AudiLab Software

Software developed here

A number of applications for 3-D modelling have been and are being developed here (including Fie, Tr3, Thrup'ny and others) and are available as executable binaries.

Applications have also been developed for handling bibliographic references and for miscellaneous tasks.

Libraries developed here include:

• Gut: General utilities, including the sublibraries
  • Txt: (text-string handling),
  • Font: (Far* font definitions used by mvch* routines in Gut), and
  • Sysdep: (system-dependent code for Compaq Unix, GNU/Linux, MS Windows, VMS and MS-DOS).
  Included are the Angst routines for device-independent alphanumeric and graphics output to a variety of devices.
• Dip: Device-independent plotting - this is an enhancement of the old Tektronix Plot-10 library, with the addition of color, polygons, etc. See instructions for installation and use of software which uses Dip.
• Put: Plotting utilities
• Mdl: Finite-element modelling routines to read and write SAP input (.sap) & output (.res) files

Finite-element software

We are currently using SAP IV, Code_Aster, FEBio, CalculiX and an old version of the commercial package COMSOL. We have also investigated Cast3m and Modulef, and used to use the commercial packages I-DEAS. I have compiled some sketchy information about available f-e software.

Other software used here

Libraries from elsewhere that are used here include:

• IEEE Signal-Processing library (~funnell/sig/)
• Scientific Subroutine Package (~funnell/ssp)
• Linear-algebra package from Argonne National Laboratory (~funnell/netlib/linpack/)

I often use GNU emacs:

• instructions for installation and use under MS Windows
• my customisations including key bindings patterned after the BBN Pen editor

Until ~2000 I used mostly VMS and until 2008 we used DEC/Compaq Unix. Now we use Debian GNU/Linux and (alas) M$ Windows 2000 & XP.

I've collected some personal tips for MS Windows and for Unix/Linux.

Departmental environment

Workstations within BME should use fixed IP addresses that are assigned. The netmask should be 255.255.255.0 and the gateway address should be 132.206.111.1. The DNS servers should be set to 132.206.85.18, 132.206.85.19 and 132.206.85.20, and campus.mcgill.ca should be specified as the domain. See Network setup for how to do this under Debian/GNU Linux.

Departmental computing resources include printers; a shared computer with a scanner; and access to a Windows server (Probe) which hosts both individual directories (biomedusers) and shared lab directories (probeShare), all of which are backed up regularly.

Each user has a quota of 5 GB in their personal Probe directory.
AudiLab has a quota of 20 GB in probeShare/Biomed/Audilab/ and 100 GB in probeShare/BMEdisk/AudiLab/.

To access Probe from a Linux computer, in the Nautilus file-system browser do File ▶ Connect to Server. In the dialogue box select Windows share as the Service type and fill in the fields as follows:

Server	probe.campus.mcgill.ca
Folder	biomedusers or probeshare
User Name	your McGill DAS (Short) username
Domain Name	campus

Printing

M$ Windows

See departmental instructions.

Linux

Make sure CUPS is installed. (Under Debian GNU/Linux, use aptitude to install cupsys and its required packages.)

To add a new printer, in a Web browser go to http://localhost:631/admin and select Add Printer.

I've had problems printing from some applications to one or the other printer and have not attempted to resolve the problems. Printing from OpenOffice.org applications to the Kyocera printer should work.

If problems arise when printing Unix-style plain-text files because the carriage returns are missing, they can be added using unix2dos.

Kyocera black-and-white printer

The required PPD file, Kyocera_Mita_FS-9520DN_en.ppd, can be downloaded from www.linuxprinting.org. The device URI to use is lpd://132.206.111.191. Specify the following settings:

• Options Installed
  • Paper Feeder: Cassette3,4
• General
  • Media Size: Letter
  • Media Source: Cassette 3
  • Optional Disk: Hard Disk
  • Memory: 320MB(256MB Upgrade)

Dell colour printer

Use CUPS's HP Color LaserJet Series PCL 6 for the make and model. The device URI to use is lpd://132.206.111.192. Specify the following settings:

• General
  • Output Resolution: 600DPI

Organization of AudiLab software

The source files for a library are generally in the same directory as the object-library file, and are listed in a .nam file. The .nam file may include pointers to other directories for some of the modules.

For libraries developed here, there are two naming conventions: a source file contains either

• a single subprogramme with the same name, e.g., decodf.for contains the subroutine decodf; or
• a collection of subprogrammes, each with a name starting with the file name, e.g., days.for includes days_from_s_auto, days_from_s, days_from_i, etc.

Most of my software is written in Fortran 77/90 with some C. For Fortran code, the subprogrammes are usually subroutines rather than functions. For C, of course, there are only functions.