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

  • From: Ben Bolstad <bmb@xxxxxxxxxxxxx>
  • To: rmaexpress_help@xxxxxxxxxxxxx
  • Date: Wed, 05 Mar 2008 06:14:27 -0800

I am guessing that there are further corrupted CEL files in that
dataset. I did not have the energy to further examine that possibility
yesterday.

Ben


On Wed, 2008-03-05 at 06:03 -0800, Alex Feltus wrote:
> 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?  
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> > > > > >
> > 
> === 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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