<div dir="ltr">Hi Carson, <span style="color:rgb(119,119,119);font-size:12.800000190734863px;white-space:nowrap">Christopher, Daniel,</span><div><span style="color:rgb(119,119,119);font-size:12.800000190734863px;white-space:nowrap"><br></span></div><div><span style="color:rgb(119,119,119);font-size:12.800000190734863px;white-space:nowrap">Thank you for your kind help.</span></div><div><span style="color:rgb(119,119,119);font-size:12.800000190734863px;white-space:nowrap"><br></span></div><div><span style="color:rgb(119,119,119);font-size:12.800000190734863px;white-space:nowrap">N</span>ow it works without any other options on one nodes and 4 CPUs. I set the number of task to 2, but there's only one contigs in running. Should it be two contigs running at the same time?<div><br></div><div>Zelin</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div>--------------------------------------------</div>Zelin Chen [<a href="mailto:chzelin@gmail.com" target="_blank">chzelin@gmail.com</a>]<br><br></div><div><br></div><div><div>NIH/NHGRI</div><div><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,sans-serif;font-size:12px">Building 50, Room 5531</span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,sans-serif;font-size:12px"><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,sans-serif;font-size:12px">50 SOUTH DR, MSC 8004 </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,sans-serif;font-size:12px"><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,sans-serif;font-size:12px">BETHESDA, MD 20892-8004</span></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Aug 15, 2017 at 11:47 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Did it die or did you just get a warning?<div><br></div><div>Here is a list of flags to add that suppress warnings and other issues with OpenMPI. You can add them all or one at a time depending on issues you get.</div><div><br></div><div>#add if MPI not using all CPU given</div><div>--oversubscribe --bind-to none</div><div><br></div><div>#workaround for infinaband (use instead of --mca ^openib)</div><div>--mca btl vader,tcp,self --mca btl_tcp_if_include ib0</div><div><br></div><div>#add to stop certain other warnings</div><div>--mca orte_base_help_aggregate 0</div><div><br></div><div>#stop fork warnings</div><div>--mca btl_openib_want_fork_support 1 --mca mpi_warn_on_fork 0</div><div><br></div><div>—Carson</div><div><br></div><div><br></div><div><br><div><blockquote type="cite"><div>On Aug 15, 2017, at 9:34 AM, zl c <<a href="mailto:chzelin@gmail.com" target="_blank">chzelin@gmail.com</a>> wrote:</div><br class="m_7520722775390369704Apple-interchange-newline"><div><div dir="ltr"><div class="gmail_extra">Here are some latest message:<div><br></div><div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">[cn3360:57176] 1 more process has sent help message help-opal-runtime.txt / opal_init:warn-fork</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">[cn3360:57176] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages</span></div></div><div><span style="font-variant-ligatures:no-common-ligatures"><br></span></div><div><div class="m_7520722775390369704m_-1862143133597923131gmail-m_5723736450607837839gmail_signature"><div dir="ltr"><div dir="ltr"><div><div>------------------------------<wbr>--------------</div>Zelin Chen [<a href="mailto:chzelin@gmail.com" target="_blank">chzelin@gmail.com</a>]<br><br></div><div><br></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Aug 15, 2017 at 10:39 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="auto"><div>You may need to delete the .../maker/perl directory before doing the reinstall if not doing a brand new installation. Otherwise you can ignore the subroutine redefined warnings during compile.</div><div><br></div><div>Have you been able to test the alternate flags on the command line for MPI? How about an alternate perl without threads?<br><br><div><div><span style="font-size:13pt">--Carson</span></div><div><br></div><div>Sent from my iPhone</div></div></div><div><br>On Aug 15, 2017, at 8:27 AM, zl c <<a href="mailto:chzelin@gmail.com" target="_blank">chzelin@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div><div dir="ltr">When I installed by './Build install', I got following some messages:<div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">Configuring MAKER with MPI support</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">Installing MAKER...</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">Configuring MAKER with MPI support</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">Subroutine dl_load_flags redefined at (eval 125) line 8.</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">Subroutine Parallel::Application::MPI::C_<wbr>MPI_ANY_SOURCE redefined at (eval 125) line 9.</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">Subroutine Parallel::Application::MPI::C_<wbr>MPI_ANY_TAG redefined at (eval 125) line 9.</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">Subroutine Parallel::Application::MPI::C_<wbr>MPI_SUCCESS redefined at (eval 125) line 9.</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">Subroutine Parallel::Application::MPI::C_<wbr>MPI_Init redefined at (eval 125) line 9.</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">Subroutine Parallel::Application::MPI::C_<wbr>MPI_Finalize redefined at (eval 125) line 9.</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">Subroutine Parallel::Application::MPI::C_<wbr>MPI_Comm_rank redefined at (eval 125) line 9.</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">Subroutine Parallel::Application::MPI::C_<wbr>MPI_Comm_size redefined at (eval 125) line 9.</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">Subroutine Parallel::Application::MPI::C_<wbr>MPI_Send redefined at (eval 125) line 9.</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">Subroutine Parallel::Application::MPI::C_<wbr>MPI_Recv redefined at (eval 125) line 9.</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">Subroutine Parallel::Application::MPI::_c<wbr>omment redefined at (eval 125) line 9.</span></div></div><div class="gmail_extra"><br></div><div class="gmail_extra">I'm not sure whether it's correctly installed.</div><div class="gmail_extra"><br></div><div class="gmail_extra">Thanks,</div><div class="gmail_extra"><br clear="all"><div><div class="m_7520722775390369704m_-1862143133597923131gmail-m_5723736450607837839m_-7744257814608198508gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div>------------------------------<wbr>--------------</div>Zelin Chen [<a href="mailto:chzelin@gmail.com" target="_blank">chzelin@gmail.com</a>]<br><br></div><div><div>NIH/NHGRI</div><div><span style="font-family:Verdana,Geneva,sans-serif;font-size:12px">Building 50, Room 5531</span><br style="font-family:Verdana,Geneva,sans-serif;font-size:12px"><span style="font-family:Verdana,Geneva,sans-serif;font-size:12px">50 SOUTH DR, MSC 8004 </span><br style="font-family:Verdana,Geneva,sans-serif;font-size:12px"><span style="font-family:Verdana,Geneva,sans-serif;font-size:12px">BETHESDA, MD 20892-8004</span></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Mon, Aug 14, 2017 at 9:23 PM, Fields, Christopher J <span dir="ltr"><<a href="mailto:cjfields@illinois.edu" target="_blank">cjfields@illinois.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
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<div class="m_7520722775390369704m_-1862143133597923131gmail-m_5723736450607837839m_-7744257814608198508m_-5812194475710527082WordSection1"><p class="MsoNormal">Carson,<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">It was attached to the initial message (named ‘run05.mpi.o47346077’). It looks like a Perl issue with threads, though I don’t see why this would crash a cluster. The fact there is a log file would suggest it just ended the job.<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">chris<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p>
<div style="border-style:solid none none;border-top-width:1pt;border-top-color:rgb(181,196,223);padding:3pt 0in 0in"><p class="MsoNormal" style="margin-left:0.5in"><b><span style="font-size:12pt">From:
</span></b><span style="font-size:12pt">maker-devel <<a href="mailto:maker-devel-bounces@yandell-lab.org" target="_blank">maker-devel-bounces@yandell-l<wbr>ab.org</a>> on behalf of Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br>
<b>Date: </b>Monday, August 14, 2017 at 2:18 PM<br>
<b>To: </b>zl c <<a href="mailto:chzelin@gmail.com" target="_blank">chzelin@gmail.com</a>><br>
<b>Cc: </b>"<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<b>Subject: </b>Re: [maker-devel] maker MPI problem<u></u><u></u></span></p>
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<div><p class="MsoNormal" style="margin-left:0.5in"><u></u> <u></u></p>
</div><p class="MsoNormal" style="margin-left:0.5in">This is rather vague —> “crashed the computer cluster”
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<div><p class="MsoNormal" style="margin-left:0.5in">Do you have a specific error?<u></u><u></u></p>
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<div><p class="MsoNormal" style="margin-left:0.5in">—Carson<u></u><u></u></p>
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<div><p class="MsoNormal" style="margin-left:0.5in">On Aug 14, 2017, at 12:59 PM, zl c <<a href="mailto:chzelin@gmail.com" target="_blank">chzelin@gmail.com</a>> wrote:<u></u><u></u></p>
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Hello,<u></u><u></u></p>
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I ran maker 3.0 with openmpi 2.0.2 and it crashed the computer cluster. I attached the log file. Could you help me to solve the problem?<u></u><u></u></p>
<div><p class="MsoNormal" style="margin-left:0.5in"> <u></u><u></u></p>
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CMD:<u></u><u></u></p><p class="MsoNormal" style="margin-left:0.5in">
export LD_PRELOAD=/usr/local/OpenMPI/<wbr>2.0.2/gcc-6.3.0/lib/libmpi.so<u></u><u></u></p><p class="MsoNormal" style="margin-left:0.5in">
export OMPI_MCA_mpi_warn_on_fork=0<u></u><u></u></p><p class="MsoNormal" style="margin-left:0.5in">
mpiexec -mca btl ^openib -n $SLURM_NTASKS maker -c 1 –base genome -g genome.fasta<u></u><u></u></p>
<div><p class="MsoNormal" style="margin-left:0.5in"> <u></u><u></u></p>
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Thanks,<u></u><u></u></p><p class="MsoNormal" style="margin-left:0.5in">
Zelin Chen<u></u><u></u></p>
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<div><p class="MsoNormal" style="margin-left:0.5in">------------------------------<wbr>--------------<u></u><u></u></p>
</div><p class="MsoNormal" style="margin-left:0.5in">Zelin Chen [<a href="mailto:chzelin@gmail.com" target="_blank">chzelin@gmail.com</a>] Ph.D.<u></u><u></u></p>
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<div><p class="MsoNormal" style="margin-left:0.5in">NIH/NHGRI<u></u><u></u></p>
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<div><p class="MsoNormal" style="margin-left:0.5in"><span style="font-size:9pt;font-family:Verdana,sans-serif">Building 50, Room 5531<br>
50 SOUTH DR, MSC 8004 <br>
BETHESDA, MD 20892-8004</span><u></u><u></u></p>
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</div><p class="MsoNormal" style="margin-left:0.5in"><run05.mpi.o47346077>_________<wbr>______________________________<wbr>________<br>
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