[R] Memory problem

[Gang Chen]

It seems the problem lies in this line:

> try(fit.lme <- lme(Beta ~ group*session*difficulty+FTND, random =  
> ~1|Subj, Model), tag <- 1);

As lme fails for most iterations in the loop, the 'try' function  
catches one error message for each failed iteration. But the puzzling  
part is, why does the memory usage keep accumulating? Does each error  
message keep stored accumulatively in the buffer or something else?  
Or something is wrong with the way I'm using 'try'?

Thanks,
Gang


On Aug 9, 2007, at 10:36 AM, Gang Chen wrote:

> I got a long list of error message repeating with the following 3
> lines when running the loop at the end of this mail:
>
> R(580,0xa000ed88) malloc: *** vm_allocate(size=327680) failed (error
> code=3)
> R(580,0xa000ed88) malloc: *** error: can't allocate region
> R(580,0xa000ed88) malloc: *** set a breakpoint in szone_error to debug
>
> There are 2 big arrays, IData (54x64x50x504) and Stat (4x64x50x9), in
> the code. They would only use about 0.8GB of memory. However when I
> check the memory usage during the looping, the memory usage keeps
> growing and finally reaches the memory limit of my computer, 4GB, and
> spills the above error message.
>
> Is there something in the loop about lme that is causing memory
> leaking? How can I clean up the memory usage in the loop?
>
> Thank you very much for your help,
> Gang
>
> ============
>
>
> tag <- 0; dimx<-54; dimy<-64; dimz<-50; NoF<-8; NoFile<-504;
>
> IData <- array(data=NA, dim=c(dimx, dimy, dimz, NoFile));
> Stat <- array(data=NA, dim=c(dimx, dimy, dimz, NoF));
>
> for (i in 1:NoFile) {
>     IData[,,,i] <- fill in the data for array IData here;
> }
>
> for (i in 1:dimx) {
> for (j in 1:dimy) {
> for (k in 1:dimz) {
>     for (m in 1:NoFile) {
> 		Model$Beta[m] <- IData[i, j, k, m];
>     }
>     try(fit.lme <- lme(Beta ~ group*session*difficulty+FTND, random =
> ~1|Subj, Model), tag <- 1);
>     if (tag != 1) {
> 	   Stat[i, j, k,] <- anova(fit.lme)$F[-1];	
>     }
>     else {
>         Stat[i, j, k,] <- rep(0, NoF-1);
>     }
>     tag <- 0;
> }
> }
> }
>
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