Help reducing huge time overhead when executing system() or unix() commands from Matlab function

1 view (last 30 days)
I have a data processing program that goes through gigabytes of .csv text. The approach I've been taking is to use grep (Mac or Linux) to break up my massive data files into digestible files.
Here's the catch: I have to do it a few hundred times. No biggie, grep is fast, I'll knock this out in no time. A test from bash:
Sweet! 1.6s per file and I'll have this done before I finish my coffee break.
Holy Toledo, that makes a huge difference. My pre-processing is now taking multiple hours per data file. I have tried to look at Matlab environment variables and even dipped my toe into calling through java (checkout jsystem on the exchange!)
Still no luck. I can have my function generate a bash script and then I can run the script manually, I suppose, but I need this to work for other people in the office who are less command line savvy (that's saying something!)
Can anyone shed some light on what's going on or point me towards an improved time?
Thanks a bunch!
% I ran this example on a 3.23 gig text file.
% 16,706,909 lines
% 3,225,789,919 characters
[~, r] = unix('time LC_ALL=C grep -F "My Data Tag String" "/Path/To/Giant/Data/File.csv" > output.csv')
Nick Counts
Nick Counts on 17 Nov 2017
True, the single script could be run from my function. I wasn't sure if the overhead is just on spawning each instance, or if there's something deeper at work that would put me in the same position.
Also, it hurts to not have user feedback - my current implementation has a progress bar so my users believe something is happening!

Sign in to comment.

Accepted Answer

Walter Roberson
Walter Roberson on 17 Nov 2017
When I cd into a directory with a fair number of files, and
!time ls
and compare the timing to executing ls in a shell when cd'd to the same directory, then the !time ls version is showing up as slightly faster.
So the next thing for you to test: are you getting the same grep in each case?

Sign in to comment.

More Answers (0)

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!