<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>Sorry missed the ';' at the end of the eval block.</div><div><br></div><div>Should be this --></div><div><br></div><div><div><span style="font-family: Courier; "> my $select;</span></div><div><span style="font-family: Courier; "> eval{</span></div><div><span style="font-family: Courier; "> require Proc::ProcessTable;</span></div><div><span style="font-family: Courier; "> my $obj = new Proc::ProcessTable;</span></div><div><span style="font-family: Courier; "> foreach my $p (@{$obj->table}) {</span></div><div><span class="Apple-tab-span" style="white-space: pre; font-family: Courier; "> </span><span style="font-family: Courier; "> #now check for the id </span></div><div><span style="font-family: Courier; "> if ($p->pid == $id){</span></div><div><span class="Apple-tab-span" style="white-space: pre; font-family: Courier; "> </span><span style="font-family: Courier; ">$select</span><span class="Apple-tab-span" style="white-space: pre; font-family: Courier; "> </span><span style="font-family: Courier; ">= $p;</span></div><div><span style="font-family: Courier; "><span class="Apple-tab-span" style="white-space: pre; "> </span>last;</span></div><div><span style="font-family: Courier; "> }</span></div><div><span style="font-family: Courier; "> }</span></div><div><span style="font-family: Courier; "> };</span></div><div><span style="font-family: Courier; "><br></span></div><div><span style="font-family: Courier; "> return $select;</span></div></div><div><span style="font-family: Courier; "><br></span></div><div><span style="font-family: Courier; "><br></span></div><div><span style="font-family: Courier; ">--Carson</span></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> Tue, 17 Apr 2012 13:09:32 -0400<br><span style="font-weight:bold">To: </span> Scott Geib <<a href="mailto:smg283@gmail.com">smg283@gmail.com</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] mpi issue on computing cluster<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>If it's a sharedlibs issue then 'maker -help' would cause the same error. Try that.</div><div><br></div><div><br></div><div>Are you sure that you are not worried about Signal.pm causing the error? Try changing /mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm lines 136-143 from this --></div><div><br></div><div><br></div><div><div><span style="font-family: Courier; "> require Proc::ProcessTable;</span></div><div><span style="font-family: Courier; "> my $obj = new Proc::ProcessTable;</span></div><div><span style="font-family: Courier; "> foreach my $p (@{$obj->table}) {</span></div><div><span style="font-family: Courier; "> #now check for the id </span></div><div><span style="font-family: Courier; "> return $p if ($p->pid == $id);</span></div><div><span style="font-family: Courier; "> }</span></div><div><span style="font-family: Courier; "><br></span></div><div><span style="font-family: Courier; "> return undef;</span></div></div><div><br></div><div><br></div><div><br></div><div>To this --></div><div><br></div><div><br></div><div><span style="font-family: Courier; "> my $select;</span></div><div><span style="font-family: Courier; "> eval{</span></div><div><span style="font-family: Courier; "> require Proc::ProcessTable;</span></div><div><span style="font-family: Courier; "> my $obj = new Proc::ProcessTable;</span></div><div><span style="font-family: Courier; "> foreach my $p (@{$obj->table}) {</span></div><div><span class="Apple-tab-span" style="white-space: pre; font-family: Courier; "> </span><span style="font-family: Courier; "> #now check for the id </span></div><div><span style="font-family: Courier; "> if ($p->pid == $id){</span></div><div><span class="Apple-tab-span" style="white-space: pre; font-family: Courier; "> </span><span style="font-family: Courier; ">$select</span><span class="Apple-tab-span" style="white-space: pre; font-family: Courier; "> </span><span style="font-family: Courier; ">= $p;</span></div><div><span style="font-family: Courier; "><span class="Apple-tab-span" style="white-space:pre"> </span>last;</span></div><div><span style="font-family: Courier; "> }</span></div><div><span style="font-family: Courier; "> }</span></div><div><span style="font-family: Courier; "> };</span></div><div><span style="font-family: Courier; "><br></span></div><div><span style="font-family: Courier; "> return $select;</span><span style="font-family: Courier; "> </span></div><div><br></div><div><br></div><div>If it works, I can generate a cleaner workaround, but I'd like to know If that is the root of the problem.</div><div><br></div><div>Thanks,</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> Scott Geib <<a href="mailto:smg283@gmail.com">smg283@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Fri, 13 Apr 2012 09:00:29 -1000<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] mpi issue on computing cluster<br></div><div><br></div>Hi, <br>I am trying to run maker 2.24 on a compute cluster and get the following error (not worried about Signal.pm error):<br><br>an into unknown state (hex char: 29) at /mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm line 138.<br>
Fatal error in MPI_Init: Other MPI error, error stack:<br>MPIR_Init_thread(388)........:<br>MPID_Init(139)...............: channel initialization failed<br>MPIDI_CH3_Init(49)...........: progress_init failed<br>MPIDI_CH3I_Progress_init(808): This version of MPICH requires the SIGUSR1 signal, but the application has already installed a handler<br>
[proxy:0:<a href="mailto:0@r01n11.local">0@r01n11.local</a>] HYD_pmcd_pmip_control_cmd_cb (./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed<br>[proxy:0:<a href="mailto:0@r01n11.local">0@r01n11.local</a>] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status<br>
[proxy:0:<a href="mailto:0@r01n11.local">0@r01n11.local</a>] main (./pm/pmiserv/pmip.c:208): demux engine error waiting for event<br>[proxy:0:<a href="mailto:1@r01n13.local">1@r01n13.local</a>] HYD_pmcd_pmip_control_cmd_cb (./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed<br>[proxy:0:<a href="mailto:1@r01n13.local">1@r01n13.local</a>] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status<br>
[proxy:0:<a href="mailto:1@r01n13.local">1@r01n13.local</a>] main (./pm/pmiserv/pmip.c:208): demux engine error waiting for event<br>[proxy:0:<a href="mailto:3@r07n27.local">3@r07n27.local</a>] HYD_pmcd_pmip_control_cmd_cb (./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed<br>[proxy:0:<a href="mailto:3@r07n27.local">3@r07n27.local</a>] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status<br>
[proxy:0:<a href="mailto:3@r07n27.local">3@r07n27.local</a>] main (./pm/pmiserv/pmip.c:208): demux engine error waiting for event<br>[<a href="mailto:mpiexec@r01n11.local">mpiexec@r01n11.local</a>] HYDT_bscu_wait_for_completion (./tools/bootstrap/utils/bscu_wait.c:70): one of the processes terminated badly; aborting<br>
[<a href="mailto:mpiexec@r01n11.local">mpiexec@r01n11.local</a>] HYDT_bsci_wait_for_completion (./tools/bootstrap/src/bsci_wait.c:18): launcher returned error waiting for completion<br>[<a href="mailto:mpiexec@r01n11.local">mpiexec@r01n11.local</a>] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:216): launcher returned error waiting for completion<br>
[<a href="mailto:mpiexec@r01n11.local">mpiexec@r01n11.local</a>] main (./ui/mpich/mpiexec.c:404): process manager error waiting for completion<br><br>I do not know how mpich2 was compiled, I feel this may be a --enable-sharedlibs issue? <br><br>I may need to contact my cluster support, but I thought I would try here first, <br><br>Thanks<br>
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