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

[Obenchain, Valerie]

The devel build report hasn't posted yet but I took a look at the new 
compiler flag output Herve implemented. The results show tokay2 is 
indeed using

CXX11FLAGS: -O3 -march=native -mtune=native

This is inconsistent with what we have in the R/etc/<arch>/Makeconf for 
both architectures on both tokay1 and tokay2. The Makeconf looks like this:

CXX11 = $(BINPREF)g++ $(M_ARCH)
CXX11FLAGS = -O2 -Wall $(DEBUGFLAG) -mtune=generic
CXX11PICFLAGS =
CXX11STD = -std=gnu++11

I don't know why the Makeconf is not being respected on tokay2. I can 
confirm the inconsistency in an R session -

tokay2:

PS C:\Users\biocbuild\bbs-3.9-bioc\R> ./bin/R CMD config CXX11FLAGS
-O3 -march=native -mtune=native

tokay1:

PS C:\Users\biocbuild\bbs-3.8-bioc\R> ./bin/R CMD config CXX11FLAGS
-O2 -Wall -mtune=generic

I'll work with Herve to resolve this.

Val



On 12/17/18 5:05 PM, Aaron Lun wrote:
> Thanks Val. I don�t think it�s a BiocNeighbors thing, as it doesn�t try 
> to customize the compilation flags or have its own Makevars. Moreover, 
> the �-O3 -mtune=native -mtune=generic� flags seem to show up on all of 
> my packages containing C++11 code. Some cursory checks of other packages 
> suggest that the correct flags (�-O2 -mtune=generic�) are used for C++98 
> code.
> 
> -A
> 
>> On 17 Dec 2018, at 17:47, Obenchain, Valerie <Valerie.Obenchain using RoswellPark.org> wrote:
>> 
>> 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 
> <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/> 
> <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/> <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]]
>>> 
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>> 
>> 
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