Dear R-help list members, I am hoping to get you help in reproducing a problem I am having That is only reproducible on a large-memory machine. Whenever I run the following lines, get a segfault listed below:
*** caught segfault *** address 0x7f092cc46e40, cause 'invalid permissions' Traceback: 1: La.svd(x, nu, nv) 2: svd(X) 3: ginv(bigmatrix) Here is the code that I run: require(MASS) l=30000 w=30000 x=rpois(l*w,0.00126) bigmatrix=matrix(x,nrow=l,ncol=w) inverted=ginv(bigmatrix) I have tried this both with OMP_NUM_THREADS=1 and greater than 1, and the resulting is always a segfault. The max memory used in around 40G. I am running this on a machine with 128Gb of RAM. I have also done tests with 15,000x15,000 matrices, and they do not cause any segfaults, so I think the problem is related to the size of the input to the La.svd function. I have also tried this with a less sparse matrix, but again, no change in the outcome. I have submitted the bug report to the R bugzilla site ( https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15163), but I wanted to see if anyone on the r-help list has hit this problem before, or can reproduce it, and if there is a solution out there. My web searches have turned up nothing. It appears that R uses a modified version of LAPACK 3.1, and the latest version of LAPACK is 3.4.2. Is that important? Thanks so much for your help, Cyrus PS: Here is my SessionInfo: (I am using ubuntu). R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] MASS_7.3-22 Matrix_1.0-10 lattice_0.20-10 Rcpp_0.10.2 [5] devtools_0.8 loaded via a namespace (and not attached): [1] compiler_2.15.2 digest_0.6.0 evaluate_0.4.3 grid_2.15.2 [5] httr_0.2 memoise_0.1 parallel_2.15.2 RCurl_1.95-3 [9] stringr_0.6.2 tools_2.15.2 whisker_0.1 [[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 and provide commented, minimal, self-contained, reproducible code.
