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 />>//>//
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