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

[Carson Holt]

One more thing.

There are three locations where this exact line of code are called
--> @AnyDBM_File::ISA = qw(DB_File GDBM_File NDBM_File SDBM_File)
run_log
ds_utility
Bio::Fasta::DB

Because of the way perl works only the last one to run needs to be fixed
to stop the error (because it overrides the other two calls), but that
means if the line is ever removed from the last loaded module or load
order changes, then the error will come back because it is the last one to
run that fixes the issue.  So to be safe you should fix it in all
instances.

Currently ds_utility loads last, but it really doesn't need AnyDBM_File
any more to perform it's function and the call will likely be removed in
future releases, so changing the line in Bio::Fasta::DB should avoid
potential future errors on your system.

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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