From luke-tierney at uiowa.edu  Mon Aug 21 16:07:02 2017
From: luke-tierney at uiowa.edu (luke-tierney at uiowa.edu)
Date: Mon, 21 Aug 2017 09:07:02 -0500 (CDT)
Subject: [Rd] Control multi-threading in standard matrix product
In-Reply-To: <50f32a42-786d-e7c7-71e5-ed0efa975f0a@gmail.com>
References: <825dace5-8fca-3660-b8b2-fd9f115b29ac@inria.fr>
 <50f32a42-786d-e7c7-71e5-ed0efa975f0a@gmail.com>
Message-ID: <alpine.DEB.2.20.1708210905360.2616@luke-Latitude>

Many, though not all, threaded BLAS honor the OpenMP environment
variables; you might see whether setting OMP_THEAD_LIMIT or
OMP_NUM_THREADS does what you want.

Best,

luke

On Mon, 21 Aug 2017, Tomas Kalibera wrote:

> Hi Ghislain,
>
> I think you might be comparing two versions of R with different BLAS 
> implementations, one that is single threaded (is your 3.3.2 used with 
> reference blas?) and one that is multi threaded (3.4.1 with openblas). Could 
> you check with "perf"? E.g. run your benchmark with "perf record" in both 
> cases and you should see the names of the hot BLAS functions and this should 
> reveal the BLAS implementation (look for dgemm).
>
> In Ubuntu, if you install R from the package system, whenever you run it it 
> will use the BLAS currently installed via the package system. However if you 
> build R from source on Ubuntu, by default, it will use the reference BLAS 
> which is distributed with R. Section "Linear algebra" of "R Installation and 
> Administration" has details on how to build R with different BLAS/LAPACK 
> implementations.
>
> Sadly there is no standard way to specify the number of BLAS worker threads. 
> RhpcBLASctl has specific code for several existing implementations, but R 
> itself does not attempt to control BLAS multi threading in any way. It is 
> expected the user/system administrator will configure their BLAS 
> implementation of choice to use the number of threads they need. A similar 
> problem exists in other internally multi-threaded third-party libraries, used 
> by packages - R cannot control how many threads they run.
>
> Best
> Tomas
>
> On 08/21/2017 02:55 PM, Ghislain Durif wrote:
>> Dear R Core Team,
>> 
>> I wish to report what can be viewed as a bug or at least a strange
>> behavior in R-3.4.1. I ask my question here (as recommended on
>> https://www.r-project.org/bugs.html) since I am not member of the R's
>> Bugzilla.
>> 
>> When running 'R --vanilla' from the command line, the standard matrix
>> product is by default based on BLAS and multi-threaded on all cores
>> available on the machine, c.f. following examples:
>> 
>> n=10000
>> p=1000
>> q=5000
>> A = matrix(runif(n*p),nrow=n, ncol=p)
>> B = matrix(runif(p*q),nrow=p, ncol=q)
>> C = A %*% B # multi-threaded matrix product
>> 
>> 
>> However, the default behavior to use all available cores can be an
>> issue, especially on shared computing resources or when the matrix
>> product is used in parallelized section of codes (for instance with
>> 'mclapply' from the 'parallel' package). For instance, the default
>> matrix product is single-threaded in R-3.3.2 (I ran a test on my
>> machine), this new features will deeply affect the behavior of existing
>> R packages that use other multi-threading solutions.
>> 
>> Thanks to this stackoverflow question
>> (https://stackoverflow.com/questions/45794290/in-r-how-to-control-multi-threading-in-blas-parallel-matrix-product),
>> I now know that it is possible to control the number of BLAS threads
>> thanks to the package 'RhpcBLASctl'. However, being able to control the
>> number of threads should maybe not require to use an additional package.
>> 
>> In addition, the doc 'matmult' does not mention this point, it points to
>> the 'options' doc page and especially the 'matprod' section, in which
>> the multi-threading is not discussed.
>> 
>> 
>> Here is the results of the 'sessionInfo()' function on my machine for
>> R-3.4.1:
>> R version 3.4.1 (2017-06-30)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 16.04.3 LTS
>> 
>> Matrix products: default
>> BLAS: /usr/lib/openblas-base/libblas.so.3
>> LAPACK: /usr/lib/libopenblasp-r0.2.18.so
>> 
>> locale:
>>    [1] LC_CTYPE=fr_FR.utf8       LC_NUMERIC=C
>>    [3] LC_TIME=fr_FR.utf8        LC_COLLATE=fr_FR.utf8
>>    [5] LC_MONETARY=fr_FR.utf8    LC_MESSAGES=fr_FR.utf8
>>    [7] LC_PAPER=fr_FR.utf8       LC_NAME=C
>>    [9] LC_ADDRESS=C              LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods base
>> 
>> loaded via a namespace (and not attached):
>> [1] compiler_3.4.1
>> 
>> 
>> 
>> and for R-3.3.2:
>> R version 3.3.2 (2016-10-31)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 16.04.3 LTS
>> 
>> locale:
>>    [1] LC_CTYPE=fr_FR.utf8       LC_NUMERIC=C
>>    [3] LC_TIME=fr_FR.utf8        LC_COLLATE=fr_FR.utf8
>>    [5] LC_MONETARY=fr_FR.utf8    LC_MESSAGES=fr_FR.utf8
>>    [7] LC_PAPER=fr_FR.utf8       LC_NAME=C
>>    [9] LC_ADDRESS=C              LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods base
>> 
>> 
>> Thanks in advance,
>> Best regards
>> ||
>> 
>
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> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu



[Rd] Control multi-threading in standard matrix product
luke-tierney at uiowa.edu