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

[Carson Holt]

That is extremely odd.  It fails to even generate the indexes. Could you
check the drive space of your working directory and your /tmp directory?

It is odd because Bioperl uses the stat command to check on the file right
before making a tied hash.  So it was there for the stat but not the tie,
which is immediately following.

If you check manually does it exist now? -->
/home/ramonf/makertrials/mgallocut7/sca29310_8.maker.output/mpi_blastdb/sca2
9310_8%2Efa.mpi.1/sca29310_8%2Efa.mpi.1.0.index

Are you running in an NFS mounted directory?

--Carson


From:  Ramón Fallon <ramonfallon at gmail.com>
Date:  Thursday, 7 March, 2013 9:40 AM
To:  Carson Holt <carson.holt at oicr.on.ca>
Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] thread terminated, causing all processes to fail

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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