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

  • From: Alex Feltus <yaqona2@xxxxxxxxx>
  • To: rmaexpress_help@xxxxxxxxxxxxx
  • Date: Wed, 5 Mar 2008 06:03:54 -0800 (PST)

Ben:

Thanks for your help with this.  I removed those two
.CEL files which allowed me to get to the BA stage
(further than before).  However, I still get a
segmentation fault.  

Alex

Here is the gdb output (appears to break as before):

Starting program: /usr/local/bin/RMAExpress 
[Thread debugging using libthread_db enabled]
[New Thread 47990231476192 (LWP 8626)]
[New Thread 1082132816 (LWP 24051)]
[New Thread 1090525520 (LWP 24052)]
[Thread 1090525520 (LWP 24052) exited]
[Thread 1082132816 (LWP 24051) exited]
[New Thread 1082132816 (LWP 24053)]
[New Thread 1090525520 (LWP 24054)]
[New Thread 1098918224 (LWP 24055)]
[Thread 1090525520 (LWP 24054) exited]
[Thread 1098918224 (LWP 24055) exited]
[Thread 1082132816 (LWP 24053) exited]
[New Thread 1082132816 (LWP 24056)]
[New Thread 1098918224 (LWP 24057)]
[Thread 1098918224 (LWP 24057) exited]
[Thread 1082132816 (LWP 24056) exited]

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 47990231476192 (LWP 8626)]
0x0000000000427480 in max_density (z=0x378a8440,
rows=0, cols=<value optimized out>, column=0) at
Preprocess/rma_background3.c:301
301         if (dens_y[i] == max_y)

--- Ben Bolstad <bmb@xxxxxxxxxxxxx> wrote:

> 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
> > > > > > 
> > > > > > 
> > > > > >      
> > > > > >
> > > > >
> > >
> >
>
____________________________________________________________________________________
> > > > > > Looking for last minute shopping deals?  
> > > > > > Find them fast with Yahoo! Search. 
> > > > > >
> > > > >
> 
=== message truncated ===


--
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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