Hi Aaron, The only compilation flags that are different for tokay1 (release) and tokay2 (devel) are C++14 flags. BiocNeighbors is not using C++14 but C++11 so I think the changes we discussed previously actually don't apply to your case.
All compilation flags we use are listed at the top of the build report, e.g., for tokay2: https://www.bioconductor.org/checkResults/devel/bioc-LATEST/tokay2-NodeInfo.html I can look into this further but right now I'm not sure where the '-O3 -march=native -mtune=native' is coming from in the check output for BiocNeighbors. We don't use 'native' on the builders for build/check or for creating binaries. Herve might have more insight on this. Val On 12/15/18 10:56 PM, Aaron Lun 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 > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
