From istazahn at gmail.com  Thu Jan 11 13:56:06 2018
From: istazahn at gmail.com (Ista Zahn)
Date: Thu, 11 Jan 2018 07:56:06 -0500
Subject: [Rd] OpenBLAS in everyday R?
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On Jan 10, 2018 8:24 PM, "Benjamin Tyner" <btyner at 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 <btyner at 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 <btyner at 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>>
>>>>>> />/escribi?: />//>>/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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>>>>>
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>>>>
>>>
>>
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[Rd] OpenBLAS in everyday R?
Ista Zahn