[maker-devel] MAKER seg faulting

[Seth Munholland]

Hi Carson,

Just an update, that was indeed my issue.  Thanks for your help!

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 Wed, May 11, 2016 at 11:35 AM, Seth Munholland <munholl at uwindsor.ca>
wrote:

> 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
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>>
>>
>>
>
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