<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); "><div><span class="Apple-style-span" style="font-size: 12px; font-family: Consolas, monospace; ">I don't think you will need to reinstall perl (you may but I don't think so). </span><span class="Apple-style-span" style="font-size: 12px; font-family: Consolas, monospace; ">MVAPICH2 doesn't work because they have overridden malloc with their own version which causes weirdness with shared libraries in Perl. I've submitted some bug reports to the MVAPICH2 developers and made modifications to the development version of MAKER, and had some progress, but I am still not getting reliable</span><span class="Apple-style-span" style="font-size: 12px; font-family: Consolas, monospace; "> behavior </span><span class="Apple-style-span" style="font-size: 12px; font-family: Consolas, monospace; ">in MVAPICH2 when compiling for the OFA-IB-Nemesis or OFA-IB-CH3 interfaces. So for now using MPICH2 is your best choice. You lose some of the infiniband optimizations but IO rather than messages passing is MAKER's true bottleneck (so you won't get a performance hit by using MPICH2).</span></div><div><span class="Apple-style-span" style="font-size: 12px; font-family: Consolas, monospace; "><br></span></div><div><span class="Apple-style-span" style="font-size: 12px; font-family: Consolas, monospace; ">--Carson</span></div><div><span class="Apple-style-span" style="font-size: 12px; font-family: Consolas, monospace; "><br></span></div><div><span class="Apple-style-span" style="font-size: 12px; font-family: Consolas, monospace; "><div><br></div></span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><br></div><span id="OLK_SRC_BODY_SECTION" style="font-size: 14px; font-family: Calibri, sans-serif; "><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 5:20 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>, "<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> Re: [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; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div><div><div>Hi Carson,</div><div>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?</div><div>Oscar</div><div><div><div>-- </div><div><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; ">Dian (Oscar) Jiao, Ph.D.,<br>
Research Associate, Life Sciences Computing Group<br>
Texas Advanced Computing Center<br>
University of Texas at Austin<br>
<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a> | (832) 303-1166</span></div></div></div></div></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>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Date: </span>Thursday, October 4, 2012 3:53 PM<br><span style="font-weight:bold">To: </span>Oscar Jiao <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>>, "<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>Re: [maker-devel] maker mpi failed<br></div><div><br></div><div><div 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><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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