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

[Ramón Fallon]

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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