Thanks for your reply.

Does what you said by resources mean memory or something else? Inside my
loop, I removed the objects that are created but not used by the next loop
and did garbage collection as well. Do you have any idea how I should
modify my code such that the system won't kill it? Thanks.





On Thu, Aug 23, 2012 at 5:06 PM, Jeff Newmiller <jdnewmil@dcn.davis.ca.us>wrote:

> Yes. Operating systems kill processes that consume excessive resources.
> That excess may arise from one large computation or from a small one on top
> of many other allocations... the "straw that broke the camel's back"
> problem.
> ---------------------------------------------------------------------------
> Jeff Newmiller                        The     .....       .....  Go Live...
> DCN:<jdnewmil@dcn.davis.ca.us>        Basics: ##.#.       ##.#.  Live
> Go...
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> Sent from my phone. Please excuse my brevity.
>
> flora flora <floraflora196@gmail.com> wrote:
>
> >I tried to use gpuCor function in the gputools package of R to calcuate
> >the
> >pairwise correlations of a matrix of 40,000 columns.
> >
> >Becuase there would be memory issues if I use the whole matrix at a
> >time, I
> >splitted the matrix into submatrix of 10,000 columns and then calculate
> >the
> >pairwise correlation of different submatrices. There are altogether 4
> >submatrices, so I need to calculate the pearson correlation of sub
> >matrix 1
> >with sub matrix 1,2,3,4, and sub matrix 2 with submatrix 1,2,3,4, etc.
> >
> >The program runs well at first, but at the last step, which is
> >calculating
> >the correlation between submatrix 4 with itself, the program was killed
> >and
> >gave no error messages.
> >
> >Have anybody else encountered this before?
> >
> >Actually it doesn't have to be related with gpuCor. Just generally
> >speaking, in what circumstances would a R program be killed
> >spontaneously
> >without any error messages?
> >
> >Thanks.
> >
> >       [[alternative HTML version deleted]]
> >
> >______________________________________________
> >R-help@r-project.org mailing list
> >https://stat.ethz.ch/mailman/listinfo/r-help
> >PLEASE do read the posting guide
> >http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> >and provide commented, minimal, self-contained, reproducible code.
>
>

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