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

  • From: Ben Bolstad <bmb@xxxxxxxxxxxxx>
  • To: rmaexpress_help@xxxxxxxxxxxxx
  • Date: Tue, 04 Mar 2008 20:35:20 -0800

I have investigated this issue further by first downloading all
available ATH1 arrays (GPL198) from GEO. I can duplicate this error, but
it is not due to a dataset size problem. Instead it is because one of
CEL files is corrupted (GSM260954.cel for the record). There is actually
also another file in that set that is corrupted, at least at my end
(GSM226522_S17_3.CEL) though the corruption mode is different. Fixes for
detecting these corruption types during the parsing face are imminent
for the next beta release. I'm not sure the timing on this next beta,
though it will probably be within the next couple of weeks.

I don't expect these situations to be particularly common so I don't
believe that 1.0 beta 8 is critically damaged, and it is still a
definite improvement over 1.0 beta 7 and earlier versions for (super)
large datasets.

Best,

Ben 


On Mon, 2008-03-03 at 10:04 -0800, Alex Feltus wrote:
> Ben:
> 
> I can RMA 31 arrays of this type no problem, so the
> data is good.  I have ~300GB of disk space that can be
> used for temp files.  I also never even hit swap since
> I have 16GB RAM.  I am using the default buffer
> settings: 150 arrays/50,000 probe sets.
> 
> Here is GDB output for 460 GPL198 arrays:
> 
> GNU gdb 6.6-debian
> Copyright (C) 2006 Free Software Foundation, Inc.
> GDB is free software, covered by the GNU General
> Public License, and you are
> welcome to change it and/or distribute copies of it
> under certain conditions.
> Type "show copying" to see the conditions.
> There is absolutely no warranty for GDB.  Type "show
> warranty" for details.
> This GDB was configured as "x86_64-linux-gnu"...
> Using host libthread_db library
> "/lib/libthread_db.so.1".
> (gdb) R
> Starting program: /usr/local/bin/RMAExpress 
> [Thread debugging using libthread_db enabled]
> [New Thread 47608618407904 (LWP 16114)]
> [New Thread 1082132816 (LWP 16117)]
> [New Thread 1090525520 (LWP 16118)]
> [Thread 1090525520 (LWP 16118) exited]
> [Thread 1082132816 (LWP 16117) exited]
> [New Thread 1082132816 (LWP 16119)]
> [New Thread 1090525520 (LWP 16120)]
> [Thread 1090525520 (LWP 16120) exited]
> [Thread 1082132816 (LWP 16119) exited]
> [New Thread 1082132816 (LWP 16121)]
> [New Thread 1090525520 (LWP 16122)]
> [Thread 1090525520 (LWP 16122) exited]
> [Thread 1082132816 (LWP 16121) exited]
> 
> Program received signal SIGSEGV, Segmentation fault.
> [Switching to Thread 47608618407904 (LWP 16114)]
> 0x0000000000427480 in max_density (z=0x3767c660,
> rows=0, cols=<value optimized out>, column=0) at
> Preprocess/rma_background3.c:301
> 301         if (dens_y[i] == max_y)
> 
> 
> Alex
> 
> 
> --- Ben Bolstad <bmb@xxxxxxxxxxxxx> wrote:
> 
> > At least for the one dataset of this type, that I
> > currently have
> > accessible, consisting of only 24 arrays every thing
> > processes fine with
> > out complaint or crashing.
> > 
> > What values are you using in your Buffer settings?
> > Do you have ample
> > disk space in the location you are trying to use for
> > your temporary
> > space?
> > 
> > Ben
> > 
> > 
> > 
> > On Mon, 2008-03-03 at 07:53 -0800, Ben Bolstad
> > wrote:
> > > Ok, that makes more sense since the first one you
> > gave me did not seem
> > > to be an Affymetrix array type. I know that things
> > worked with
> > > Arabidopsis ATH1 Arrays in the past, though I have
> > not tested with this
> > > array type in quite awhile.
> > > 
> > > Ben
> > > 
> > > 
> > > 
> > > On Mon, 2008-03-03 at 07:46 -0800, Alex Feltus
> > wrote:
> > > > My mistake.  The GEO accession for the array I
> > am
> > > > using is GPL198.
> > > > 
> > > > Alex
> > > > 
> > > > --- Alex Feltus <yaqona2@xxxxxxxxx> 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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> > > > > 
> > > > 
> > > > 
> > > > --
> > > > 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
> > > > 
> > > > 
> > > >      
> >
> ____________________________________________________________________________________
> > > > Never miss a thing.  Make Yahoo your home page. 
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> > > 
> > > 
> > 
> > 
> 
> 
> 
>       
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