[maker-devel] WARNING: Multiple MAKER processes have been started in the same directory.

[Michael Thon]

I meant the warning that is in the subject line of my first email:

WARNING: Multiple MAKER processes have been started in the same directory.

I get that warning when I run mpi maker.  For now, I'm running it without mpi.  When the run finishes I can try it again with mpi and make sure I get the same output.

For me, just editing  ds_utility.pm and runlog.pm in maker/lib was enough to fix the seg fault.  I didn't have to change anything in Bio::DB::Fasta.

best
Mike

On Aug 3, 2012, at 7:11 AM, Carson Holt <carsonhh at gmail.com> wrote:

> I'm sorry I'm confused.  Which warning? the segmentation fault you
> mentioned before?  For now I would say it's best to first try maker once
> outside of MPI to verify that the segmentation fault no longer happens
> before moving onto the MPI environment.
> 
> Make sure to run with the -f flag when retrying after the fix suggested by
> Felix, so maker completely restarts from scratch.  That way you can see
> that the fasta database is being generated from start to finish (and is
> not just being reread from the successful run under the --debug flag).
> 
> Make sure that the fix Felix sent is also applied to the Bioperl
> Bio::DB::Fasta module and not just the /maker/lib/ directory or the seg
> fault will not go away otherwise (if it is infact one of perl's DB modules
> causing the issue, which it likely is).  Your error sounds similar to an
> error Felix and Thomas encountered some time ago
> (http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/2012-Marc
> h/000941.html).  Basically one of perl's native DB modules or the database
> the module relies on are broken, so the command line snippet is cutting
> any calls to those other databases out of maker and Bioperl (which should
> be ok if you have at minimum a working Berkley DB and DB_File module on
> your system).
> 
> Use this command line to get the correct directory for applying the
> changes to Bioperl as well -->
> perl -e 'use Bio::DB::Fasta; ($dir = $INC{"Bio/DB/Fasta.pm"}) =~
> s/[^\/]+$//; print "$dir\n"'
> 
> Then copy the directory location-->
> 
> cd <to_that_directory>
> sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/'\
>  $(grep -l 'DB_File GDBM_File NDBM_File SDBM_File' *)
> 
> 
> 
> Finally run maker with the -f flag.  If it works let me know, and then you
> can give MPI a shot.  Make said yes to the "compile for MPI question"
> asked during the maker install process or mpiexec will fail when running
> maker.  If it doesn¹t work without MPI or if it works and then MPI fails,
> make sure to collect the STDERR in a text file and send it to me.  I will
> probably have you run it with the --debug flag as well following any
> initial failure (just to get the extra status messages about your system
> configuration).
> 
> Thanks,
> Carson
> 
> 
> 
> On 12-08-03 12:30 AM, "Michael Thon" <mike.thon at gmail.com> wrote:
> 
>> I get this warning when running the mpi version of maker.  Should I be
>> concerned?  the command I use is this:
>> 
>> mpiexec -n 8 maker
>> 
>> -Mike
>> 
>> 
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