[Bioc-devel] Compilation flags, CHECK errors and BiocNeighbors

Kasper Daniel Hansen k@@perd@nielh@n@en @ending from gm@il@com
Mon Dec 17 05:02:53 CET 2018

I would hope we do not distribute binaries compiled with
That seems very wrong.

On Sun, Dec 16, 2018 at 1:56 AM Aaron Lun <
infinite.monkeys.with.keyboards using gmail.com> wrote:

> Sometime between 6-18 November, BiocNeighbors’ BioC-devel builds began
> failing on Windows 64-bit, and have continued to fail since:
> http://bioconductor.org/checkResults/devel/bioc-LATEST/BiocNeighbors/ <
> http://bioconductor.org/checkResults/devel/bioc-LATEST/BiocNeighbors/>
> The most interesting part is the nature of the failures. They are not
> segmentation faults but rather “incorrect” output in the unit tests:
> - BiocNeighbors uses the Annoy algorithm for approximate nearest neighbor
> search, which is provided as a header-only C++ library in the RcppAnnoy
> package.
> - I have compiled the BiocNeighhbors C++ code with an “#include" for these
> libraries to use the Annoy routines. For testing, I compared the output of
> my C++ code to the output of the code in the RcppAnnoy package.
> - It is these tests that are failing (i.e., the output does not match up)
> during CHECK on Windows 64-bit only, despite the fact that the same library
> is being “#include”d in both the BiocNeighbors and RcppAnnoy sources!
> What makes this particularly intriguing is that the differences between
> BiocNeighbors and RcppAnnoy are very minor. Less than 1% of the neighbor
> identities differ, and only for some of the scenarios, so it’s not an
> obvious bug that would be changing the output en masse. Now, the package
> also uses/tests Annoy in BioC-release but builds fine on tokay1:
> http://bioconductor.org/checkResults/release/bioc-LATEST/BiocNeighbors/ <
> http://bioconductor.org/checkResults/release/bioc-LATEST/BiocNeighbors/>
> The major difference between the Bioc-release/devel builds is the
> compilation flags, which have changed from “-O2 -mtune=generic” to “-O3
> -march=native -mtune=native” in tokay2. I am told (thanks Val) that the
> timing of this change is consistent with the start of the BiocNeighbors
> build failures on tokay2. I would guess that RcppAnnoy is also compiled
> with “-O2 -mtune=generic” on the CRAN build systems, introducing
> differences in optimization levels between the BiocNeighbors and RcppAnnoy
> binaries. These could be responsible for the discrepancies in the search
> results.
> I was able to reproduce this on my Unix cluster (gcc 6.5.0) where setting
> “-march=native” with either “-O3” or “-O2” caused a difference in the
> calculations. After much trial and error, I eventually narrowed this down
> to the “-mfma” flag, which seems to change the precision of
> multiply-and-add operations and thus the search results. This occurs even
> when AVX support is turned off; I guess the compiler tries to be smart if
> it detects you are doing some kind of simultaneous multiply and addition,
> which is a pretty common thing to do when computing Euclidean distances.
> In summary: can we not use “-march=native” on tokay2? (Val, I know we
> discussed this, but whatever changes you made to the compilation flags
> don’t seem to have propagated to the build machines.) As the case study
> with BiocNeighbors shows, this leads to inconsistencies between the CRAN
> and BioC-devel binaries for the same code, which unnecessarily complicates
> downstream usage and unit tests. I also wonder how binaries specialized for
> tokay2’s architecture would behave on other CPUs with different instruction
> sets, if they would run at all.
> Cheers,
> Aaron
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