[maker-devel] maker mpi failed

[Dian "Oscar" Jiao]

Hi Carson,
I didn't know maker does not work with MVAPICH2. The cluster I was installing maker on only has mvapich2. So I guess I will have to install mpich2 under my directory. However, I installed perl threading based on mvapich2. Does that mean I need to reinstall perl with mpich2 before reinstalling maker?
Oscar
--
Dian (Oscar) Jiao, Ph.D.,
Research Associate, Life Sciences Computing Group
Texas Advanced Computing Center
University of Texas at Austin
jiao at tacc.utexas.edu | (832) 303-1166

From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Thursday, October 4, 2012 3:53 PM
To: Oscar Jiao <jiao at tacc.utexas.edu<mailto:jiao at tacc.utexas.edu>>, "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] maker mpi failed

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<mailto:jiao at tacc.utexas.edu>>
Date: Thursday, 4 October, 2012 4:42 PM
To: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto: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 ……

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/dpp_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/dpp_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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