#193616 mpqc has many missing libs in the linkages

Package:
mpqc
Source:
mpqc
Description:
Massively Parallel Quantum Chemistry Program
Submitter:
Jack Howarth
Date:
2014-10-27 00:21:05 UTC
Severity:
normal
#193616#5
Date:
2003-05-17 04:27:42 UTC
From:
To:
of the shared libs are missing direct linkages to libs they
are getting symbols from. A list of such libs include...

prelink: Warning: /usr/lib/libSCpsi.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCdft.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCscf.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCwfn.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCsolvent.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCintv3.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCoint3.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCbasis.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCmolecule.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCisosurf.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCoptimize.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCscmat.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCgroup.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCsymmetry.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCrender.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCmisc.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCstate.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCkeyval.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCclass.so.4 has undefined non-weak symbols
prelink: Warning: /usr/lib/libSCref.so.4 has undefined non-weak symbols

The error "has undefined non-weak symbols" is indicative of this linkage
mistake. You can look at each of these by hand and figure out the missing
libs that need to be added when each shared lib is created...

ldd -r /usr/lib/libSCcontainer.so.4
        libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x0ef20000)
        libm.so.6 => /lib/libm.so.6 (0x0fdf0000)
        libc.so.6 => /lib/libc.so.6 (0x0fe80000)
        libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x0f080000)
        /lib/ld.so.1 => /lib/ld.so.1 (0x08000000)
undefined symbol: _ZN2sc6indentERSt9basic_iosIcSt11char_traitsIcEE      (/usr/lib/libSCcontainer.so.4)
undefined symbol: _ZN2sc5ExEnv4out0Ev   (/usr/lib/libSCcontainer.so.4)

This tells us that /usr/lib/libSCcontainer.so.4 is missing a linkage against
libSCmisc.so.4.0.0 which provides the missing symbols...

nm -D libSCmisc.so.4.0.0 | grep  _ZN2sc6indentERSt9basic_iosIcSt11char_traitsIcEE
0f899f38 T _ZN2sc6indentERSt9basic_iosIcSt11char_traitsIcEE

nm -D libSCmisc.so.4.0.0 | grep  _ZN2sc5ExEnv4out0Ev
0f89eef4 T _ZN2sc5ExEnv4out0Ev

Of course all of these corrections need to be passed back upstream.
#193616#10
Date:
2003-05-17 08:53:05 UTC
From:
To:
Hi Jack,
[...]
[..]

Uhm, how do you propose I fix this? I'm not gonna hand-comb through all
those libraries and hack the already hacked-up build-system. You're free
to send a patch of course.

Would combining those libraries into three big ones (libutil, libmath,
libchemistry, along the source) help? That's something I wanted to
suggest to upstream anyway.

Michael
#193616#15
Date:
2007-05-18 18:49:04 UTC
From:
To:
tags 193616 + upstream
forwarded 193616 http://sourceforge.net/tracker/index.php?func=detail&aid=1721480&group_id=6610&atid=106610
thanks

FYI: I reported the issue to upstream.

Regards, Daniel
#193616#22
Date:
2007-05-18 18:49:04 UTC
From:
To:
tags 193616 + upstream
forwarded 193616 http://sourceforge.net/tracker/index.php?func=detail&aid=1721480&group_id=6610&atid=106610
thanks

FYI: I reported the issue to upstream.

Regards, Daniel
#193616#27
Date:
2011-12-28 16:18:03 UTC
From:
To:
user debian-gcc@lists.debian.org
usertags 193616 + ld-as-needed
thanks

any progress on this?
the missing links cause build failures with ld --as-needed [0]
See e.g. ghemical build log in ubuntu:
https://launchpadlibrarian.net/87304470/buildlog_ubuntu-precise-i386.ghemical_3.0.0-1_FAILEDTOBUILD.txt.gz

[0] http://wiki.mandriva.com/en/Underlinking
#193616#32
Date:
2011-12-29 11:42:13 UTC
From:
To:
Hi,

Not from my side, and I won't have time to look into this in the near
future.

I guess somebody needs to check all the libSC* libraries for
inter-dependencies.  Alternatively, maybe we can try to just link in all
other SC libs when linking one of them.


Michael
#193616#37
Date:
2012-01-21 12:35:25 UTC
From:
To:
the build system is a mess so I just made a minimal patch to fix
ghemicals build with as-needed. I merged it into the 11_as_needed patch.
See the attachment.
It would be great if you can apply it to the debian package even though
its not necessary in debian.

I also did some brief testing linking everything with everything, but
there seem to be circular dependencies between the libraries, so thats
won't work properly either.
#193616#42
Date:
2012-01-21 15:07:34 UTC
From:
To:
Hi,

Many thanks, applied.


Michael
#193616#47
Date:
2014-10-27 00:19:37 UTC
From:
To:
libSCbasis to liblapack to resolve dgesvd_.

[1] https://bugs.launchpad.net/ubuntu/+source/ghemical/+bug/1277718