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jeffdaily / parasail

Pairwise Sequence Alignment Library
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Parasail-2.4 is slower #73

Open nahmedraja opened 5 years ago

nahmedraja commented 5 years ago

Hello,

I was using Parasail version 1.2 previously.

I switched to version 2.4 by replacing "libparasail.a" and "parasail.h" of version 1.2 with that of version 2.4.

I noticed that the "parasail_nw_scan_avx2_256_16()" of version 2.4 is considerably slower than that of version 1.2.

My guess is that this is happening because parasail-2.4 is also recording the traceback information while performing the alignment.

Is it correct?

regards

Nauman

jeffdaily commented 5 years ago

What platform are you running on? linux? osx? and what ISAs does your CPU support? I need more information to guess what's happening.

parasail-2.4 only records the traceback if you request it. parasail_nw_scan_avx2_256_16() will only record the final alignment score, whereas parasail_nw_trace_scan_avx2_256_16() would additionally capture the traceback for use with the traceback-printing routines. That said, the slowdown you are experiencing must be caused by something else.

jeffdaily commented 5 years ago

A lot has changed since version 1.2. It's hard to say what specifically might have caused the slowdown in global alignment performance.