Perl on Ubuntu 16.04 does not inherit exported shell functions

[junghans]

The perl behavior on Ubuntu 16.04 (perl-5.22.2-1) has changed:

$ bash
$ fct() { echo "Hello from within function";}
$ export -f fct
$ perl -e '$x=`bash -c "fct"`; print $x'
bash: fct: command not found

In contrast in early versions (e.g. Ubuntu 14.04):

$ bash
$ fct() { echo "Hello from within function";}
$ export -f fct
$ perl -e '$x=`bash -c "fct"`; print $x'
Hello from within function

However on Fedora 23 (perl-5.22.1) and Gentoo (perl-5.22.2) it works as expected.

This was found by a user here: https://groups.google.com/d/msg/votca/MnIiwjO3iC4/ceda5If3AgAJ

[junghans]

Debian upstream bug report: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824511

[shadowcat-mst]

Have you checked this isn't actually some sort of anti-shellshock-like-things mitigation in the shell rather than something specific to the perl build?

[junghans]

It could well be something in bash itself, but hopefully Debian's Perl maintainer (@ntyni) will know.

[junghans]

@shadowcat-mst, good guess as @ntyni point out in #824511, this actually a problem in dash, which is used as /bin/sh, the issue is already reported as https://bugs.debian.org/814358!

A workaround is:

sudo ln -fs bash /bin/sh

[junghans]

Over a year later and the bug in debian is still not fixed, maybe we should just change the 5 affected perl scripts (kbibi_ramp_correction.pl, lj_126.pl, pressure_cor_simple.pl,
pressure_cor_wjk.pl and of course update_ibi_pot.pl) to not call csg_get_interaction_property() and csg_get_property() anymore.

[abrukhno]

Looks like it might be a bit more complicated than just csg_get_property() for kBT:
(but I certainly support the move!)

inverse $ git grep csg_get *pl
kbibi_ramp_correction.pl:my $kbt=csg_get_property("cg.inverse.kBT");
kbibi_ramp_correction.pl:my $int_start=csg_get_interaction_property("inverse.post_update_options.kbibi.start");
kbibi_ramp_correction.pl:my $int_stop=csg_get_interaction_property("inverse.post_update_options.kbibi.stop");
kbibi_ramp_correction.pl:my $ramp_factor=csg_get_interaction_property("inverse.post_update_options.kbibi.factor");
kbibi_ramp_correction.pl:my $r_min=csg_get_interaction_property("min");
kbibi_ramp_correction.pl:my $r_max=csg_get_interaction_property("max");
kbibi_ramp_correction.pl:my $delta_r=csg_get_interaction_property("step");
kbibi_ramp_correction.pl:my $r_ramp=csg_get_interaction_property("--allow-empty","inverse.post_update_options.kbibi.r_ramp");
lj_126.pl:my $max=csg_get_interaction_property("max");
lj_126.pl:my $min=csg_get_interaction_property("min");
lj_126.pl:my $delta_r=csg_get_interaction_property("step");
lj_126.pl:my $c12=csg_get_interaction_property("inverse.post_update_options.lj.c12");
lj_126.pl:my $c6=csg_get_interaction_property("inverse.post_update_options.lj.c6");
pressure_cor_simple.pl:my $kBT=csg_get_property("cg.inverse.kBT");
pressure_cor_simple.pl:my $max=csg_get_interaction_property("max");
pressure_cor_simple.pl:my $min=csg_get_interaction_property("min");
pressure_cor_simple.pl:my $delta_r=csg_get_interaction_property("step");
pressure_cor_simple.pl:my $scale_factor=csg_get_interaction_property("inverse.post_update_options.pressure.simple.scale");
pressure_cor_simple.pl:my $p_target=csg_get_interaction_property("inverse.p_target");
pressure_cor_wjk.pl:my $kBT=csg_get_property("cg.inverse.kBT");
pressure_cor_wjk.pl:my $max=csg_get_interaction_property("max");
pressure_cor_wjk.pl:my $min=csg_get_interaction_property("min");
pressure_cor_wjk.pl:my $delta_r=csg_get_interaction_property("step");
pressure_cor_wjk.pl:my $partDens=csg_get_interaction_property("inverse.particle_dens");
pressure_cor_wjk.pl:my $name=csg_get_interaction_property("name");
pressure_cor_wjk.pl:my $scale_factor=csg_get_interaction_property("inverse.post_update_options.pressure.wjk.scale");
pressure_cor_wjk.pl:my $p_target=csg_get_interaction_property("inverse.p_target");
skeleton.pl:my $kBT=csg_get_property("cg.inverse.kBT");
update_ibi_pot.pl:#my $pref=csg_get_property("cg.inverse.kBT");

[junghans]

I am on it - #218

[tdthatcher]

This bug seems to still persist in the ubuntu 18.04 package, votca-csg/bionic 1.4.1-1build1, but it looks like it's fixed in the 1.5 release in 19.04. Are there any plans for an 18.04 stable-release-update to the package to fix this? Otherwise, that leaves the 18.04 package fundamentally flawed...

[junghans]

Please ask the Ubuntu package maintainer to bump the version in 18.04, otherwise, sudo ln -fs bash /bin/sh.

[tdthatcher]

Please ask the Ubuntu package maintainer to bump the version in 18.04, otherwise, sudo ln -fs bash /bin/sh.

Thanks for the reply. That workaround isn't something viable in my environment, so I'll get ahold of the package maintainers.