[R] R-1.6.0 crashing on RedHat6.3
dgrove at fhcrc.org
Mon Oct 28 22:55:19 CET 2002
> > Hi,
> > 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):
> > library(mva)
> > 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 problem stems from some outdated shared library.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 ?
Sorry, I was told it was running 6.3. I just checked and
it's running 6.2.
> 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....
Yep, it's 144x5300. The machine has 2GB of RAM, and this uses about 1.5GB.
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