On Wed, 18 Feb 2009, Jong wrote:
Hi all,
I've compiled R (version 2.8.1) from the source code with "--with-
blas=" option in order to use external multi-threaded blas package.
However, it's very hard to verify that compilation is correct and R is
using multi-threads correctly or not. Which command or operation in R
will run with multi-threads?
I assumed that matrix multiplication %*% may call multi-threaded blas
operation. So, I run the following code:
n <- 2000
T = matrix(runif(n*n), nrow=n, ncol=n)
system.time(T %*% T)
that should have done it. On my (Core 2 Duo) MacBook
x <- matrix(rnorm(1e6),100)
system.time(t(x)%*%x) ## user + system < elapsed
user system elapsed
4.221 0.951 2.719
system.time(crossprod(x)) ## ditto
user system elapsed
2.933 0.898 2.665
showing the vecLib (Mac's BLAS) is multithreaded.
HTH,
Chuck
and watch R process by using unix top command with show-all-threads
option. However, it seems like my R doesn't use multi-threads but just
run with single thread. Is there any other command that I can use to
verify multi-threads use?
Regarding the with-blas option, I have tried to use either atlas or
gotoblas with the following configure option:
--with-blas="-lptf77blas -lpthread -latlas"
--with-blas="-lgotocblas -lgotoblas -lpthread"
Not sure if my options are correct or not.
Thank you for your and comment or advice in advance.
Thanks,
Jong
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Charles C. Berry (858) 534-2098
Dept of Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu UC San Diego
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