[maker-devel] MAKER seg faulting

[Seth Munholland]

Hi Carson,

I am not using an MPI.  Given the association to tblastx I suspect my c++
install of BLAST is what's seg faulting.  Thanks!

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

On Tue, May 10, 2016 at 7:02 PM, Carson Holt <carsonhh at gmail.com> wrote:

> So MAKER is written in Perl, and Perl can’t really seg fault (it doesn’t
> give developers that kind of low level access to memory). However if you
> are using MPI, then it could be causing a seg fault, or one of the programs
> MAKER is calling could be seg faulting (like BLAST).
>
> So if you are using MPI, let me know which flavor and I can make
> suggestions (for example MVAPICH2 is incompatible with programs that do
> system calls, and OpenMPI may require special setting for LD_PRELOAD to
> work properly with shared libraries). If your not using MPI, then you will
> need to look at the installed programs MAKER is calling and reinstall them,
> update them, or roll back a version (i.e. BLAST, Exonerate, etc.)
>
> —Carson
>
>
>
> On May 10, 2016, at 12:18 PM, Seth Munholland <munholl at uwindsor.ca> wrote:
>
> Hello Everyone,
>
> For reasons unknown my MAKER (2.31.8 on Ubuntu 14.04) runs keep seg
> faulting.  I've changed the the dataset I'm running MAKER on, by parsing
> out smaller sections of the larger assembly, and I still seg fault on
> sections that the larger assembly moved past without issue.
>
> The only commonality I see is every tme it seg faults it appears to have
> jsut finished a tblastx.  Any suggestions for how I can debug and correct
> this issue?
>
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: (519) 253-3000 Ext: 4755
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20160511/2bcef9e2/attachment-0003.html>