Moving allocations

[RaviGaddipati]

Was there a reason to do pvHStore, pvHLoad, pvHmax, and pvE memory allocations in the gssw_sw_sse2 functions? Moving the allocations up to graph_fill and reusing the same allocations for each node gave a huge performance boost.

[ekg]

Do you have a patch? It would require a recycler no? The size of the
allocated matrix will vary.
On Nov 26, 2015 10:00 PM, "Ravi Gaddipati" [email protected] wrote:

Was there a reason to do pvHStore, pvHLoad, pvHmax, and pvE memory
allocations in the gssw_sw_sse2 functions? Moving the allocations up to
graph_fill and reusing the same allocations for each node gave a huge
performance boost.

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#3.

[RaviGaddipati]

No patch for this yet.
The size is dependent on segLen (i.e. readLen), and since that's the same for all nodes the allocation size is the same. Not sure what you mean by recycler.
I've been still getting accurate results with a modified version of gssw that does this (https://github.com/gaddra/gssw/tree/positional).

[ekg]

There is also pH, if I remember correctly. The entire score matrix. This
allocation could be recycled. The others yes absolutely. They should
definitely be refused directly!!!
On Nov 26, 2015 10:22 PM, "Ravi Gaddipati" [email protected] wrote:

No patch for this yet.
The size is dependent on segLen (i.e. readLen), and since that's the same
for all nodes the allocation size is the same.
I've been still getting accurate results with a modified version of gssw
that does this (https://github.com/gaddra/gssw/tree/positional).

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#3 (comment).

[RaviGaddipati]

Ah yes, I had no use for traceback so I had removed mH. I'll make a pull request sometime soon.