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

[Carson Holt]

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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