[rmaexpress_help] Re: RMAExpress still crashes after 1.0 beta 8

  • From: Ben Bolstad <bmb@xxxxxxxxxxxxx>
  • To: rmaexpress_help@xxxxxxxxxxxxx
  • Date: Sun, 02 Mar 2008 21:03:21 -0800

I have run it up to 2500 HGU-133 Plus 2.0 arrays in recent testing
without it exploding at my end. The cause of the crash that was fixed in
1.0 beta 8 was that i was using a 32 bit integer to index data
(basically the previous situation was causing an overflow condition),
this has been changed to indexing data via row/column style coordinates.
Making the fix allowed me to go right up to 2500 with out problem (I
don't have to many more CEL files of this type lying around right now,
though I suppose I could look for more on GEO).

If you could give me the backtrace from a debugger it would be somewhat
useful for narrowing down the problem. If I understand you correctly it
is seg-faulting somewhere between reading the data and doing anything
else?

Best,

Ben



On Sun, 2008-03-02 at 20:51 -0800, Alex Feltus wrote:
> Hey:
> 
> I have been able to normalize hundreds of arrays with
> RMAExpress 1.0 beta 8 compiled from source on an
> Ubuntu 7.10 system with 8 Xeon cores and 16GB RAM.
> 
> However, I am unable to normalize a set of 2887
> arrays.  They appear to load but then I get a
> segmentation fault.  Your beta 8 bug fix (- Fix a
> potential crash situation in extremely large datasets
> (eg would crash at approximately 1578 HGU-133 plus 2.0
> CEL files)) sounds like my problem, but maybe the
> extra arrays kill it?
> 
> Thanks,
> Alex
> 
> --
> Alex Feltus, Ph.D.
> Assistant Professor
> Clemson University
> Department of Genetics & Biochemistry
> Biosystems Research Complex Rm 302C
> 51 New Cherry Street
> Clemson, SC 29634
> 864-656-3231 (office) - (864) 656-6879 (fax)
> http://www.clemson.edu/genbiochem/faculty/afeltus.html
> 
> 
>       
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