[Rcpp-devel] How to free memory in Rcpp
Honglang Wang
wanghonglang2008 at gmail.com
Fri Dec 14 17:17:43 CET 2012
Thanks, Romain.
Best wishes!
Honglang Wang
Office C402 Wells Hall
Department of Statistics and Probability
Michigan State University
1579 I Spartan Village, East Lansing, MI 48823
wangho16 at msu.edu
On Fri, Dec 14, 2012 at 11:04 AM, Romain Francois
<romain at r-enthusiasts.com>wrote:
> I dont know. This looks like a deeply hidden problem.
>
> Maybe you can enable some rcpp debugging by adding
>
> #define RCPP_DEBUG_LEVEL 1
>
> Before you include Rcpp.h, this will give you verbose output, maybe this
> will help locating the issue.
>
> Romain
>
> Envoyé de mon iPhone
>
> Le 14 déc. 2012 à 16:31, Honglang Wang <wanghonglang2008 at gmail.com> a
> écrit :
>
> Hi Romain,
> Thanks very much. I tried your method. And now the old error has gone,
> which is really good for me. But a new error is :
> Error in betahat(ker, x, X, y, t, h, m) :
> (list) object cannot be coerced to type 'double'
> Calls: system.time ... apply -> FUN -> betahat -> .External ->
> cpp_exception
> Execution halted
>
> What should I do? Do I have to do like:
> arma::colvec betahat0(betahat.begin(),betahat.size()/2,false);
> NumericVector betahat00(p);
> betahat00 = betahat0;
> return List::create(Named("betahat") = betahat00);
>
> Best wishes!
>
> Honglang Wang
>
> Office C402 Wells Hall
> Department of Statistics and Probability
> Michigan State University
> 1579 I Spartan Village, East Lansing, MI 48823
> wangho16 at msu.edu
>
>
>
> On Fri, Dec 14, 2012 at 2:09 AM, Romain Francois <romain at r-enthusiasts.com
> > wrote:
>
>> Le 14/12/12 03:15, Honglang Wang a écrit :
>>
>>> Hi,
>>> Here is the sample code:
>>> // [[Rcpp::export]]
>>> List betahat(Function ker, double t0, NumericMatrix Xr, NumericMatrix
>>> yr, NumericVector tr, double h, int m) {
>>> int n = Xr.nrow(), p = Xr.ncol();
>>> arma::mat X(Xr.begin(), n, p, false);
>>> arma::mat y(yr.begin(), n, 1, false);
>>> arma::colvec t(tr.begin(), tr.size(), false);
>>> arma::mat T = X;
>>> T.each_col() %= (t-t0)/h;
>>> arma::vec K =as<arma::vec>(ker(tr-t0,h))/
>>> m;
>>> double L1 = arma::accu(K%X.col(0)%X.col(0)**);
>>> double L2 = arma::accu(K%X.col(0)%X.col(1)**);
>>> double L3 = arma::accu(K%X.col(1)%X.col(1)**);
>>> double L4 = arma::accu(K%X.col(0)%T.col(0)**);
>>> double L5 = arma::accu(K%X.col(1)%T.col(0)**);
>>> double L6 = arma::accu(K%X.col(1)%T.col(1)**);
>>> double L7 = arma::accu(K%T.col(0)%T.col(0)**);
>>> double L8 = arma::accu(K%T.col(0)%T.col(1)**);
>>> double L9 = arma::accu(K%T.col(1)%T.col(1)**);
>>> double R1 = arma::accu(K%X.col(0)%y);
>>> double R2 = arma::accu(K%X.col(1)%y);
>>> double R3 = arma::accu(K%T.col(0)%y);
>>> double R4 = arma::accu(K%T.col(1)%y);
>>> arma::mat L(2*p,2*p);
>>> L(0,0)=L1;L(0,1)=L2;L(0,2)=L4;**L(0,3)=L5;
>>> L(1,0)=L2;L(1,1)=L3;L(1,2)=L5;**L(1,3)=L6;
>>> L(2,0)=L4;L(2,1)=L5;L(2,2)=L7;**L(2,3)=L8;
>>> L(3,0)=L5;L(3,1)=L6;L(3,2)=L8;**L(3,3)=L9;
>>> arma::mat R(2*p,1);
>>> R(0,0)=R1;R(1,0)=R2;R(2,0)=R3;**R(3,0)=R4;
>>> arma::vec betahat = arma::solve(L,R);
>>>
>>> arma::colvec betahat0(betahat.begin(),**betahat.size()/2,false);
>>> return List::create(Named("betahat") = betahat0);
>>> }
>>>
>>> I will call this function repeatedly, and at some point, it went wrong
>>> with the following error:
>>> Error in betahat(ker, x, X, y, t, h, m) :
>>> promise already under evaluation: recursive default argument
>>> reference or earlier problems?
>>> Calls: system.time ... apply -> FUN -> betahat -> .External ->
>>> cpp_exception
>>> Execution halted
>>>
>>> I have no idea what's this error. I am just wondering whether I need to
>>> free some memory in this code. Thanks.
>>>
>>
>> You don't. The explicit constructor/destructor scheme of C++ takes care
>> of this automatically for you.
>>
>> So there is a chance you are victim of a well hidden bug. These are
>> usually related to garbage collection and us not making enough precaution
>> somewhere. This is very hard to track.
>>
>> As a wild guess, I think it is because Function return you an unprotected
>> SEXP. It does not matter most of the time because you consume it, but
>> sometimes the GC will run and collect your object before as<mat> has a
>> chance to process it.
>>
>> If my guess is correct, then doing yourself some protection might do the
>> trick, something like:
>>
>> NumericVector result = ker(tr-t0,h) ;
>> arma::vec K =as<arma::vec>(result)/m;
>>
>> will do the trick since the result of the function call then gets
>> protected by the "result" object.
>>
>> If this does not work, then you can do some debugging as indicated by
>> others.
>>
>> Romain
>>
>> Best wishes!
>>> Honglang Wang
>>> Office C402 Wells Hall
>>> Department of Statistics and Probability
>>> Michigan State University
>>> 1579 I Spartan Village, East Lansing, MI 48823
>>> wangho16 at msu.edu <mailto:wangho16 at msu.edu>
>>>
>>>
>>>
>>>
>>> On Thu, Dec 13, 2012 at 4:57 PM, <romain at r-enthusiasts.com
>>> <mailto:romain at r-enthusiasts.**com <romain at r-enthusiasts.com>>> wrote:
>>>
>>>
>>> Hello,
>>>
>>> What memory do you want to free ? Can you give an example of code
>>> where there is memory you'd like to "free" ?
>>>
>>> Romain
>>>
>>> Le 2012-12-13 22:52, Honglang Wang a écrit :
>>>
>>> Dear All,
>>> How to free memory in Rcpp? What's the command? Thanks.
>>>
>>> Best wishes!
>>>
>>> Honglang Wang
>>>
>>> Office C402 Wells Hall
>>> Department of Statistics and Probability
>>> Michigan State University
>>> 1579 I Spartan Village, East Lansing, MI 48823
>>> wangho16 at msu.edu <mailto:wangho16 at msu.edu> [1]
>>>
>>>
>>> Links:
>>> ------
>>> [1] mailto:wangho16 at msu.edu <mailto:wangho16 at msu.edu>
>>>
>>
>>
>> --
>> Romain Francois
>> Professional R Enthusiast
>> +33(0) 6 28 91 30 30
>>
>> R Graph Gallery: http://gallery.r-enthusiasts.**com<http://gallery.r-enthusiasts.com>
>>
>> blog: http://romainfrancois.blog.**free.fr<http://romainfrancois.blog.free.fr>
>> |- http://bit.ly/RE6sYH : OOP with Rcpp modules
>> `- http://bit.ly/Thw7IK : Rcpp modules more flexible
>>
>>
>
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