[Rcpp-devel] Rcpp-devel Digest, Vol 57, Issue 18

[Alessandro Mammana]

Sorry,  I read this post just by chance,
did I understand correctly, the class Rcpp::Matrix are not thread safe?
Is there any problem in writing code such as:

mat(i,j) = something

in a multithreaded environment (such as inside a "#pragma omp parallel
for" loop)?
My scripts are full of such loops. I have assumed that it was the same as doing:

double* M = mat.begin();
M[i + ncol*j] = something;

This at least should be thread safe, right?

Thx a lot!
Ale



On Tue, Jul 15, 2014 at 12:00 PM,
<rcpp-devel-request at lists.r-forge.r-project.org> wrote:
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>    1. Re: parallel distance matrix calculation (JJ Allaire)
>    2. Re: parallel distance matrix calculation (JJ Allaire)
>
>
> ----------------------------------------------------------------------
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> Message: 1
> Date: Mon, 14 Jul 2014 10:45:06 -0400
> From: JJ Allaire <jj.allaire at gmail.com>
> To: Dirk Eddelbuettel <edd at debian.org>
> Cc: "rcpp-devel at lists.r-forge.r-project.org"
>         <rcpp-devel at lists.r-forge.r-project.org>
> Subject: Re: [Rcpp-devel] parallel distance matrix calculation
> Message-ID:
>         <CAKw=oCxkxeHkM4Q=aFMk+9SrQaM1e-Hao1Mh=qgKzn22HCOB5g at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Here's a parallel version:
>
> https://github.com/jjallaire/RcppParallel/blob/master/inst/examples/parallel-distance-matrix.cpp
>
> To make the code reasonable I introduced a new RMatrix<T> class in
> RcppParallel that makes offsetting into rows and columns safe and
> straightforward. This class has no connection on the R or Rcpp APIs so is
> guaranteed to be thread-safe.
>
> On a 4 core machine (8 with hyperthreading) I'm observing a 10x speedup.
> The parallel related speedup is 4x. There is an additional 2.5x speedup
> which appears to be related to the lower level access to the Matrix memory
> done by RMatrix<T> (and perhaps some elimination of copying).
>
>
>
>
> On Sun, Jul 13, 2014 at 7:27 AM, Dirk Eddelbuettel <edd at debian.org> wrote:
>
>>
>> On 12 July 2014 at 12:37, JJ Allaire wrote:
>> | If you could send the full source code to your example (including
>> js_distance
>> | and whatever R code you are using to test/exercise the functions) I'll
>> see if I
>> | can come up with the code you'd use to parallelize the outer loop.
>> Depending on
>> | how it turns out perhaps we can even convert this into another gallery
>> article!
>>
>> That's the spirit!  [ I had another quick look at the inner-product example
>> which is short and nice, but there is just too little of a pickup there...
>> ]
>>
>> Dirk
>>
>> --
>> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>>
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> ------------------------------
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> Message: 2
> Date: Mon, 14 Jul 2014 12:48:25 -0400
> From: JJ Allaire <jj.allaire at gmail.com>
> To: Dirk Eddelbuettel <edd at debian.org>
> Cc: "rcpp-devel at lists.r-forge.r-project.org"
>         <rcpp-devel at lists.r-forge.r-project.org>
> Subject: Re: [Rcpp-devel] parallel distance matrix calculation
> Message-ID:
>         <CAKw=oCyCdv98hTUHRUf+XLbKKFUMp3L64hJX4Ku6uoDjjarvSw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
>> On a 4 core machine (8 with hyperthreading) I'm observing a 10x speedup.
>> The parallel related speedup is 4x. There is an additional 2.5x speedup
>> which appears to be related to the lower level access to the Matrix memory
>> done by RMatrix<T> (and perhaps some elimination of copying).
>>
>
> It turns out that the additional slowdown in the serial version was due to
> repeatedly calling Vector::length as a loop termination condition. I
> re-wrote the serial version using iterators and now the speedup from
> parallel is about 5x (more in line with expectations).
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> End of Rcpp-devel Digest, Vol 57, Issue 18
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-- 
Alessandro Mammana, PhD Student
Max Planck Institute for Molecular Genetics
Ihnestraße 63-73
D-14195 Berlin, Germany