On Jan 10, 2018 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? What are you barking about? I don't understand what you are trying to accomplish. 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 [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel