multithreading - Boosting the grep search using GNU parallel

Question

I am using the following grep script to output all the unmatched patterns:

grep -oFf patterns.txt large_strings.txt | grep -vFf - patterns.txt > unmatched_patterns.txt

patterns file contains the following 12-characters long substrings (some instances are shown below):

6b6c665d4f44
8b715a5d5f5f
26364d605243
717c8a919aa2

large_strings file contains extremely long strings of around 20-100 million characters longs (a small piece of the string is shown below):

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

How can we speed up the above script (gnu parallel, xargs, fgrep, etc.)? I tried using --pipepart and --block but it doesn't allow you to pipe two grep commands.

Btw these are all hexadecimal strings and patterns.

The working code below is a little faster than the traditional grep:

rg -oFf patterns.txt large_strings.txt | rg -vFf - patterns.txt > unmatched_patterns.txt

grep took an hour to finish the process of pattern matching while it took ripgrep around 45 mins.

question from:https://stackoverflow.com/questions/65878582/boosting-the-grep-search-using-gnu-parallel

Answer 1

If you do not need to use grep try:

build_k_mers() {
    k="$1"
    slot="$2"
    perl -ne 'for $n (0..(length $_)-'"$k"') {                                                                                               
       $prefix = substr($_,$n,2);                                                                                                            
       $fh{$prefix} or open $fh{$prefix}, ">>", "tmp/kmer.$prefix.'"$slot"'";                                                                
       $fh = $fh{$prefix};                                                                                                                   
       print $fh substr($_,$n,'"$k"'),"
"                                                                                                   
    }'
}
export -f build_k_mers

rm -rf tmp
mkdir tmp
export LC_ALL=C
# search strings must be sorted for comm                                                                                                     
parsort patterns.txt | awk '{print >>"tmp/patterns."substr($1,1,2)}' &

# make shorter lines: Insert 
(last 12 char before 
) for every 32k                                                                         
# This makes it easier for --pipepart to find a newline                                                                                      
# It will not change the kmers generated                                                                                                     
perl -pe 's/(.{32000})(.{12})/$1$2
$2/g' large_strings.txt > large_lines.txt
# Build 12-mers                                                                                                                              
parallel --pipepart --block -1 -a large_lines.txt 'build_k_mers 12 {%}'
# -j10 and 20s may be adjusted depending on hardware
parallel -j10 --delay 20s 'parsort -u tmp/kmer.{}.* > tmp/kmer.{}; rm tmp/kmer.{}.*' ::: `perl -e 'map { printf "%02x ",$_ } 0..255'`
wait
parallel comm -23 {} {=s/patterns./kmer./=} ::: tmp/patterns.??

I have tested this on patterns.txt: 9GBytes/725937231 lines, large_strings.txt: 19GBytes/184 lines and on my 64-core machine it completes in 3 hours.