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

[Carson Holt]

That's good to know the seg fault is gone.  Sorry for the confusion, but I
don't seem to have received your other e-mail about the "multiple process
warning".

Could you run '/maker/src/Build status' and send me the output?

Thanks,
Carson

On 12-08-03 3:56 AM, "Michael Thon" <mike.thon at gmail.com> wrote:

>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-Ma
>>rc
>> 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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>> 
>> 
>
>
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