Linux in a Scientific Laboratory

The authors tell us how they use Linux daily to fulfill the requirements of their lab.
RS-232 (Serial) Ports

The easiest and quite common situation is for the instrument to have a built-in serial port. We can then talk to it using regular serial communication, just like talking to a modem. Examples of such instruments in our lab include stepper motor controllers, temperature controllers and various precise time measurement apparatus.

The simplicity of a serial-line (RS-232) interface has a cost: a serial connection is rather slow and unsuitable for situations requiring quick response or large amounts of data. It also has the annoying feature of being a very loosely defined standard. There are many variations: DTE vs. DCE configuration; hardware vs. software handshake; various settings of data, stop and parity bits. With so many possibilities, the probability that two randomly selected devices will talk to each other right after plugging in the cable is vanishingly small. The ubiquitous “break-out box” is helpful here: it is a small enclosure connected in series with our serial cable, showing the status of data lines and allowing us to reroute individual signal lines with jumper wires.

Compared to the difficulty of figuring out the proper cabling and communication parameters, the actual programming of serial-port communications is trivial, since Linux already provides good quality serial-port drivers. (Linux, of course, does not rely on serial-port routines in PC BIOS and MS-DOS, since they are so inadequate that a whole cottage industry was created providing so-called “communication libraries”.)

One problem with serial-port communications: RS-232 is inherently a point-to-point link—there is no standard and reliable way of connecting multiple devices to the same serial line. There is a scheme where several devices are daisy-chained, i.e., the computer's transmit line goes to the receive input of device 1, its transmit goes to device 2's receive, and so on, until the transmit line of the last device returns to the computer's receive pin. This requires that all devices cooperate by passing on data not destined for them; it is also not reliable when there can be asynchronous responses from devices in the chain. One of the two standard serial ports usually provided on a PC platform is occupied by the mouse, so we need a multi-port expansion board if we need more than one serial line. Fortunately, Linux has built-in support for several inexpensive multi-port boards. We have used Cyclades and STB boards; they are very easy to configure, and their drivers present themselves to the programmer as a regular serial port.

For initial exploration and testing, we normally use either the Seyon or Kermit terminal emulators. Seyon comes with most Linux distributions, while Kermit has to be obtained from Columbia University's FTP site, as its license terms prohibit third-party distribution. The minicom program is harder to configure, so we do not use it much.

Nick wrote a Tool Command Language (Tcl) serial communication extension for flexible serial-port I/O, with timeouts and terminator characters. Tcl fits well within our environment because it can be conveniently embedded as a scripting tool for heavy-duty FORTRAN and C programs, and it allows for rapid development, while being robust enough to be deployed in a production environment. We will discuss the benefits of scripting in our environment later in the article.


Another hardware interface popular in scientific and engineering communities is the GPIB—General Purpose Interface Bus. It was designed and popularized by Hewlett Packard (hence its original name HP-IB), and later became an official industry standard, IEEE-488. It is a medium-speed parallel bus, capable of over 100Kbps bandwidth. Many scientific instruments support it, and there are relatively inexpensive controllers for PCs, made by Hewlett Packard, National Instruments and others. Fortunately, Linux kernel drivers, written by Claus Schroeter, already exist for most common GPIB cards. (See “GPIB: Cool, It Works With Linux” by Timotej Ecimovic, Linux Journal, March 1997.)

Versabus Module Europe (VME)

For those applications requiring very fast data transfer, the VME bus is a common choice. VME is popular in the telecommunications industry, as well as for industrial and military test and measurement applications. It is typically housed in large (and expensive) backplane crates, containing 24 card slots. Usually one of these slots is occupied by a controller that controls the I/O modules in the remaining slots. Originally, VME was designed to work with Motorola 68k-series CPUs, and so most crate controllers were 68k-based, but recently PowerPC and even Pentium-based controllers seem to be more popular.

It turns out that there are Linux ports to all of these architectures, but again, it was simplest for us to use an x86-based VME controller. In most respects, it is a standard Pentium/PCI miniature motherboard, with the only unusual feature being an on-board PCI-VME bridge chip. We use a controller made by VMIC with a VIC bridge chip set; Nick wrote a driver for it, based on another VME-bridge driver we found on the Net.

All VME I/O is done via memory mapping. The I/O modules are accessed by reading and writing their specific memory locations; the VME bridge chip is needed to translate CPU native bus cycles onto the VME bus. A program simply needs to map the appropriate memory area (using mmap), and it can then execute regular memory load and store operations to access the VME peripherals.

We are currently completing a large data-acquisition system that collects precise timing information from events observed at over 800 detectors. We have designed a front-end processor on a VME card module that handles 32 detectors, and another module which multiplexes data from these front-end modules into the crate controller. As the maximum possible data rate in this application is 300,000 events per second, VME is an appropriate platform.


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