Hi List, I'm using npRmpi to run some density equality tests and place the output into a matrix. I've put together some crude functions for the purpose, but I'm receiving the following error when npdeneqtest() reached the bootstrap;
FATAL ERROR: Memory allocation failure (type DBL_VECTOR). Program terminated. I'm running Ubuntu Lucid 64bit with 4 cores and 12GB of memory. My R install is also 64bit. platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 12.0 year 2010 month 10 day 15 svn rev 53317 language R version.string R version 2.12.0 (2010-10-15) Here's the home-brew function I'm using; npdenseqtestMatrix <- function(df1_row,df2_col,var_names,...) { dim_nms_row <- unique(df1_row[,'cat']) dim_nms_col <- unique(df2_col[,'cat']) tn_pval <- c() col_bw <- list() for(i in dim_nms_col) { col_bw[[which(dim_nms_col==i)]] <- npudensbw(df2_col[which(df2_col[,'cat']==i),var_names],...) } for(i in dim_nms_row) { df1_row_bw <- npudensbw(df1_row[which(df1_row[,'cat']==i),var_names],...) for(j in dim_nms_col) { tn_pval <- c(tn_pval,npdeneqtest(df1_row[which(df1_row[,'cat']==i),var_names],df2_col[which(df2_col[,'cat']==j),var_names],bw.x=df1_row_bw,bw.y=col_bw[[which(dim_nms_col==j)]],...)$Tn.P) } } print(tn_pval) return(matrix(tn_pval,length(dim_nms_row),length(dim_nms_col),dimnames=list(dim_nms_row,dim_nms_col),byrow=TRUE)) } Keep in mind that 'cat' is just a shorthand for Category in this case and it's acting as a database key (largely because the data come from GRASS). I think that my memory allocation should be unlimited (well to the hardware potential) since I'm using 64 bit installs. I have no experience with coding anything for parallel processing. It may also be relevant to point out that I commonly use screen and work remotely, but I've tried with and without screen and the result is the same error. I can't really provide the data here because my dataset is quite large (though I don't think large enough to fill 12GB of memory). Any thoughts would be appreciated, Chris ______________________________________________ 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.