Iam doing a basic pattern search of about 20GB text file. (split into 10 text files each of 2GB). I use egrep (since I have multiple patterns, using | option). It is slow. Before I try to do the same in perl to do benchmarking, I request the wisdom of esteemed monks, if you have any insight into solving similar issues.
Thanks,
dba
Update1
I do use 10 parallel egrep to search 2 GB each. But for a single process it takes 35 minutes.
Non-perl question: Is there a way for me to tell perl or egrep to use more memory than it normally uses. I have a lot of memory on the server.
Update2
The text files are not compressed.
This is my sample perl code to benchmark timings:
use strict;
open(OFILE,">output.txt") or die "Unable to open output file";
open(IFILE,"<input.txt") or die "Unable to open input file";
while ( <IFILE>)
{
print OFILE unless /^CPXX1|^KLXX1|^KMXX1|^MEXX1|^PAXX1|^PMXX1|^SLXX1|
+^SZXX1|^WXXX1|^YZXX1/
}
close(IFILE);
close(OFILE);
Any suggestions to tune this?
Update3
Thank you monks for your great suggestions. I did some benchmarking. Instead of working with 2GB file, I
split the text file to the first 1 million rows (approximately 300MB) and used it to benchmark.
I also modified the regex to
/^(CP|KL|KM|ME|PA|PM|SL|SZ|WX|YZ)XX1/
1. for
cat to just copy, it took 5 seconds
2. for
perl it took 14 seconds
3. for
egrep it took 22 seconds
(Both perl and egrep used the same regex as above. I actually ran the tests twice to avoid any discrepencies)
Observations
The change in regex made a world of difference in both egrep and perl.
perl performed better than egrep to my surprise.
Update4
Thanks again for all your great suggestions. I will try demerphq's solution and update with the results.
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