<div dir="ltr"><div>"ls -al" is instantaneous in all directories...<br><br></div><div>I'll try installing it on my workstation, although it's not possible to do annotation on my machine! And the machine I currently have installed it, is our server and I can't really make any big changes there.<br>
<br></div><div>Anyway, I'll let you know how it goes.<br></div><div><br></div>P<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, May 28, 2014 at 6:16 PM, 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;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div>You may also want to look into if you need to reinstall perl on another drive.</div>
<div><br></div><div>--Carson</div><div><br></div><div><br></div><span><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" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Wednesday, May 28, 2014 at 10:15 AM<br>
<span style="font-weight:bold">To: </span> Panos Ioannidis <<a href="mailto:panos.ioannidis@gmail.com" target="_blank">panos.ioannidis@gmail.com</a>><div><div class="h5"><br><span style="font-weight:bold">Cc: </span> Daniel Ence <<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>>, "<<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>
<span style="font-weight:bold">Subject: </span> Re: [maker-devel] Problem with installation<br></div></div></div><div><div class="h5"><div><br></div><div><div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif">
<div>Normally it takes 30 seconds, but if your IO response is slow (I.e. 3 seconds per query which is why you should do the 'ls -al' test), it can take several minutes because it's an IO issue.</div><div><br>
</div>
<div>--Carson</div><div><br></div><span><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> Panos Ioannidis <<a href="mailto:panos.ioannidis@gmail.com" target="_blank">panos.ioannidis@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Wednesday, May 28, 2014 at 10:13 AM<br>
<span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Daniel Ence <<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>>, "<<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>
<span style="font-weight:bold">Subject: </span> Re: [maker-devel] Problem with installation<br></div><div><br></div><div dir="ltr"><div><div><div><div><div><div>Hello Daniel and Carson,<br><br></div>Thank you both for your comments.<br>
<br></div>Carson, I gave it a lot more than 30 seconds. I gave it about 5 minutes but still nothing happens.<br><br></div>Daniel, the same is true for <span style="font-family:'courier new',monospace">maker -CTL</span>; it appears as if it's doing something, but if you give a <span style="font-family:'courier new',monospace">top</span> you'll see that the CPU usage is ALWAYS 0%.<br>
<br></div>Three things that might be helpful:<br>1. Ctrl-C doesn't work for killing maker; you have to give "kill -9 <PID>"<br></div>2. when I give <span style="font-family:'courier new',monospace">top</span> I see that there are two maker processes running. Is this normal?<br>
</div>3. When I press Ctrl-C, the resources in <span style="font-family:'courier new',monospace">top</span> (labeled VIRT, RES and SHR - I guess that's memory) for one of the two maker processes go to zero, but it doesn't go away.<br>
<br><br><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, May 28, 2014 at 4:32 PM, 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;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div>Perl is a scripting language rather than a compiled language, and one thing that happens when you first use a new module or script Is that the interpreter follows the dependency tree validating that everything executes/loads correctly. Since you installed a number of dependencies and MAKER itself, the first time you launch MAKER Perl has to do this check on the dependency tree. This only happens the first time, and after that Perl remembers it already ran the check so the dependencies and MAKER will just start from then on. Normally this proccess takes less than 30 seconds; however, on some systems (especially clusters) there may a heavy IO burden and this process can take a while. For example does it take a moment for 'ls -al' to return in some directories rather than returning instantaneously like it is supposed to? If it takes 3 seconds to return or example, then each dependency check may take up to 3 seconds. If you just installed a bunch of new perl modules then there may be a hundred or more dependencies that may have to be validated for the first time.</div>
<div><br></div><div>--Carson</div><div><br></div><div><br></div><div><br></div><span><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> Daniel Ence <<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Date: </span> Wednesday, May 28, 2014 at 7:29 AM<br>
<span style="font-weight:bold">To: </span> Panos Ioannidis <<a href="mailto:panos.ioannidis@gmail.com" target="_blank">panos.ioannidis@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> "<<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>
<span style="font-weight:bold">Subject: </span> Re: [maker-devel] Problem with installation<br></div><div><div><div><br></div><div><div style="word-wrap:break-word">
Hi Panos, When you go to the src directory and type "./Build status", what message do you get? Also, what version of maker are you running?
<div><br></div><div>Thanks,</div><div>Daniel</div><div><br></div><div><br><div><div><span style="font-family:Tahoma;font-size:small">Daniel Ence</span></div><div><span style="font-family:Tahoma;font-size:small">Graduate Student</span></div>
<div><a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a><br style="font-family:Tahoma;font-size:small"><span style="font-family:Tahoma;font-size:small">Eccles Institute of Human Genetics</span><br style="font-family:Tahoma;font-size:small">
<span style="font-family:Tahoma;font-size:small">University of Utah</span><br style="font-family:Tahoma;font-size:small"><span style="font-family:Tahoma;font-size:small">15 North 2030 East, Room 2100</span><br style="font-family:Tahoma;font-size:small">
<span style="font-family:Tahoma;font-size:small">Salt Lake City, UT 84112-5330</span></div></div><br><div><div>On May 28, 2014, at 1:28 AM, Panos Ioannidis <<a href="mailto:panos.ioannidis@gmail.com" target="_blank">panos.ioannidis@gmail.com</a>></div>
<div> wrote:</div><br><blockquote type="cite"><div dir="ltr"><div><div><div><div><div><div><div><div>Hello Maker community,<br><br></div>
I just finished installing Maker and even though everything seems to be okay, when I give<br><br></div><span style="font-family:'courier new',monospace">./maker -h</span><br><br></div>
or<br><br></div><span style="font-family:'courier new',monospace">./maker</span><br><br></div>
the program apparently hangs without giving any output or warning or error.<br><br></div>
Just so you know, I have installed all dependencies (Perl libraries and third-party programs) and am executing from
<span style="font-family:'courier new',monospace">bin/</span>, not <span style="font-family:'courier new',monospace">
src/bin/</span>.<br><br></div>
Any ideas?<br><br></div>
Panos<br></div>
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