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

[Michael Thon]

./Build status


==============================================================================
STATUS MAKER 2.26
==============================================================================
PERL Dependencies:	VERIFIED
External Programs:	VERIFIED
External C Libraries:	VERIFIED
MPI SUPPORT:		ENABLED
MWAS Web Interface:	DISABLED
MAKER PACKAGE:		CONFIGURATION OK

...

I was impatient and I ran maker with MPI.  In the master log file I see a lot of failed contigs.  Now I'm running it without MPI to see if those contigs fail again. 

On Aug 3, 2012, at 2:37 PM, Carson Holt <carsonhh at gmail.com> wrote:

> 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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> 
>