<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>The cause of this is most likely a corrupt MPI message.</div><div><br></div><div>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 --></div><div><br></div><div>export LD_PRELOAD=<openmpi_location>/lib/libmpi.so</div><div>#replace <openmpi_location> with the location of OpenMPI</div><div><br></div><div>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. </div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> hueytyng <<a href="mailto:cynsb1987@gmail.com">cynsb1987@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, June 9, 2014 at 10:22 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] ERROR: This MpiChunk is not part of this level<br></div><div><br></div><div dir="ltr">Hi Carson,<br><br>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.<br><div><br>#---------------------------------------------------------------------<br>
Now starting the contig!!<br>SeqID: 1AL_NODE_4659_length_8657_cov_8.758115<br>Length: 8739<br>#---------------------------------------------------------------------<br><br><br>setting up GFF3 output and fasta chunks<br>ERROR: This MpiChunk is not part of this level<br>
at /ws/ws-group/app/maker/bin/../lib/Process/MpiTiers.pm line 439.<br> Process::MpiTiers::update_chunk(Process::MpiTiers=HASH(0x63e64c0), Process::MpiChunk=HASH(0x6155138)) called at /ws/ws-group/bin/maker line 1537<br>
main::update_chunk(ARRAY(0x40c69d0), Process::MpiChunk=HASH(0x6155138)) called at /ws/ws-group/bin/maker line 929<br>--> rank=4, hostname=safs-raijen<br>deleted:0 hits<br>deleted:0 hits<br><br><br></div><div>Attached is my maker_opts.ctl file.<br><br></div><div>Thank you,<br></div><div>Jenny<br></div></div>
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