[maker-devel] ERROR: This MpiChunk is not part of this level

[Carson Holt]

The cause of this is most likely a corrupt MPI message.

It could be random (it happens with MPI messages). In which case it should
succeed on retry. It could mean you need to reinstall you MPI communicator,
or give fewer nodes to mpiexec when running your job (MPICH2 starts having
communication issues after around 100 processes for example - even sooner on
some systems).  It may also mean that you set MAKER up with one communicator
during the installation (like MPICH2) and then used mpiexec from another
communicator to launch the job (OpenMPI for example or even a different
version of MPICH2).   Make sure you are not using MVAPICH2 because MAKER
won't work with MVAPICH2.  Also if you are using OpenMPI, you must preload
libmpi.so or otherwise shared libraries won't work and it will fail while
running MAKER.  To do that you have to export the following environmental
variable -->

export LD_PRELOAD=<openmpi_location>/lib/libmpi.so
#replace <openmpi_location> with the location of OpenMPI

Also because a corrupt message has the chance to cause other issues, you may
want to completely delete the folder for the failed contig (look in the
datastore_index.log to see where that folder is).  Also make sure you are
using the latest version of MAKER because it has been vetted on OpenMPI
using 8000+ cpus. Earlier version (I.e. 2.28 and below) may have issues on
OpenMPI or on some systems with slow NFS storage or limited memory.

--Carson


From:  hueytyng <cynsb1987 at gmail.com>
Date:  Monday, June 9, 2014 at 10:22 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] ERROR: This MpiChunk is not part of this level

Hi Carson,

I run Maker 2.31 on my assembled contigs. From the
"master_datastore_index.log", 529 contigs run through, before I get the
error below. Maker halts after this.

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 1AL_NODE_4659_length_8657_cov_8.758115
Length: 8739
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
ERROR:  This MpiChunk is not part of this level
 at /ws/ws-group/app/maker/bin/../lib/Process/MpiTiers.pm line 439.
    Process::MpiTiers::update_chunk(Process::MpiTiers=HASH(0x63e64c0),
Process::MpiChunk=HASH(0x6155138)) called at /ws/ws-group/bin/maker line
1537
    main::update_chunk(ARRAY(0x40c69d0), Process::MpiChunk=HASH(0x6155138))
called at /ws/ws-group/bin/maker line 929
--> rank=4, hostname=safs-raijen
deleted:0 hits
deleted:0 hits


Attached is my maker_opts.ctl file.

Thank you,
Jenny
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