[maker-devel] running mpi MAKER

[Le-shin Wu]

Hi Carson,

Thanks a lot for your information. When I run './Build status', it shows as
below and looks like MPI SUPPORT is enabled.

==============================================================================
STATUS MAKER 2.27
==============================================================================
PERL Dependencies:      VERIFIED
External Programs:      VERIFIED
External C Libraries:   VERIFIED
MPI SUPPORT:            ENABLED
MWAS Web Interface:     DISABLED
MAKER PACKAGE:          CONFIGURATION OK

But when I run 'which mpiexec' it shows
"/N/soft/mason/openmpi/1.5.4/gcc/bin/mpiexec". So I think I did not use the
correct version of mpiexec while running my MAKER job. Thanks again. I will
try my MAKER job again with the correct mpiexec from mpich2.

Best

LW


____________________________________________

Le-Shin Wu
Center for Computational Cytomics, Indiana University
http://www.cs.indiana.edu/~lewu
____________________________________________


On Wed, Sep 18, 2013 at 4:27 PM, Carson Holt <carsonhh at gmail.com> wrote:

> It means either maker as not properly configured for MPI support, or the
> communication ring is not launching properly.
>
> Three things:
> 1. In the .../maker/src/ directory, run './Build status'. Does it say
> MPI_SUPPORT is configured or installed?
> 2. Run 'which mpiexec' on the command line?  What is the path?  Is is
> MPICH2 mpiexec, or OpenMPI, or something else?
> 3. Run 'mpiexec -n 64 -hostfile $PBS_NODEFILE hostname' on the command
> line.  What does it print out?
>
> Thanks,
> Carson
>
>
> On 9/18/13 1:35 PM, "Le-Shin Wu" <leshin at gmail.com> wrote:
>
> >Hi,
> >
> >I am new to MAKER and just started to use MAKER for doing some genome
> >annotations. I compiled MAKER package with mpi-supported configuration on
> >our cluster. But when I used "mpiexec -n 64 -hostfile $PBS_NODEFILE maker
> >maker_opts.ctl maker_bopts.ctl maker_exe.ctl" command to run my MPI MAKER
> >job, I got whole bunch of warring message as shown below in my error log
> >file. I wonder is there anything wrong with this warring message? Thank
> >you. (I request 64 processors on two nodes)
> >
> >STATUS: Processing and indexing input FASTA files...
> >WARNING: Multiple MAKER processes have been started in the
> >same directory.
> >
> >
> >Best
> >
> >LW
> >_______________________________________________
> >maker-devel mailing list
> >maker-devel at box290.bluehost.com
> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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