A collection of computer systems and programming tips that you may find useful.
Brought to you by Craic Computing LLC, a bioinformatics consulting company.

Friday, January 27, 2012

Getting absolute paths with the Unix ls command

The standard Unix command ls lists filenames and directories in the specified directory. The default behaviour is to list just the filenames as including the full pathname would clutter the screen.

But sometimes you want the absolute paths. I need this all the time if I want to create a file containing a list fo filenames. The obvious command to get all the YAML files, for example, is:
$ ls -1 *yml

In order to get the full pathnames you need to use this:
ls -1 -d $PWD/*yml

Wednesday, January 25, 2012

Wolfram CDF Player and Chrome Browser

Wolfram Computable Document Format (CDF) is a way to embed interactive documents into web pages, in particular those that perform calculations in response to a user changing the parameters. For example you can create graphs of functions that will change as the function is modified. It is an extension of the Wolfram Mathematica software.

It looks really promising for some applications and you should check out their demonstrations - some impressive, some not so much.

You 'play' CDF files using a browser plugin - just like Flash - and these are available for all the current browsers.

I'm running it on Google Chrome on Mac OS X on a fairly recent laptop. It performs OK depending on the specific application and the amount of data it is asked to push around. But when you close that window or move to another page the CDF player process continues to run. In my case that was taking 5% of my cpu and 66MB of memory and it continued to do so for perhaps 10 minutes after the page was closed.

This sort of drain on your cpu, due to the plugin, is fairly common - just look at everything going on in Activity Monitor when you are browsing an 'active' web page with ads, etc.

In Chrome you can go to Window -> Task Manager, select a process and End it - but that didn't appear to do anything in my case.

CDF looks very interesting but if it requires too many resources, and then fails to release them properly, then it is not likely to be broadly adopted. It is something to keep an eye on, for sure.

Wednesday, January 4, 2012

Disabling Spotlight (mds) on Mac OS X (Snow Leopard)

I run a lot of command line scripts on my laptop - some of which can run for hours. I want to continue using the machine for reading mail, etc., but I don't want any other intensive task sucking up the cpu cycles. So I shut down iTunes, don't watch any videos, etc.

But sometimes I see some other process taking all my cycles. The odds are that it is either something to do with Flash or it is a process called mds.

mds is the indexing software that powers Spotlight - the built in Mac search facility.

I suspect that when I'm generating gigabytes of data and hundreds of files in one of my compute jobs, mds is responding by trying to index them at the same time.

I don't use spotlight at all, so let's turn it off and see if that helps.

This turns it off:
$ sudo mdutil -a -i off 

This turns it back on:
$ sudo mdutil -a -i on

Turning it back on will presumably trigger a big mds run as it plays catch up, so run this command only when you can afford the cycles.

Archive of Tips