Myujth

I want to match strings from a pattern file to look into Source.txt file.

pattern_list.txt has 139k lines

Source.txt more than 5 millions lines

If I use grep like this it tooks 2 seconds to get the output.

grep -F -f pattern_list.txt Source.txt > Output.txt

But if I try with this AWK script it gets stuck and after 10 min I need to stop because nothing happens.

awk 'NR==FNR a[$1]; next 

for (i in a) if ($0 ~ i) print $0

 ' FS=, OFS=, pattern_list.txt Source.txt > Output.txt

pattern_list is like this

21051
99888
95746

and source.txt like this

72300,2,694
21051,1,694
63143,3,694
25223,2,694
99888,8,694
53919,2,694
51059,2,694

What it wrong with my AWK script?

I'm running on Cygwin in Windows.

if you are doing literal match this should be faster than your approach

$ awk -F, 'NR==FNRa[$0]; next $1 in aprint $1,$3,$8,$20' pattern_list source > output

However, I think sort/join will still be faster than grep and awk.

If increasing performance is your goal, you'll need to multithread this (AWK is unlikely faster, perhaps slower?).

If I were you, I'd partition the source file, then search each part:

$ split -l 100000 src.txt src_part
$ ls src_part* | xargs -n1 -P4 fgrep -f pat.txt > matches.txt
$ rm src_part*