Question: segfault ReadAffy cause 'memory not mapped'
5.7 years ago by
Brian D. Peyser PhD • 70
Brian D. Peyser PhD • 70 wrote:
Below is some previous info on this issue; Dr Bolstad, did you issue a patch to affyio? I had just pulled the latest source from SVN with the hope that I could manage to hack it and noticed this at the top of read_abatch.c: ** Sept 18, 2013 - improve 64bit support for read_abatch I haven't tried running these big calcs since then. Should I give a try now? -Brian On Wed, 2013-08-21 at 16:21 -0700, Ben Bolstad wrote: > Well, internally read_abatch is using allocMatrix() to actually allocate > the main block of memory that will be used to store the probe intensities. > However, there are a lot of places where "int" is used as the indexing > variable. Probably if I had had better foresight when I wrote this code 10 > years ago, I'd have used something a bit more specific (eg int64_t). I'm > guessing it is one of these sorts of things that is causing the crash. > I'll try to get around to refactoring the code at some point. > > If you'd like you could send me the gdb backtrace at the point of the > segfault and I could investigate further. > > Best, > > Ben > > > > On 8/1/13 5:33 PM, Loraine, Ann wrote: > >> Hello, > >> > >> I am trying to process several thousand CEL files using the ReadAffy > >> command. > >> > >> The machine has 96 Gb RAM. > >> > >> However I get this error: > >> > >> > expr=ReadAffy(filenames=d.uniq$cel,celfile.path='CEL',sampleNam es=d.uniq$gsm,compress=T) > >> > >> *** caught segfault *** > >> address 0x7fc79b4b1048, cause 'memory not mapped' > >> > > > > I also have a problem loading many (3750) Affy hgu133plus2 arrays into > > an AffyBatch. I was able to run this with ~2900 arrays, but not since > > adding ~800 more. At right around 16 GiB allocated, I get a segfault > > like: > > > > *** caught segfault *** > > address 0x2aa6b6067048, cause 'memory not mapped' > > > > Traceback: > > 1: .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra, > > ref.cdfName, dim.intensity[c(1, 2)], verbose, PACKAGE = "affyio") > > 2: read.affybatch(filenames = as.character(pdata$Filename)) > > <snip> -- Brian D. Peyser PhD Special Assistant to the Associate Director Office of the Associate Director Developmental Therapeutics Program Division of Cancer Treatment and Diagnosis National Cancer Institute National Institutes of Health 301-524-5587 (mobile)
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