Yes, the resources operating systems usually kill for are memory. No, you have not provided a reproducible example. In general, you need to do something different, such as choose a different algorithm, run on a different computer, or split your problem into smaller pieces. --------------------------------------------------------------------------- Jeff Newmiller The ..... ..... Go Live... DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --------------------------------------------------------------------------- Sent from my phone. Please excuse my brevity.
flora flora <floraflora...@gmail.com> wrote: >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 ><jdnew...@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:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live >> Go... >> Live: OO#.. Dead: OO#.. >Playing >> Research Engineer (Solar/Batteries O.O#. #.O#. with >> /Software/Embedded Controllers) .OO#. .OO#. >rocks...1k >> >--------------------------------------------------------------------------- >> Sent from my phone. Please excuse my brevity. >> >> flora flora <floraflora...@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. >> >> ______________________________________________ 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 and provide commented, minimal, self-contained, reproducible code.