slw287r / izlib

Drop in replacement for zlib.h by isa-l.

izlib

Drop in replacement for zlib.h by isa-l.

Usage

• Install Intel(R) Intelligent Storage Acceleration Library
• Replace "zlib.h" with "izlib.h" and re-compile your file (seqtk for example)

Type	Files	Include	Link flag
zlib	zlib.h	"zlib.h"	-lz
izlib	izlib.h, igzip_lib.h (from isa-l)	"izlib.h"	-lisal

Benchmark

• Data

Reads	Bases	Q20_bases	Q30_bases	GC_bases	File size (toy.fq.gz)
59,581,851	2,979,092,550	2,899,802,990	2,710,969,020	1,188,643,406	2,942,110,279

• Command

time seqtk seq -FE toy.fq.gz > /dev/null

• Results

seqtk version	zlib	izlib	speed up
Runtime	1m18.050s	0m23.648s	3.3×

Caveats

Isa-l's igzip program sometimes complains about big concatenated gzip file. I'm not sure whether the issue resists in the above API. Use at your own risk.

igzip (version 2.30.0) compiled with newer gcc (gcc version 11.2.1 on my end) works without the aforementioned issue.

Credits