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

[Carson Holt]

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<mailto:ramonfallon at gmail.com>>
Date: Wednesday, 6 March, 2013 12:57 PM
To: <maker-devel at yandell-lab.org<mailto: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<mailto: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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