[maker-devel] MAKER can't find forks in @INC, but it is there

Seth Munholland munholl at uwindsor.ca
Tue Feb 21 15:26:23 MST 2017 

I found my errors.

1) In my machine file; the first entry was not the main node, so locate was
looking on a different node than Maker
2) forks (and other modules) were not properly installed on every node in
the cluster.  I used CPAN to install them on each cluster and it is now
working.

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

On Tue, Feb 21, 2017 at 1:05 PM, Seth Munholland <munholl at uwindsor.ca>
wrote:

> I wasn't sure what modules were separated (figured it was wroth a shot),
> however, I did the force install of forks and I still get the same error.
> I tried uninstalling and reinstalling all the forks installations that
> showed up and commented out the PERL5LIB export I had in my ~/.bashrc (then
> reloaded) to make sure I wasn't getting some kind of conflicting
> libraries/modules. and I'm back to:
>
> Can't locate forks.pm in @INC (you may need to install the forks module)
> (@INC contains: /Data/Apps/maker/bin/../perl/lib
> /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib
> /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
> /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
> /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22
> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at
> /Data/Apps/maker/bin/maker line 42.
> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
>
> along with:
>
> $ sudo updatedb
> $ locate forks.pm
> /home/seth/.cpan/build/forks-0.36-0/blib/lib/forks.pm
> /home/seth/.cpan/build/forks-0.36-0/lib/forks.pm
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/forks.pm
>
> Now it's a maker issue, not a forks issue (if I'm reading it correctly),
> so I reinstalled Maker (made sure to direct to mpicc and mpi.h properly)
> and got:
>
> $ sudo ./Build install
> Installing MAKER...
> Configuring MAKER with MPI support
> Skip /Data/Apps/maker/src/../perl/config-x86_64-linux-gnu-thread-multi-5.022001
> (unchanged)
>
> I don't believe that's an error or even a warning, but I get the same
> "can't locate forks" error when I try to run it.
>
>
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: (519) 253-3000 Ext: 4755
>
> On Tue, Feb 21, 2017 at 12:19 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> forks::signals is part of forks. It’s not a separate package. If it’s
>> missing, there is a problem with the forks installation. So you need to do
>> a force install of forks to force the reinstall.
>>
>> Example —>         cpan[1]> force install forks
>>
>> —Carson
>>
>>
>> On Feb 21, 2017, at 10:17 AM, Seth Munholland <munholl at uwindsor.ca>
>> wrote:
>>
>> I tried this and still get the same error.  Then I tried forcing a
>> reinstall of forks/signals and got:
>>
>> cpan[1]> install forks::signals
>> Warning: Cannot install forks::signals, don't know what it is.
>> Try the command
>>
>>     i /forks::signals/
>>
>> to find objects with matching identifiers.
>>
>> but scrolling through the install scroll of the forks reinstall I do see
>> it got installed properly.
>>
>>
>> Seth Munholland, B.Sc.
>> Department of Biological Sciences
>> Rm. 304 Biology Building
>> University of Windsor
>> 401 Sunset Ave. N9B 3P4
>> T: (519) 253-3000 Ext: 4755
>>
>> On Fri, Feb 17, 2017 at 3:39 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>
>>> Do a force reinstall of forks via CPAN. The error is coming from
>>> forks.pm line 83, so the problem is the forks installation itself.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>> On Feb 17, 2017, at 1:11 PM, Seth Munholland <munholl at uwindsor.ca>
>>> wrote:
>>>
>>> Hi Everyone,
>>>
>>> After sorting my MPICH/OpenMPI issue I have come across another: When I
>>> try to run MAKER on the demo data via
>>>
>>> $ mpiexec -machinefile /Data/machinefile -n 4 /Data/Apps/maker/bin/maker
>>> /Data/Apps/maker/data/maker_exe.ctl /Data/Apps/maker/data/maker_opts.ctl
>>> /Data/Apps/maker/data/maker_bopts.ctl
>>>
>>> (-n 4 because I have 4 nodes in my MPI cluster and I wanted to get it
>>> working before opening up, if I change the -n value then the error repeats
>>> once for each process I attempt to run via MPICH) I got the following:
>>>
>>> Can't locate forks.pm in @INC (you may need to install the
>>> forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib
>>> /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib
>>> /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
>>> /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
>>> /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
>>> /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base
>>> .) at forks.pm line 83.
>>> BEGIN failed--compilation aborted at forks.pm line 84.
>>> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
>>> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
>>> Undefined subroutine &threads::_END called at (eval 2) line 1.
>>> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
>>> Can't locate forks.pm in @INC (you may need to install the
>>> forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib
>>> /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib
>>> /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
>>> /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
>>> /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
>>> /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base
>>> .) at forks.pm line 83.
>>> BEGIN failed--compilation aborted at forks.pm line 84.
>>> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
>>> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
>>> Undefined subroutine &threads::_END called at (eval 2) line 1.
>>> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
>>> Can't locate forks.pm in @INC (you may need to install the
>>> forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib
>>> /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib
>>> /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
>>> /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
>>> /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
>>> /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base
>>> .) at forks.pm line 83.
>>> BEGIN failed--compilation aborted at forks.pm line 84.
>>> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
>>> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
>>> Undefined subroutine &threads::_END called at (eval 2) line 1.
>>> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
>>> Can't locate forks.pm in @INC (you may need to install the
>>> forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib
>>> /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib
>>> /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
>>> /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
>>> /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
>>> /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base
>>> .) at forks.pm line 83.
>>> BEGIN failed--compilation aborted at forks.pm line 84.
>>> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
>>> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
>>> Undefined subroutine &threads::_END called at (eval 2) line 1.
>>> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
>>>
>>> However I also see
>>> $ locate forks.pm
>>> /home/seth/.cpan/build/forks-0.36-0/blib/lib/forks.pm
>>> /home/seth/.cpan/build/forks-0.36-0/lib/forks.pm
>>> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/forks.pm
>>>
>>> Since /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 is in INC I initially
>>> thought this was a Perl error.  I hit up perlmonks and found that there is
>>> an issue between forks and Storable, where Storable now has a verion number
>>> of X.Y_Z but forks is only looking for X.Y (no _Z).  I followed these
>>> instructions https://rt.cpan.org/Public/Bug/Display.html?id=102730 and
>>> tried again.  Now I get:
>>>
>>> $ mpiexec -machinefile /Data/machinefile -n 4 /Data/Apps/maker/bin/maker
>>> /Data/Apps/maker/data/maker_exe.ctl /Data/Apps/maker/data/maker_opts.ctl
>>> /Data/Apps/maker/data/maker_bopts.ctl
>>> Can't locate forks/signals.pm in @INC (you may need to install the
>>> forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib
>>> /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib
>>> /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
>>> /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
>>> /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
>>> /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base
>>> .) at forks.pm line 83.
>>> BEGIN failed--compilation aborted at forks.pm line 84.
>>> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
>>> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
>>> Undefined subroutine &threads::_END called at (eval 2) line 1.
>>> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
>>> Can't locate forks/signals.pm in @INC (you may need to install the
>>> forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib
>>> /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib
>>> /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
>>> /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
>>> /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
>>> /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base
>>> .) at forks.pm line 83.
>>> BEGIN failed--compilation aborted at forks.pm line 84.
>>> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
>>> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
>>> Undefined subroutine &threads::_END called at (eval 2) line 1.
>>> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
>>> Can't locate forks/signals.pm in @INC (you may need to install the
>>> forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib
>>> /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib
>>> /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
>>> /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
>>> /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
>>> /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base
>>> .) at forks.pm line 83.
>>> BEGIN failed--compilation aborted at forks.pm line 84.
>>> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
>>> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
>>> Undefined subroutine &threads::_END called at (eval 2) line 1.
>>> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
>>> Can't locate forks/signals.pm in @INC (you may need to install the
>>> forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib
>>> /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib
>>> /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
>>> /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
>>> /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
>>> /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base
>>> .) at forks.pm line 83.
>>> BEGIN failed--compilation aborted at forks.pm line 84.
>>> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
>>> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
>>> Undefined subroutine &threads::_END called at (eval 2) line 1.
>>> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
>>>
>>> Clearly MAKER has an issue with forks, but it is installed, it is up to
>>> date (I double checked via cpan and apt-get to be sure), and it is in a
>>> directory that is in @INC.  Should I pursue this as a MAKER error or as a
>>> Perl error?
>>>
>>> Seth Munholland, B.Sc.
>>> Department of Biological Sciences
>>> Rm. 304 Biology Building
>>> University of Windsor
>>> 401 Sunset Ave. N9B 3P4
>>> T: (519) 253-3000 Ext: 4755
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>>
>>
>>
>
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