Hi, sorry for double posting but I saw my messages were scrubbed from html garbage and don't know if nobody replies for that, but just in case... apologize if not. I am having trouble with this error when calculating a density on a point pattern dataset with 34480 points. My script exit when calculating z<-density(mypattern, 3000, dimyx=3000) The machine the script it's running on it's a debian/amd64 OS with 16Gb RAM, I have set to unlimited the memory limits (the output of ulimit -a follows) Any ideas? Regards -raffaele ------------------------ rmorelli at amb-asa1:~/R$ ulimit -a core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 128594 max locked memory (kbytes, -l) unlimited max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 8192 cpu time (seconds, -t) unlimited max user processes (-u) 128594 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited -- L'unica speranza di catarsi, ammesso che ne esista una, resta affidata all'istinto di ribellione, alla rivolta non isterilita in progetti, alla protesta violenta e viscerale. (V. Evangelisti)
[plain text] Error: cannot allocate vector of size 274.7 Mb
6 messages · Raffaele Morelli, Roman Luštrik, Mauricio Zambrano-Bigiarini
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On 13/11/12 11:20, Raffaele Morelli wrote:
Hi, sorry for double posting but I saw my messages were scrubbed from html garbage and don't know if nobody replies for that, but just in case... apologize if not. I am having trouble with this error when calculating a density on a point pattern dataset with 34480 points. My script exit when calculating z<-density(mypattern, 3000, dimyx=3000) The machine the script it's running on it's a debian/amd64 OS with 16Gb RAM, I have set to unlimited the memory limits (the output of ulimit -a follows) Any ideas?
Try: ?memory.limit ?gc and read 'Circle 2' of the R_inferno (www.burns-stat.com/pages/Tutor/R_inferno.pdf) IHTH, Mauricio
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2012/11/13 Roman Lu?trik <roman.lustrik at gmail.com>:
Would it be at all possible if you made your problem reproducible? Cheers, Roman
I can upload my .RData (~45Mb) on a server and the script if you're willing to try. In the meanwhile I am doing some test with my owin taken from the maps dataset, I guess the one I am using is too much detailed. -r
2012/11/13 Mauricio Zambrano-Bigiarini <mauricio.zambrano at jrc.ec.europa.eu>:
On 13/11/12 11:20, Raffaele Morelli wrote:
Hi, sorry for double posting but I saw my messages were scrubbed from html garbage and don't know if nobody replies for that, but just in case... apologize if not. I am having trouble with this error when calculating a density on a point pattern dataset with 34480 points. My script exit when calculating z<-density(mypattern, 3000, dimyx=3000) The machine the script it's running on it's a debian/amd64 OS with 16Gb RAM, I have set to unlimited the memory limits (the output of ulimit -a follows) Any ideas?
Try: ?memory.limit ?gc and read 'Circle 2' of the R_inferno (www.burns-stat.com/pages/Tutor/R_inferno.pdf) IHTH, Mauricio
Circle 2 is interesting but it's not my case, I do not costruct object that way and fetch data from a postgres/postgis database. Putting in the code lines such as
cat('point 1 mem', memory.size(), memory.size(max=TRUE), 'nn')
doesn't help because those commands are windows specific and I work on linux. Here follows a link to my script and RData, lines commented are not needed because objects are in the RData http://cen.isprambiente.it/~rmorelli/R/ I've just purged unusued objects from RData. Regards -r
2012/11/13 Roman Lu?trik <roman.lustrik at gmail.com>:
Would it be at all possible if you made your problem reproducible? Cheers, Roman
Here follows a link to my script and RData, lines commented are not needed because objects are in the RData http://cen.isprambiente.it/~rmorelli/R/ Regards -r