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

[Seth Munholland]

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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