[BioC] rhdf5 segfault

[Harris A. Jaffee]

On Dec 23, 2013, at 10:56 PM, Ben Bolstad <bmb at bmbolstad.com> wrote:

> You might try changing your stack size limits in your shell, before launching R. e.g.
> 
> ulimit -s unlimited


I don’t think that is possible, at least as you put it.  The soft limit tends
to be smaller than the hard limit and is the only thing that can be increased.
You may not get unlimited, but this should work and might help:

	limit -Ss `ulimit -Hs`

> I know I encountered a similar issue with rhdf5 not to long ago reading from a file with a fairly large number of strings, and that was a suitable work around.  Note within R Cstack_info() will also tell you stack size.
> 
> At the time I looked into it, at least in my case I tracked it down to a segfault occuring in the H5Dread_helper_STRING function of file H5D.C at line 244, but it looked like the issue might be with the allocation:
> 
> char bufSTR[n][size]
> 
> in the previous line and I can only assume that n*size is too large for the C stack (in my instance, and perhaps yours) at the default settings in your shell.
> 
> 
> Best,
> 
> Ben
> 
> 
> 
> On Dec 23, 2013, at 4:11 PM, Brad Friedman <friedman.brad at gene.com> wrote:
> 
>> Dear Bernd and List Members:
>> 
>> I'm getting a segmentation fault reading in a character vector (attached)
>> written by rhdf5. If anyone can make a suggestion how to get rhdf5 to read
>> this without throwing the error I would appreciate it. The file appears to
>> be written correctly since h5dump can read it.
>> 
>> I got the same error with the same vector on both my mac laptop and our
>> linux server, in both cases using the latest version of rhdf5 (2.7.4).
>> 
>> Brad
>> 
>>> library(rhdf5)
>>> load("charvec.rda")  ## provides "charvec"
>> 
>> 
>>> str(charvec)
>> chr [1:16630] "lincRNA:chr8:119735533-119736887 forward strand" ...
>>> hdf5.file <- tempfile()
>>> h5createFile(hdf5.file)
>> [1] TRUE
>>> h5write(charvec, hdf5.file, "foo")
>>> got <- h5read(hdf5.file, "foo")
>> Error: segfault from C stack overflow
>>> sessionInfo()
>> R version 3.0.1 (2013-05-16)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>> 
>> locale:
>> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>> [1] rhdf5_2.7.4
>> 
>> loaded via a namespace (and not attached):
>> [1] zlibbioc_1.6.0
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> 
> 
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