[R-sig-Fedora] Centos / Fedora rpm - issue with openblas

[enzo at smartinsightsfromdata.com]

Martyn

From  a pure R point of view, isn’t a limit to use only the distributed blas?

I understand that Julia, often compared with R, allows dynamic linking and openblas is very much part of the picture.

It would be a good think to provide standard benchmarks, similar to what done here:

http://speed.julialang.org/timeline/#/?exe=3,1,2&base=none&ben=grid&env=1&revs=50&equid=off

Many thanks again for the help in clarifying this issue.

Enzo

On 16 Jun 2014, at 14:38, Martyn Plummer <plummerm at iarc.fr> wrote:

> Enzo,
> 
> I am copying in Tom Callaway from Red Hat (Tom: Enzo wrote to us
> privately on the same issue, but this is on the R-SIG-Fedora list).
> 
> This is a choice made by Red Hat Software, not by the R Development Core
> Team, so there is nothing to change in the R-admin manual. Everything
> depends on how you configure R. In the SPEC file that builds the Fedora
> RPM, R is configured using the options "--with-blas" and
> "--with-lapack", neither of which is the default (and the latter is
> quite strongly discouraged). These options cause R to be linked directly
> to external blas and lapack libraries.
> 
> This has clear advantages for a software distributor like Red Hat. The
> blas used by R is the synchronized with the rest of the system. Updates
> and bug fixes to blas and lapack apply immediately without needing to
> push an update to R.
> 
> Something like the previous behaviour could be put in place by adding
> the option --enable-BLAS-shlib when R is configured. Then libRblas.so
> will be built as before. However, this libRblas will not contain a copy
> of the reference blas that comes with R. Instead it will be just be a
> stub that redirects BLAS calls to the external BLAS library. (NB You
> must also use --enable-R-shlib for this to work, but this is the case
> for the Fedora SRPM so not a problem).
> 
> This option gives you the best of both worlds. However, such a change
> would have to wait until the next major release of R.
> 
> Martyn
> 
> On Mon, 2014-06-16 at 13:05 +0100, enzo at smartinsightsfromdata.com wrote:
>> Martyn
>> 
>> Many thanks for your clear reply.  I’m sure that this has been done
>> for good reasons, but I am disappointed that  I need to organise
>> myself to compile R from sources *just* to link another library: it
>> looks like a functional regression to me, compared to 3.02 (and
>> previous releases).
>> 
>> May I suggest at some point to amend R standard docs to clarify that
>> the option described is no longer viable with Linux / Fedora?
>> 
>> Many thanks again.
>> 
>> Enzo
>> 
>> On 16 Jun 2014, at 11:49, Martyn Plummer <plummerm at iarc.fr> wrote:
>> 
>>> This is a change in the way that the RPM is built. The RPM for R 3.1.0
>>> does not build its own blas and lapack libraries, but links directly to
>>> external blas and lapack provided by Fedora.  This means that you can no
>>> longer swap out libRblas.so by replacing it with a symbolic link to
>>> openblas.
>>> 
>>> If you really want openblas then you should install R from source using
>>> the configure option --with-blas="openblas" (Recall that you need to
>>> install the openblas-devel RPM).
>>> 
>>> Martyn
>>> 
>>> On Mon, 2014-06-16 at 08:53 +0000, enzo at smartinsightsfromdata.com wrote:
>>>> 
>>>> I�ve installed R 3.1 with the latest Fedora rpm
>>>> (R-3.1.0-5.el6.x86_64.rpm) and I run into some issues with openblas.
>>>> 
>>>> I�ve documented this with an open question on stack overflow here:
>>>> http://stackoverflow.com/questions/24158372/openblas-r-3-1-and-fedora-centos-dist
>>>> 
>>>> Basically before 3.1 I had 3.02 and I was able to install and use
>>>> openblas following the instruction from official CRAN documentation,
>>>> symlinking the openblas library instead of the �official� one, with a
>>>> significant improvement in performance.
>>>> 
>>>> Now I do not know how to dynamic-link the openblas libraries anymore,
>>>> as it seems that either the address of the standard libs is changed,
>>>> or the working of the libraries has changed.
>>>> 
>>>> Could somebody be so kind to shed some light?
>>>> 
>>>> Many thanks in advance!
>>>> 
>>>> Enzo Martoglio
>>>>       [[alternative HTML version deleted]]
>>>> 
>>>> 
>>>> _______________________________________________
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>>>> R-SIG-Fedora at r-project.org
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>>>> 
>>> 
>> 
>