[R] ERROR: cannot allocate vector of size?

[Uwe Ligges]

At first, I'd try with an R version from 2010 rather than one from 2007.
Next, I'd try to be sure to really have a 64-bit version of R rather 
than a 32 bit one which is what I suspect.

Best,
Uwe Ligges


On 20.05.2010 20:10, Yesha Patel wrote:
> 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 at 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.