I've looked through all of the posts about this issue (and there are
plenty!) but I am still unable to solve the error. ERROR: cannot allocate
vector of size 455 Mb
I am using R 2.6.2 - x86_64 on a Linux x86_64 Redhat cluster system. When I
log in, based on the specs I provide [qsub -I -X -l arch=x86_64] I am
randomly assigned to a x86_64 node.
I am using package GenABEL. My data (~ 650,000 SNPs, 3,000 people) loads in
okay and I am able to look at the data using basic commands [nids, nsnps,
names(phdata)]
The problem occurs when I try to run the extended analysis: xs <-
mlreg(GASurv(age,dm2)~sex,dta)
******************
1) I have looked through the memory limits on R
mem.limits()
nsize vsize
NA NA
2) Code:
gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 961605 51.4 1710298 91.4 1021138 54.6
Vcells 64524082 492.3 248794678 1898.2 68885474 525.6
gc(reset=TRUE)
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 961119 51.4 1710298 91.4 961119 51.4
Vcells 64523417 492.3 199035742 1518.6 64523417 492.3
3) Linux Memory Allocation - Note: Max Memory Size, Virtual Memory & Stack
Size are all unlimited
bash-3.2$ core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 31743
max locked memory (kbytes, -l) 32
max memory size (kbytes, -m) unlimited
open files (-n) 32768
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) unlimited
cpu time (seconds, -t) unlimited
max user processes (-u) 31743
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
4) free -mt
total used free shared buffers cached
Mem: 3901 99 3802 0 1 24
-/+ buffers/cache: 73 3827
Swap: 1027 37 990
Total: 4929 136 4792
5) ps -u
USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND
xxxxxx 22352 0.0 0.0 65136 956 pts/0 S 03:09 0:00 -tcsh
xxxxxx 22354 0.0 0.0 13496 1792 pts/0 S 03:09 0:00
/usr/sbin/pbs_m
xxxxxx 22355 0.0 0.0 6232 60 pts/0 S 03:09 0:00 pbs_demux
xxxxxx 29872 0.0 0.0 63736 920 pts/0 R+ 09:45 0:00 ps -u
******************
Any solutions? Thank you!
[[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.
