在R中如何控制BLAS并行矩阵产品中的多线程 [英] In R how to control multi-threading in BLAS parallel matrix product

问题描述

我对在R中使用BLAS并行矩阵乘积有疑问(至少从R-3.4起可能是更早的默认乘积).

现在(至少在我的计算机上)默认行为是矩阵产品(请参见下面的示例)使用计算机上所有可用的内核，这可能是一个问题.

您知道如何控制R中用于标准矩阵产品的核数吗?

预先感谢

示例:

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

会话信息:

> sessionInfo()
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

解决方案

包 RhpcBLASctl 确实做到了.

根据其描述:

控制"BLAS"(又称为"GotoBLAS"，"ACML"和"MKL")上的线程数.并可以控制"OpenMP"中的线程数.如果可行的话，获得一些逻辑核心和物理核心.

我们在 HPC上的CRAN任务视图中提到了它. /p>

I have a question regarding the use of BLAS parallelized matrix product in R (being the default matrix product at least since R-3.4, maybe earlier).

The default behavior (at least on my machine) is now for the matrix product (c.f. example below) to use all the cores available on the machine, which can be a problem.

Do you know how to control the number of cores used for standard matrix product in R?

Thanks in advance

Example:

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

Session info:

> sessionInfo()
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

解决方案

The package RhpcBLASctl does just that.

From its DESCRIPTION:

Control the number of threads on 'BLAS' (Aka 'GotoBLAS', 'ACML' and 'MKL'). and possible to control the number of threads in 'OpenMP'. get a number of logical cores and physical cores if feasible.

We mention it in the CRAN Task View on HPC.

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