I’m not really familiar with conda, but if they’re being packaged together then an omp build might be more appropriate.
Perhaps another point for Juan’s list: whether OpenBLAS is the right choice to pair with. The library itself hasn’t produced optimized kernels for any of the Intel *Lake chips yet; might be worth considering its near- and long-term future (vs something else). Keith > On Jan 10, 2018, at 8:24 PM, Benjamin Tyner <bty...@gmail.com> wrote: > > Thanks Keith. We checked, and indeed libopenblas is not linked against libomp > nor libgomp. We suspect this is because we used conda to install R and > OpenBLAS. So I guess we should be barking up the conda tree instead? > > By the way, I also noticed on my home machine (Ubuntu), > /usr/lib/libopenblas.so.0 is also not linked against those, for what that's > worth. > > Regards, > Ben > > On 01/10/2018 12:04 AM, Keith O'Hara wrote: >> Check if libopenblas is linked against libomp or libgomp. >> >> I’d be curious to see any errors that arise when an OpenMP version of >> OpenBLAS is linked with R. >> >> Keith >> >> >>> On Jan 9, 2018, at 11:01 PM, Benjamin Tyner <bty...@gmail.com> wrote: >>> >>> I didn't do the compile; is there a way to check whether that was used? If >>> not, I'll inquire with our sysadmin and report back. >>> >>> In any case, my suggestion was motivated by the fact that some parts of R >>> use OpenMP while others do not, in the hope that the former could have >>> their OpenBLAS omelet without breaking the OpenMP eggs, so to speak. >>> >>> >>> On 01/09/2018 06:41 PM, Keith O'Hara wrote: >>>> Do those issues still arise when OpenBLAS is compiled with USE_OPENMP=1 ? >>>> >>>> Keith >>>> >>>>> On Jan 9, 2018, at 6:03 PM, Benjamin Tyner <bty...@gmail.com> wrote: >>>>> >>>>> Please pardon my ignorance, but doesn't OpenBLAS still not always play >>>>> nicely with multi-threaded OpenMP? (for example, don't race conditions >>>>> sometimes crop up)? If so, it might be nice to have the ability to >>>>> temporarily disable multi-threaded OpenMP (effectively: >>>>> omp_set_num_threads(1)) for the duration of operations using OpenBLAS. >>>>> >>>>> Regards >>>>> Ben >>>>> >>>>>> Julia using OpenBLAS is *very* reassuring. >>>>>> >>>>>> I agree that having it included as an options(...) feature should be OK. >>>>>> >>>>>> On Sun, Dec 17, 2017, 3:22 PM Juan Telleria <jtelleriar at gmail.com >>>>>> <https://stat.ethz.ch/mailman/listinfo/r-devel>> wrote: >>>>>> >>>>>>> /Julia Programming Language uses also OpenBlas, and it is actively >>>>>>> />/maintained with bugs being fixed as I have checked it out: >>>>>>> />//>/http://www.openblas.net/Changelog.txt />//>/So I still see it ok >>>>>>> to be included as an options(...) feature (by default />/off, just for >>>>>>> safety), over other Blas libraries. />//>/R could not use Intel MKL for >>>>>>> legal reasons (I think), because as long />/that R ships with GPL >>>>>>> libraries, shipping R by default with Non-GPL is />/illegal. >>>>>>> />//>/Cheers, />/Juan />//>/El 17/12/2017 2:50 a. m., "Avraham Adler" >>>>>>> <avraham.adler at gmail.com >>>>>>> <https://stat.ethz.ch/mailman/listinfo/r-devel>> />/escribió: />//>>/On >>>>>>> Sat, Dec 16, 2017 at 7:41 PM, Kenny Bell <kmbell56 at gmail.com >>>>>>> <https://stat.ethz.ch/mailman/listinfo/r-devel>> wrote: />>/> It seems >>>>>>> like many of the multi-threaded BLASes have some sort of />>/> >>>>>>> fundamental problem preventing use in the way Juan suggests: />>/> >>>>>>> />>/> - Dirk's vignette states that ATLAS "fixes the number of cores >>>>>>> used at />>/> compile-time and cannot vary this setting at run-time", >>>>>>> so any />>/> user-friendly implementation for R would have to compile >>>>>>> ATLAS for 1-16 />>/> threads to allow the user to switch at run-time. >>>>>>> This might dramatically />>/> affect install times. />>/> />>/> - MKL >>>>>>> seems like it's been outright rejected in the past based on not />>/> >>>>>>> being "free-enough". />>/> />>/> - OpenBLAS causes crashes. />>/> />>/> >>>>>>> Has anyone tried ExBLAS for use with R? />>/> />>/> On Sun, Dec 17, >>>>>>> 2017 at 1:03 PM, Peter Langfelder < />>/> peter.langfelder at gmail.com >>>>>>> <https://stat.ethz.ch/mailman/listinfo/r-devel>> wrote: />>/> />>/>> I >>>>>>> would be very cautious about OpenBLAS in particular... from time to >>>>>>> />>/>> time I get complains from users that compiled code calculations >>>>>>> in my />>/>> WGCNA package crash or produce wrong answers with large >>>>>>> data, and they />>/>> all come from OpenBLAS users. I am yet to >>>>>>> reproduce any of their />>/>> crashes when using MKL and ATLAS BLAS >>>>>>> implementations. />>/>> />>/>> Just my 2 cents... />>/>> />>/>> Peter >>>>>>> />>//>>/I've been building R on Windows 64 bit with OpenBLAS for years >>>>>>> and my />>/builds pass check-devel. For a while in the past it failed >>>>>>> one check />>/as the tolerance was 5e-5 and with my build of OpenBLAS >>>>>>> the error was />>/5.4e-5 or 5.7e-5, but that was changed around R 3.3, >>>>>>> if I recall />>/correctly. I provide descriptions here [1], but I >>>>>>> haven't gone so far />>/as to post compiled Rblas.dlls just yet. My >>>>>>> personal build sets 4 />>/threads when compiling OpenBLAS itself as I'm >>>>>>> currently on a quad-core />>/SandyBridge. In tests I ran a few years >>>>>>> ago, both single and multi />>/threaded BLAS compile and then can be >>>>>>> compiled into R with no issues />>/(on my platforms, at least). Most >>>>>>> matrix operations performed better />>/with multi-threaded except for >>>>>>> R's eigenvalue decomposition, to the />>/nest of my recollection. >>>>>>> />>//>>/Avi />>//>>/[1] >>>>>>> https://www.avrahamadler.com/r-tips/build-openblas-for-windows-r64/ >>>>>>> />>//>>/______________________________________________ />>/R-devel at >>>>>>> r-project.org <https://stat.ethz.ch/mailman/listinfo/r-devel> mailing >>>>>>> list />>/https://stat.ethz.ch/mailman/listinfo/r-devel />>//>// >>>>>> [[alternative HTML version deleted]] >>>>> ______________________________________________ >>>>> R-devel@r-project.org mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/r-devel >>> > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
