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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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-tier...@uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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