNIX'' for hackers--it is now a fully functional UNIX environment which is just as stable (if not more) as the various commercial UNIX systems on the market.
Software support for Linux is already immense, and growing rapidly. Of particular importance was our need to use the RSI Inc. Interactive Data Language (IDL) to develop processing tools and visualize our data in near real time. IDL is a powerful data-visualization tool, and RSI Inc. recognized the power of Linux several years ago by choosing to support it. Using Linux IDL, a complete data-processing suite was developed for two new instruments deployed during the AMT which are still in active use today. We also had a need to effectively communicate and work on collective documents during our time at sea. Most users choose MS Word for this purpose, and using Caldera Wabi 2.0, we were easily able to supply this application. This, coupled with Linux's ability to mount Novell Netware volumes, meant that we truly had the best of both worlds: access to all our UNIX file systems plus the Netware volumes and associated applications. In fact, we found certain applications ran significantly more reliably under Wabi than they did under their native operating system.
For example, the Wabi interface allowed us to manipulate (independent of the ship's logging system) a Campbell Scientific Data Logger located on the forward mast via short-haul modem communications connected to the Linux desktop. Using Campbell's own data logger software under Windows 95, we found that significant drifts in the system date-time stamp of 10min/day were confusing the data logger, which is auto-adjusted to keep the data logger time in sync with the PC time. The only solution was a system restart every 6 hours or so in order for Windows 95 to grab a correct time on startup. We found that under Linux Wabi, these problems no longer existed.
The British Antarctic Survey has written custom software to allow its ships and bases to send and receive electronic mail with the rest of the world using standard Internet e-mail addresses. It was decided to write custom software so that mail could be compressed more efficiently than when using standard protocols, and this in turn reduces costs as it decreases the amount of expensive satellite air time required.
When considering all the requirements, it became clear that a system based around Sendmail running on a UNIX workstation was an almost ideal solution. This solution could be easily implemented on our ships and bases which already had Sun SPARC workstations. As for two smaller bases, it was decided to send PCs running Debian Linux. Again, Linux proved to be an inexpensive but professional solution to a problem. It would have been difficult to justify the expense of Sun SPARCs for the smaller bases, whereas it was relatively inexpensive to install Linux on a couple of older PCs which still performed well. The fact that BAS chose to use Linux to perform Antarctic communications with two of its bases shows its trust in the stability of Linux, as the communications systems are vital to the normal operation of bases.
Without Linux, the computing options for these types of operations are simple: either pay large amounts of money for proprietary systems, or suffer at the hands of a less versatile operating system. Linux changes all that. We are able to function at a professional level at a minimum cost with all of the connectivity, reliability, software choices and versatility that Linux offers. Support for Linux within the British Antarctic Survey and Colorado Center for Astrodynamics Research is increasing. Indeed, it is an officially supported operating system at both institutions and not a toy which the IT hackers play with.
Many more users are requesting Linux for reasons as diverse as wanting to run geophysical processing software on remote islands in the southern Atlantic to simply wanting to run their PC as an intelligent X terminal. Today Linux offers a truly cost-effective off-the-shelf solution for all of our requirements that rivals anything else available in the marketplace. Linux is now being recognized for what it is-a truly outstanding operating system that has grown immensely over the last few years thanks to dedicated individuals and groups working in cooperation with others.
Craig Donlon is a research fellow at the Colorado Center for Astrodynamics Research. In between moving from the mile-high community of Boulder, Craig can be found at the Applied Space Institute, European Joint Research Centre in Ispra, Italy, and hacking satellite and ship data on his Linux machine. He can be contacted at cjdn@colorado.edu.
James Crawshaw works for the British Antarctic Survey as a UNIX support engineer based at their headquarters in Cambridge, although two to three months a year are spent in Antarctica serving on board their research ships and bases providing general computing support. He can be contacted in Cambridge at james.crawshaw@bas.ac.uk.
