[R] R-1.6.0 crashing on RedHat6.3
Peter Dalgaard BSA
p.dalgaard at biostat.ku.dk
Mon Oct 28 22:20:01 CET 2002
Douglas Grove <dgrove at fhcrc.org> writes:
> I'm having what I believe are OS problems with my installation
> of R-1.6.0. The machine I'm using was previously running R-1.4.0.
> The install seemed fine to me. I didn't note an error messages
> in 'make' or 'make check'.
> My problem is that I've been running some memory intesive code,
> and the code that ran under 1.4.0 but won't run under R.1.6.0
> (or under 1.5.1). The code crashes with the message:
> Error: cannot allocate vector of size 13 Kb
> Execution halted
> There's nothing special about the code I'm trying to run,
> in fact it's pretty simple (just memory intensive):
> pc.norm <- princomp(D,scores=FALSE)
> D is a matrix of dim 144x5300
> My only guess, based on my very limited knowledge, is the
> problem stems from some outdated shared library.
> The machine is an two-processor intel-based PC running RedHat6.3.
> I would provide more info, but I'm not really sure what's relevant
> and I'm not very system-savvy.
> I know the OS should probably be updated, but this isn't feasible
> in the short term due to our sys-admin time constraints.
> Is there is anything I can do short of updating the entire OS?
> BTW, I realize that there isn't much *I* can do, as I'm not the
> system administrator, but I'm trying to figure out where the
> problem(s) may lie so that I can tell him what to update.
Are you sure that it is 6.3?? To my knowledge, there is nothing
between 6.2 and 7.0. What's in /etc/redhat-release ?
The Fortran in RH6.x was rather badly broken for some packages, but
one would expect that you had run into that before. 1.6.0 has a memory
leak but it generally affects repeated applications of model fits,
rather than big matrices.
Do you really mean 144x5300 ? (more columns than rows) That's big: The
covariance matrix at 5300x5300 will take more than 200 MB (OK, it
might only be storing upper or lower triangle.) I tried a matrix like
that on a 1.6.1beta system with about 0.75 GB and got an out of memory
error. A 144x2500 problem is currently running in
PID USER PRI NI SIZE RSS SHARE STAT %CPU %MEM TIME COMMAND
16111 pd 17 0 207M 163M 18536 R 99.8 65.8 1:58 R.bin
and seems to be staying there....
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
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