On Fri, 3 Oct 2008, Ubuntu.Diego wrote:
I'm trying to get some "easy coding" to reproduce the error. In the
meantime I have R code that run for 20 or more hours and suddenly i got
a "segfault 'memory not mapped'" error. I have to clarify that the error
not alway occurs and sometimes the process end satisfactorily. The
process is basically a search using an MCMC strategy, sometimes the
algorithm converge and stops others I got the error message. I was
wondering if it could be meaning that I run out of RAM.
The 'memory not mapped' error means that your code is reading from or
writing to memory that it doesn't own. This should have nothing to do with
running out of RAM.
If this is pure R code you have found a bug in R. If you are calling your
own C code it is more likely to be a bug there. If your C code uses
PROTECT/UNPROTECT it is even more likely to be there.
Usually the best way to track down these bugs is to run the code under
Valgrind, but this is slow, which will be a problem for code that already
takes many hours.
If you are extremely lucky, the crash will have happened on the first
incorrect memory access. Running R under a debugger such as gdb you can
use backtrace after the crash occurs to find where the bug happened.
Unfortunately it is quite likely that the crash happened because some
earlier piece of code overwrote a stored variable or something similar.
The fact that the segfault occurs only some of the time reinforces this,
especially if you don't always get the crash even with the same sequence
of random numbers.
If you have a Linux computer that you can use for a week or so it would be
worth running your code under Valgrind to see if it finds the problem.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
