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sambamba index 0.6.7 takes 4x longer than 0.6.6 on the same files #345

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carsonhh opened this issue Mar 27, 2018 · 3 comments
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sambamba index 0.6.7 takes 4x longer than 0.6.6 on the same files #345

carsonhh opened this issue Mar 27, 2018 · 3 comments
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@pjotrp
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0.6.8

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@carsonhh
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Simple command --> sambamba index -t 20 any_large_file.bam

0.6.7 rarely uses more than 5 threads under top while 0.6.6 uses all 20 I gave it.

Test on 105GB bam file using 20 threads.
0.6.6 --> 3m35.989s
0.6.7 --> 12m44.751s

I see the same pattern on all files on multiple machines (both AMD and Intel).
@pjotrp
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pjotrp commented Mar 27, 2018

Can you try http://files.genenetwork.org/software/contrib/sambamba-0.6.8-pre1 instead and report the result?

3d6a286947daebb44ac87b4ff2f16c66 sambamba-0.6.8-pre1

@pjotrp pjotrp self-assigned this Mar 27, 2018
@pjotrp pjotrp added this to the 0.6.8 milestone Mar 27, 2018
@carsonhh
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sambamba-0.6.8-pre1 is performing better.

0.6.8-pre1 --> 3m13.100s
0.6.6 --> 3m45.064s

@pjotrp
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pjotrp commented Mar 29, 2018

Thanks for trying. Yes, it is a compilation thing. The new Dlang+LLVM is faster.

@pjotrp pjotrp closed this as completed Mar 29, 2018
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