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

[Ramón Fallon]

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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