AudiLab Software

Modelling software developed here

Debugging is twice as hard as writing the code in the first place. Therefore, if you write the code as cleverly as possible, you are, by definition, not smart enough to debug it.
– Brian W. Kernighan

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

Finite-element software (developed elsewhere)

We are currently using FEBio, Code_Aster, SAP IV, 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 developed elsewhere

We use Gmsh for generating tetrahedral meshes from surface meshes. Gmsh can also be used with the finite-element solver GetDP through ONELAB, although we have not tried it.

We use, have played with or have considered playing with the following, among many others: 3D Slicer, VisIt, ParaView, CIBC software (Seg3D, ImageVis3D, map3D, etc., from Utah).

Other software developed here

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

Libraries developed here include:

Other software used here

Libraries from elsewhere that are used here include:

I often use Emacs.

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

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

Guillimin

Guillimin is McGill's High Performance Computing facility. We use it for intensive computation.

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) that hosts both directories for individuals and shared lab directories, all of which are backed up regularly.
Each user has a quota of 5 GB in their personal Probe directory in biomedusers/.
AudiLab also has a space allocation in probeShare/Biomed/AUDILAB/.

To access Probe from a Linux computer (assuming that the package cifs-tools is installed), 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

The following alternative procedure for accessing Probe from Linux requires an Administrator account and uses sudo.

You can download smbmount.pl, a Perl script that issues the appropriate smbmount commands to connect to Probe. Save the script somewhere and make it executable. For example, save it in ~/bin/ and then in a terminal window do

cd ~/bin/ chmod +x smbmount.pl

Thereafter, each time you login you can give the command ~/bin/smbmount.pl to establish the connections to Probe. (Or the script can be dragged to the GNOME launch panel.) You will be asked for your sudo password and then for your Mcgill password three times. The contents of the biomedusers, probeShare and BMEdisk directories will now appear in probe, probeShare and probeBMEdisk, respectively, in your home directory. The script relies on a hard-wired list of Linux usernames and corresponding McGill short usernames. If you get the message Unrecognized username, ask to have your usernames added to the list.

Printing

M$ Windows

See departmental instructions.

Linux

See instructions for setting up access to McGill's uPrint service. Their instructions say they apply to Ubuntu 12.10 and up; they apply to Debian 8 (‘jessie’, now testing, expected to become stable early in 2015).

Make sure CUPS is installed. (Under Debian GNU/Linux, use aptitude or some other method to install cups and its required packages.) In order to use the Print to file feature within applications, you also need the cups-pdf package.

The command lpstat -p can be used to see what printers are available. To look at the job queues, etc., in a Web browser go to http://localhost:631/.

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

Printing from the command line

I haven't figured out how to print from within applications because of the need to specify a username for uPrint. Instead, I produce PDF files and print them from the command line.

Example:
lp -U username -d printername -o sides=two-sided-long-edge -n 3 -o number-up=2 -P pagelist filename

username is your McGill short username, or the short username associated with a McGill uPrint card.
printername should be mcgill_mono or (only if necessary) mcgill_color.
filename is the name of the file to be printed (usually a PDF file).
In the example there are several optional specifiers:

I have a script lp.tcl which prompts for various options and submits the appropriate lp command.

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

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.


AudiLab home page
R. Funnell
Last modified: 2017-02-02 18:13:05