[maker-devel] thread terminated, causing all processes to fail

[Ramón Fallon]

Hi Carson,

I send you a zip of the text file of my repeated maker session, this time
having deleted the mpi_blastdb dir and with the -a flag added to "mpiexec
-n 8 maker -debug". Command line.

Cheers / Ramón.


On Wed, Mar 6, 2013 at 7:49 PM, Ramón Fallon <ramonfallon at gmail.com> wrote:

> OK, will do.
>
> Will get back to you tomorrow on it.
>
> Many thanks!
>
>
> On Wed, Mar 6, 2013 at 7:22 PM, Carson Holt <Carson.Holt at oicr.on.ca>wrote:
>
>>   Could you delete your ../*maker.output/mpi_blastdb directory, and then
>> when rerunning maker, run with the –a flag.
>>
>>  Thanks,
>> Carson
>>
>>
>>   From: Ramón Fallon <ramonfallon at gmail.com>
>> Date: Wednesday, 6 March, 2013 1:15 PM
>> To: Carson Holt <carson.holt at oicr.on.ca>
>> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>>
>> Subject: Re: thread terminated, causing all processes to fail
>>
>>  OK great, here goes .. many thanks!
>>
>>
>>
>> On Wed, Mar 6, 2013 at 7:04 PM, Carson Holt <Carson.Holt at oicr.on.ca>wrote:
>>
>>>   If you do reply all to this message, I should get the attachment.  It
>>> will be stripped from the one going to the list though.
>>>
>>>  Thanks,
>>> Carson
>>>
>>>
>>>
>>>   From: Ramón Fallon <ramonfallon at gmail.com>
>>> Date: Wednesday, 6 March, 2013 12:57 PM
>>> To: <maker-devel at yandell-lab.org>
>>> Subject: Re: thread terminated, causing all processes to fail
>>>
>>>  Hi,
>>>
>>>  Many thanks for your quick reply and hint.
>>>
>>>  Yes, you're right .. further up there is indeed
>>>
>>>  Calling FastaDB::new at /opt/src/maker_svn/bin/../lib/FastaSeq.pm line
>>> 148 thread 1.
>>>  Thread 1 terminated abnormally: ERROR: Could not reestablish DB to
>>> thaw FastaSeq for Storable
>>> --> rank=5, hostname=fatnode, at /opt/src/maker_svn/bin/maker line 1457
>>> thread 1.
>>>
>>>  I run a "script" session and have maker on -debug so I have everything
>>> in one file. Do you prefer to have it attached to a post to this mailing
>>> list (if it accepts txt attachments)
>>>
>>>  Cheers.
>>>
>>>
>>> On Wed, Mar 6, 2013 at 6:34 PM, Ramón Fallon <ramonfallon at gmail.com>wrote:
>>>
>>>> Hi,
>>>>
>>>>  I'm using the maker_svn rev 995 version and hand-compiled MPICH2 on a
>>>> single multicore machine.
>>>>
>>>>  I've successfully run the dpp_contig.fasta (MPI/8 processes) example
>>>> but am having trouble with larger contigs fasta files of my own, which are
>>>> well formed.
>>>>
>>>>  I've run into a problem whereby an mpiexec run of 8 processes will
>>>> stop due to a perl-thread related problem which says
>>>>
>>>>  FATAL: Thread terminated, causing all processes to fail
>>>>
>>>> this corresponds to line 924 in the maker executable (which is for the
>>>> secondary/worker threads), and is the result of a test on !$thr OR'd with
>>>> !$thr->is_running, so clearly one of these is failing.
>>>>
>>>>  $thr itself is a threads->new(\&$node_thread, $gdbfile). Despite
>>>> being a programmer, I've only recently started to look at the code and have
>>>> not got the hang of the parallelisation setup here, though I gather the
>>>> master must use threads to initially generate the parallel instances which
>>>> then use the message passing. Of course threads don't have message passing
>>>> ability, so I guess something clever is going on and will take some time
>>>> for me to understand.
>>>>
>>>>  Clearly however, it has worked before on dpp_contigs, so it may be is
>>>> something wrong with my datafile or the way I am carrying out the analysis.
>>>>
>>>>  Any clues that can be put my way are welcome.
>>>>
>>>>  Thank you!
>>>>
>>>
>>>
>>
>
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