<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>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.</div><div><br></div><div>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).</div><div><br></div><div>You may have to reinstall MPICH2.</div><div><br></div><div>MAKER can try and do this for you using necessary flags to make it easier</div><div>To do this --></div><div>cd ./maker/src</div><div>./Build mpich2</div><div><br></div><div>Then reinstall maker</div><div><div>cd ./maker/src</div><div>perl Build.PL</div><div><say yes to mpi question></div><div>./Build clean</div></div><div>./Build install</div><div><br></div><div>Then use this executable to launch --> ./maker/exe/mpich2/bin/mpiexec</div><div><br></div><div>Note you cannot use other launchers. You have to use the one you compiled with.</div><div><br></div><div>--Carson</div><div><br></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> "Dian \"Oscar\" Jiao" <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>><br><span style="font-weight:bold">Date: </span> Thursday, 4 October, 2012 4:42 PM<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] maker mpi failed<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html; charset=Windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">
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 ……</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">
What is this Iterator::Fasta::skip_file? Any idea what is going on here?</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">
Oscar</div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><div style="color: rgb(0, 0, 0); "><br></div><div style="color: rgb(0, 0, 0); ">STATUS: Processing and indexing input FASTA files...</div><div style="color: rgb(0, 0, 0); ">STATUS: Setting up database for any GFF3 input...</div><div style="color: rgb(0, 0, 0); ">A data structure will be created for you at:</div><div style="color: rgb(0, 0, 0); ">/work/02045/jiao/modules/Maker-GMOD/maker2.26/data/dpp_contig.maker.output/dpp_contig_datastore</div><div style="color: rgb(0, 0, 0); "><br></div><div style="color: rgb(0, 0, 0); ">To access files for individual sequences use the datastore index:</div><div style="color: rgb(0, 0, 0); ">/work/02045/jiao/modules/Maker-GMOD/maker2.26/data/dpp_contig.maker.output/dpp_contig_master_datastore_index.log</div><div style="color: rgb(0, 0, 0); "><br></div><div><font class="Apple-style-span" color="#ff0000">ERROR: Log file does not exist in Iterator::Fasta::skip_file</font></div><div style="color: rgb(0, 0, 0); ">MPI process (rank: 8) terminated unexpectedly on c341-213.ls4.tacc.utexas.edu</div><div style="color: rgb(0, 0, 0); ">Exit code -5 signaled from c341-213</div></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><br></div></div></div></div></div>
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