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

[Ramón Fallon]

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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