[maker-devel] Problem with installation

[Carson Holt]

You may also want to look into if you need to reinstall perl on another
drive.

--Carson


From:  Carson Holt <carsonhh at gmail.com>
Date:  Wednesday, May 28, 2014 at 10:15 AM
To:  Panos Ioannidis <panos.ioannidis at gmail.com>
Cc:  Daniel Ence <dence at genetics.utah.edu>, "<maker-devel at yandell-lab.org>"
<maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Problem with installation

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.

--Carson

From:  Panos Ioannidis <panos.ioannidis at gmail.com>
Date:  Wednesday, May 28, 2014 at 10:13 AM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Daniel Ence <dence at genetics.utah.edu>, "<maker-devel at yandell-lab.org>"
<maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Problem with installation

Hello Daniel and Carson,

Thank you both for your comments.

Carson, I gave it a lot more than 30 seconds. I gave it  about 5 minutes but
still nothing happens.

Daniel, the same is true for maker -CTL; it appears as if it's doing
something, but if you give a top you'll see that the CPU usage is ALWAYS 0%.

Three things that might be helpful:
1.  Ctrl-C doesn't work for killing maker; you have to give "kill -9 <PID>"
2. when I give top I see that there are two maker processes running. Is this
normal?
3. When I press Ctrl-C, the resources in top (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.





On Wed, May 28, 2014 at 4:32 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 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.
> 
> --Carson
> 
> 
> 
> From:  Daniel Ence <dence at genetics.utah.edu>
> Date:  Wednesday, May 28, 2014 at 7:29 AM
> To:  Panos Ioannidis <panos.ioannidis at gmail.com>
> Cc:  "<maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org>
> Subject:  Re: [maker-devel] Problem with installation
> 
> 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?
> 
> Thanks,
> Daniel
> 
> 
> Daniel Ence
> Graduate Student
> dence at genetics.utah.edu
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> 
> On May 28, 2014, at 1:28 AM, Panos Ioannidis <panos.ioannidis at gmail.com>
>  wrote:
> 
>> Hello Maker community,
>> 
>> I just finished installing Maker and even though everything seems to be okay,
>> when I give
>> 
>> ./maker -h
>> 
>> or
>> 
>> ./maker
>> 
>> the program apparently hangs without giving any output or warning or error.
>> 
>> Just so you know, I have installed all dependencies (Perl libraries and
>> third-party programs) and am executing from bin/, not src/bin/.
>> 
>> Any ideas?
>> 
>> Panos
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> _______________________________________________ maker-devel mailing list
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