Hi!
Thanks for your reply!  After running the command below I am certain I am
using a 64-bit R.  I am running R through a linux cluster system where R is
globally available for all users.  I have asked the system administrators if
they would update their version R but they are not receptive of making the
change. If I must, I will try to install an updated version in my local
directory.

Though before I do that I want to make sure there are no other underlying
issues I should consider.  Could there be something else I need to look
into?

> .Machine$sizeof.pointer
[1] 8

Thank you!




2010/5/21 Uwe Ligges <ligges@statistik.tu-dortmund.de>

> 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@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.
>>
>

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