<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
</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>
<div>
<div>If you do reply all to this message, I should get the attachment. It will be stripped from the one going to the list though.</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Carson</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">
</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>Ramón Fallon <<a href="mailto:ramonfallon@gmail.com">ramonfallon@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Wednesday, 6 March, 2013 12:57 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>Re: thread terminated, causing all processes to fail<br>
</div>
<div><br>
</div>
Hi,
<div><br>
</div>
<div>Many thanks for your quick reply and hint.</div>
<div><br>
</div>
<div>Yes, you're right .. further up there is indeed</div>
<div><br>
</div>
<div>Calling FastaDB::new at /opt/src/maker_svn/bin/../lib/FastaSeq.pm line 148 thread 1.</div>
<div>
<div>Thread 1 terminated abnormally: ERROR: Could not reestablish DB to thaw FastaSeq for Storable</div>
<div>--> rank=5, hostname=fatnode, at /opt/src/maker_svn/bin/maker line 1457 thread 1.</div>
<div><br>
</div>
<div>I run a "script" session and have maker on -debug so I have everything in one file. Do you prefer to have it attached to a post to this mailing list (if it accepts txt attachments)</div>
<div><br>
</div>
Cheers.</div>
<div><br>
</div>
<div><br>
<div class="gmail_quote">On Wed, Mar 6, 2013 at 6:34 PM, Ramón Fallon <span dir="ltr">
<<a href="mailto:ramonfallon@gmail.com" target="_blank">ramonfallon@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,
<div><br>
</div>
<div>I'm using the maker_svn rev 995 version and hand-compiled MPICH2 on a single multicore machine.</div>
<div><br>
</div>
<div>I've successfully run the dpp_contig.fasta (MPI/8 processes) example but am having trouble with larger contigs fasta files of my own, which are well formed.</div>
<div><br>
</div>
<div>I've run into a problem whereby an mpiexec run of 8 processes will stop due to a perl-thread related problem which says</div>
<div><br>
</div>
<div>FATAL: Thread terminated, causing all processes to fail</div>
<div> </div>
<div>this corresponds to line 924 in the maker executable (which is for the secondary/worker threads), and is the result of a test on !$thr OR'd with !$thr->is_running, so clearly one of these is failing. </div>
<div><br>
</div>
<div>$thr itself is a threads->new(\&$node_thread, $gdbfile). Despite being a programmer, I've only recently started to look at the code and have not got the hang of the parallelisation setup here, though I gather the master must use threads to initially generate
the parallel instances which then use the message passing. Of course threads don't have message passing ability, so I guess something clever is going on and will take some time for me to understand. </div>
<div><br>
</div>
<div>Clearly however, it has worked before on dpp_contigs, so it may be is something wrong with my datafile or the way I am carrying out the analysis.</div>
<div><br>
</div>
<div>Any clues that can be put my way are welcome.</div>
<div><br>
</div>
<div>Thank you!</div>
</blockquote>
</div>
<br>
</div>
</span>
</body>
</html>