[R] .Call function crashes initializing matrix

[Erik Wright]

Hi Bill,

You were right, thanks!

Now I have:

int size = 5000;
double *matrix = (double *) R_alloc(size^2, sizeof(double));

Which works for larger sizes!  But now I have discovered a new problem with it.  When I go to set the value of the elements it *sometimes* crashes:

for (i = 0; i < (size - 1); i++) {
    for (j = i; j < (size - 1); j++) {
        *(matrix + j*length + i) = 5;
    }
}

About ever tenth time I run this code I get:

R(2535,0xa07f64e0) malloc: *** error for object 0x16830404: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug

Any idea why this is happening?

Thanks again!,
Erik


On Apr 10, 2010, at 5:35 PM, William Dunlap wrote:

>> -----Original Message-----
>> From: r-help-bounces at r-project.org 
>> [mailto:r-help-bounces at r-project.org] On Behalf Of Erik Wright
>> Sent: Saturday, April 10, 2010 3:23 PM
>> To: r help
>> Subject: [R] .Call function crashes initializing matrix
>> 
>> Hello,
>> 
>> I have a C function that I call from R using .Call.  I 
>> recently discovered a bug in my code, and I am not sure if it 
>> is a problem with what I am doing in C or if it has something 
>> to do with my use of .Call.
>> 
>> I have narrowed my problem down to these two C statements:
>> int size = 5000;
>> double matrix[size][size];
>> 
>> When I run this in R it crashes, with this message:
>> *** caught segfault ***
>> address 0xb4141d70, cause 'memory not mapped'
> 
> You may be overflowing the stack.  Allocate
> the space for 'matrix' with the allocation
> functions described in section 5.9 of "Writing
> R Extensions".  They allocate space on the 'heap',
> which has much more space than the stack (where
> space for 'automatic' variables is allocated).
> Typical stack sizes are on the order of few
> megabytes and typical heap sizes are in the gigabytes. 
> 
> Bill Dunlap
> Spotfire, TIBCO Software
> wdunlap tibco.com  
> 
>> 
>> It has no problem when size is smaller, like 50.  Any idea 
>> what is going on?
>> 
>> Thanks!,
>> Erik
>> 
>> 
>> sessionInfo()
>> R version 2.10.1 (2009-12-14) 
>> i386-apple-darwin9.8.0 
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods  
>> [7] base
>> 
>> ______________________________________________
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>> PLEASE do read the posting guide 
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>