Displaying 20 results from an estimated 900 matches similar to: "Why is matrix product slower when matrix has very small values?"
2019 Nov 20
0
Why is matrix product slower when matrix has very small values?
Hi Florian,
just a guess, but couldn't it be that the multiplication of very small
values leads to FP underflow exceptions which have to be handled by BLAS
in a less efficient way than "normal" multiplications handled by SIMD
instructions ?
Best regards,
Hilmar
On 19/11/2019 15:09, Florian Gerber wrote:
> Hi,
>
> I experience surprisingly large timing differences for
2016 Aug 04
1
R, OpenBLAS and OMP_NUM_THREADS
Hi,
I was be half asleep in the heat ...
2016-08-04 0:04 GMT+09:00 Dirk Eddelbuettel <edd at debian.org>:
>
> On 3 August 2016 at 16:45, Gordon Ball wrote:
> | On 02/08/16 03:10, Ei-ji Nakama wrote:
> | > Hi,
> | >
> | > Create /etc/profile.d/openblas.sh.
> | > Write the following during in this file.
> | > OPENBLAS_NUM_THREADS = 1
> | > export
2016 Aug 03
2
R, OpenBLAS and OMP_NUM_THREADS
On 02/08/16 03:10, Ei-ji Nakama wrote:
> Hi,
>
> Create /etc/profile.d/openblas.sh.
> Write the following during in this file.
> OPENBLAS_NUM_THREADS = 1
> export OPENBLAS_NUM_THREADS
>
> OPENBLAS_NUM_THREADS environment variable does not affect the OMP_NUM_THREADS.
>
Thanks for the response.
This works fine for R run from the command line (as does setting the
same
2017 Apr 24
2
Crash after (wrongly) applying product operator on object from LIMMA package
Hi Hilmar,
weird. The memory problem seems be due to recursion (my R, version 3.3.3,
says: Error: evaluation nested too deeply: infinite recursion /
options(expressions=)?, just write traceback() to see how it happens), but
why does it segfault with xlsx? Nb xlsx is the culprit: neither rJava nor
xlsxjars cause the problem.
On the other hand, quick googling for r+xlsx+segfault returns tons of
2017 May 09
3
A few suggestions and perspectives from a PhD student
Hi,
On 08/05/17 16:37, Ista Zahn wrote:
> One of the key strengths of R is that packages are not akin to "fan
> created mods". They are a central and necessary part of the R system.
>
I would tend to disagree here. R packages are in their majority not
maintained by the core R developers. Concepts, features and lifetime
depend mainly on the maintainers of the package (even
2019 Sep 11
2
'==' operator: inconsistency in data.frame(...) == NULL
Dear Martin,
On 11/09/2019 09:56, Martin Maechler wrote:
>
> > I wonder if data.frame(<some non-empty data>) == NULL should also return
> > a value instead of an error. R help reads:
>
> > "At least one of |x| and |y| must be an atomic vector, but
> > if the other is a list R attempts to coerce it to the
> > type of the atomic
2017 Apr 18
3
Crash after (wrongly) applying product operator on object from LIMMA package
Hi,
this is a problem that occurs in the presence of two libraries (limma,
xlsx) and leads to a crash of R. The problematic code is the wrong
application of sweep or the product ("*") function on an LIMMA MAList
object. To my knowledge, limma does not define a "*" method for MAList
objects.
If only LIMMA is loaded but not package xlsx, the code does not crash
but rather
2016 Aug 01
2
R, OpenBLAS and OMP_NUM_THREEADS
What is the correct way to globally configure R to default to single (or
at least, << NUM_CPUS) threaded operation?
Using R 3.3.1 (both in debian unstable or using the CRAN repository for
xenial) with OpenBLAS (0.2.18) defaults to using one thread per
available CPU, which isn't ideal for machines more than a couple of CPUs.
Setting the environment (OMP_NUM_THREADS or
2019 Sep 04
2
'==' operator: inconsistency in data.frame(...) == NULL
Dear all,
I just stumbled upon some behavior of the == operator which is at least
somewhat inconsistent.
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
> list(a=1:3, b=LETTERS[1:3]) == NULL
logical(0)
> matrix(1:6, 2,3) == NULL
logical(0)
> data.frame(a=1:3,
2017 Aug 21
2
Control multi-threading in standard matrix product
Hi Tomas,
Thanks for your answer.
Indeed, I checked and my R-3.4.1 installed from the ubuntu repository
use 'libopenblasp-r0.2.18.so' while my R-3.3.2 that I did compiled on my
machine use 'libRblas.so' which explain the difference of behavior.
I will use RhpcBLASctl to avoid issue when combining matrix product and
other multi-threading package.
Maybe this point regarding
2017 Aug 21
3
Control multi-threading in standard matrix product
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
2013 May 24
0
Rcpp with OpenMP - Need example Makevars
Dear R experts,
recently I started developing a Rcpp package "OpenMPTest".
Within that package I want to use OpenMP, as in the following code example:
// header file
#include <omp.h>
using namespace Rcpp ;
RcppExport SEXP testOpenMP( SEXP nThreads ) ;
// cpp file
SEXP testOpenMP( SEXP nThreads ) {
BEGIN_RCPP
NumericVector numberThreads = NumericVector( nThreads );
2007 Jun 05
4
Refactor all factors in a data frame
Hi all,
Assume I have a data frame with numerical and factor variables that I
got through merging various other data frames and subsetting the
resulting data frame afterwards. The number levels of the factors seem
to be the same as in the original data frames, probably because subset()
calls [.factor without drop = TRUE (that's what I gather from scanning
the mailing lists).
I wonder if
2019 Feb 18
2
Error in rbind(info, getNamespaceInfo(env, "S3methods"))
Dear all,
I'm experiencing an unusual installation error for one package. Could
anyone suggest how I can best investigate this from here please? I'm sorry
this isn't very much to go on. Hopefully someone can point me in the right
direction.
The problem seems to be my library. It is large (3,418 packages) and I'd
like to avoid rebuilding it, if possible. All packages are up to
2019 Feb 01
2
Set the number of threads using openmp with .Fortran?
Hi everybody,
I'm trying to develop an R package with Fortran and OpenMP. I wrote a
simple hello world but I'm not able to set the number of threads. I found this
old email chain
<http://r.789695.n4.nabble.com/Set-the-number-of-threads-using-openmp-with-C-td2284685.html>
and
I tried to set my compile instructions accordingly but i had no luck.
*This is my makevars:*
2010 May 19
3
Strange case of partial matching in .[ - possible bug / wrong documentation?
Hi all,
This occurred in R-2.11.0 (WinXP).
The R-help page of .[ says that:
"Character indices can in some circumstances be partially matched (see
pmatch) to the names or dimnames of the object being subsetted (but never
for subassignment). Unlike S (Becker et al p. 358)), R has never used
partial matching when extracting by [, and as from R 2.7.0 partial matching
is not by default used by
2018 Sep 22
4
libRblas.so: cannot open shared object file: No such file or directory
R 3.5.1 is installed under Linux Mint 19 from binaries r-base and
r-base-dev from ubuntu bionic-cran35.? Mysteriously, packages using
libRblas cannot be compiled.? I get: libRblas.so: cannot open shared
object file: No such file or directory.? And indeed, I find no libRblas.so.
Any ideas about how to fix this?
Thanks,
Steve
2018 Oct 05
2
Seg fault stats::runmed
Dear all,
I just found this issue:
dd1 = c(rep(NaN,82), rep(-1, 144), rep(1, 74))
xx = runmed(dd1, 21)
-> R crashes reproducibly in R 3.4.3, R3.4.4 (Ubuntu 14.04/Ubuntu 16.04)
With GDB:
Program received signal SIGSEGV, Segmentation fault.
swap (l=53, r=86, window=window at entry=0xc59308,
outlist=outlist at entry=0x12ea2e8, nrlist=nrlist at entry=0x114fdd8,
print_level=print_level at
2018 Feb 13
2
R Compilation gets stuck on Windows 64
In the file MkRules.local.in, I see the line: USE_ATLAS = NO which I
believe needs to be changed to YES. But how do I specify the BLAS file
*libopenblas_haswell-r0.2.20.a
*and its location?
Regards,
Indrajit
On Tue, Feb 13, 2018 at 6:41 PM, Indrajit Sen Gupta <indrajitsg at gmail.com>
wrote:
> I was able to compile the R from the github by running build-r-devel.bat!
>
> Now need
2019 Feb 02
1
Set the number of threads using openmp with .Fortran?
I got this to work on Linux but it is not working on Windows. *My
understanding is that this should also work on windows, is that correct?*
If so, what should I do? differently?
To get it to work on Linux, I modified my R script as follows:
#' OpenMP Hello World
#'
#' @param nthreads The number of threads that you want to use
#' @example
#' hello(nthreads=2)
#' @export