On 7/18/21 7:04 PM, Andreas Tille wrote: > Hi Nilesh, > > thanks a lot for fixing q2-phylogeny. > > On Sun, Jul 18, 2021 at 01:14:35PM +0000, Nilesh Patra (@nilesh) wrote: >> + - Renamed binaries according to the names available in our distribution >> ... >> + with redirected_stdio(stderr=os.devnull): >> +- obs = raxml(input_sequences, raxml_version='SSE3') >> ++ obs = raxml(input_sequences, raxml_version='Standard') > > This is certainly fixing the issue in q2-phylogeny. However, I'm > wondering how many other software out there is expecting the *-SSE3 name > in raxml.> So may be the more sustainable fix is adding a symlink inside > raxml to feature the name that is expected by other software? > > What do you think?
I have to admit that I'm not fully sure there Full reasoning: Michael made a simde patch for the raxml package (many thanks Michael!) and as you might see here[1] there's 4 binaries: /usr/bin/raxmlHPC /usr/bin/raxmlHPC-PTHREADS /usr/bin/raxmlHPC-PTHREADS-AVX /usr/bin/raxmlHPC-PTHREADS-SSE3 You might notice that there's -PHTREADS-SSE3 available instead. Now, according to the dispatcher script[2] raxml will pick up the most stable available optimization starting from AVX to down baseline Now: I see a problem with the symlink (raxmlHPC-SSE3 -> raxmlHPC) that you suggest: If someone would want to actually use a SSE3 package, and ends up using raxmlHPC-SSE3 they'd instead end up using the raxmlHPC binary instead, there's also a -PTHREADS-SSE3 which causes some confusion If we can add a d/NEWS or something like that, maybe that'd work But even then, a -SSE3 binary would kind of give a false impression of being a compiler binary, which actually it isn't. And it is a sse3 compiled binary in very specific circumstances when there is on AVX support and there is SSE3 support. On the other hand, if we do not do such a symlink, we will end up with maintaining un-necessary patches (like the one above) in many packages. Nice tradeoff? :-) Let me know what you'd think, and other team member's reviews also welcome :-) [1]: https://packages.debian.org/sid/amd64/raxml/filelist [2]: https://sources.debian.org/src/raxml/8.2.12+dfsg-6/debian/bin/raxmlHPC/ Nilesh
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