MAKER can't find forks in @INC, but it is there

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MAKER can't find forks in @INC, but it is there

Seth_m55
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

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Re: MAKER can't find forks in @INC, but it is there

Carson Holt-2
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 <[hidden email]> 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
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: MAKER can't find forks in @INC, but it is there

Seth_m55
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 <[hidden email]> 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 <[hidden email]> 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
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



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Re: MAKER can't find forks in @INC, but it is there

Carson Holt-2
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




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Re: MAKER can't find forks in @INC, but it is there

Seth_m55
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
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Re: MAKER can't find forks in @INC, but it is there

Seth_m55
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org






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Re: MAKER can't find forks in @INC, but it is there

Fields, Christopher J
Just a note: when we install MAKER we generally install a clean version of perl if one isn’t already present, making sure it is on the NFS share for the cluster (which is accessible via all nodes).  This works around most of the issues you describe.   

chris

From: maker-devel <[hidden email]> on behalf of Seth Munholland <[hidden email]>
Date: Tuesday, February 21, 2017 at 4:26 PM
To: Carson Holt <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [maker-devel] MAKER can't find forks in @INC, but it is there

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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
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