[maker-devel] maker mpi failed

[Carson Holt]

You either tried to run with the -dsindex option before the log file existed
or you tried to launch via MPI when not compiled for MPI or not compiled
correctly.  It's as if you called MAKER serially multiple times in a row
which you can do, but if you start too many before one of them gets a chance
to get the log file started a race condition exists.

Which MPI flavor are you using?  MVAPICH2 won't work with MAKER, MPICH2
will, and OpenMPI may or may not (non-robust shared library behavior).

You may have to reinstall MPICH2.

MAKER can try and do this for you using necessary flags to make it easier
To do this -->
cd ./maker/src
./Build mpich2

Then reinstall maker
cd ./maker/src
perl Build.PL
<say yes to mpi question>
./Build clean
./Build install

Then use this executable to launch --> ./maker/exe/mpich2/bin/mpiexec

Note you cannot use other launchers.  You have to use the one you compiled
with.

--Carson



From:  "Dian \"Oscar\" Jiao" <jiao at tacc.utexas.edu>
Date:  Thursday, 4 October, 2012 4:42 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] maker mpi failed

Hi, I was trying to run maker 2.26. It was compiled with MPI. The non-mpi
executable works just fine. But I got the error below while running mpirun
­n maker ŠŠ

What is this Iterator::Fasta::skip_file? Any idea what is going on here?

Oscar

STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/work/02045/jiao/modules/Maker-GMOD/maker2.26/data/dpp_contig.maker.output/d
pp_contig_datastore

To access files for individual sequences use the datastore index:
/work/02045/jiao/modules/Maker-GMOD/maker2.26/data/dpp_contig.maker.output/d
pp_contig_master_datastore_index.log

ERROR: Log file does not exist in Iterator::Fasta::skip_file
MPI process (rank: 8) terminated unexpectedly on
c341-213.ls4.tacc.utexas.edu
Exit code -5 signaled from c341-213

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