[R-sig-ME] New version of lme4 - memory error

[Douglas Bates]

On 1/28/07, Andrew Robinson <A.Robinson at ms.unimelb.edu.au> wrote:
> On Sun, Jan 28, 2007 at 11:18:56AM -0600, Douglas Bates wrote:
> > On 1/27/07, Andrew Robinson <A.Robinson at ms.unimelb.edu.au> wrote:
> > >Thanks, Martin.  It was vanilla.
> > >
> > >
> > >> traceback()
> > >4: .Call(mer2_getPars, mer)
> > >3: as.double(start)
> > >2: nlminb(.Call(mer2_getPars, mer), function(x) .Call(mer2_deviance,
> > >       .Call(mer2_setPars, mer, x), as.integer(0)), lower = ifelse(const,
> > >       0, -Inf), control = list(trace = cv$msVerbose, iter.max =
> > >       cv$msMaxIter,
> > >       rel.tol = abs(0.001/.Call(mer2_deviance, mer, 0))))
> > >1: lmer2(Reaction ~ Days + (Days | Subject), sleepstudy)
> >
> > Thanks for including that traceback, Andrew.  As Martin indicated, it
> > is difficult for us to diagnose the problem because we are unable to
> > reproduce it.
> >
> > I can tell you what should be happening at that point in the lmer2
> > function.  Perhaps you could use
> >
> > debug(lmer2)
> >
> > and check under your system what is happening for you.
> >
> > As I'm sure you can determine just be looking at this traceback, this
> > is the point in lmer2 where the REML or ML criterion is to be
> > optimized using the optimizer nlminb.  The object 'mer', of class
> > 'mer2', is the internal representation of a mixed-effects model.  It
> > is described in the Implementation vignette.
> >
> > The ST slot is a list whose number of components is equal to the
> > number of random effects expressions in the model formula.  In this
> > case it should have one component and that component should be a 2x2
> > matrix (it's a matrix, not a Matrix from the Matrix package).  The C
> > code for mer2_getPars allocates a numeric vector of the correct length
> > and fills it out with elements of the lower triangles of these
> > matrices starting with the diagonal elements of each matrix.  (The
> > diagonal elements are the elements of the scale matrices S and the
> > elements of the strict lower triangle are the non-trivial elements of
> > the unit triangular matrices T.)
> >
> > I enclose some of the debugger output from my system.  Once the mer
> > object is created I check that the 'dims' slot has the expected
> > entries.  In particular the element labeled 'nf' (number of grouping
> > factors) should be 1 and the nc slot should be an integer vector of
> > length 1 and the first element should be 2.
> >
> > If the 'dims', 'nc' and 'ST' slots all have the expected contents then
> > it would be very mysterious how mer2_getPars managed to fail.  I
> > suspect that the problem originates one step back in the call to
> > mer2_create.  In either case it may be necessary to go in and examine
> > the execution of the compiled code using a symbolic debugger in order
> > to exactly what's going on.
>
> Thanks for your detailed response, Doug.  I ran debug(lmer2) as you
> suggested, and as you expected, I got the same results as you did.  Of
> course I would like to dig further into this problem.  I have limited
> experience using gdb, but I have used it.  If you don't mind providing
> a brief set of instructions, I will carry them out.

Well, actually, that wasn't what I was expecting.  I thought that
something would look wrong in those slots.

Can you be more specific about getting the same results as I did?  In
particular, did you get the same response to

.Call("mer2_getPars", mer, PACKAGE = "lme4")

If so, I'm not quite sure how it would fail in the same call
immediately afterwards.

I'll respond about how I use gdb in a susequent message.

>
> Andrew
> --
> Andrew Robinson
> Department of Mathematics and Statistics            Tel: +61-3-8344-9763
> University of Melbourne, VIC 3010 Australia         Fax: +61-3-8344-4599
> http://www.ms.unimelb.edu.au/~andrewpr
> http://blogs.mbs.edu/fishing-in-the-bay/
>