zlib built with EasyBuild yields "no version information available" error message when it's being used about easybuild-framework HOT 9 CLOSED

To reproduce this, load a zlib module built with EasyBuild, and then use a tool that links with both zlib and a library linked with the system zlib:

[kehoste@ca60c171 ~]$ module list
No Modulefiles Currently Loaded.
[kehoste@ca60c171 ~]$ module load zlib
[kehoste@ca60c171 ~]$ ar -V
ar: /home/kehoste/.local/easybuild/software/zlib/1.2.7-goalf-1.1.0-no-OFED/lib/libz.so.1: no version information available (required by /usr/lib64/libbfd-2.21.53.0.1-6.fc16.so)
GNU ar version 2.21.53.0.1-6.fc16 20110716

Also building libbfd is not a sensible option imho, since it's part of binutils.

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But the ar command failing had nothing to do with this?

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@JensTimmerman: ar fails in the PETSc build because of this problem. It was just an example, but it is relevant, since it links in zlib.

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#644 should fix this

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There is a possibly suitable way about how to handle this issue, mentioned in
easybuilders/easybuild-easyconfigs#985
apparently relying on LD_PRELOAD ; debate to be continued...

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OK I am adding some further information on possible zlib problems. According to this thread on the Stacks user mail list, the base system's zlib seems to be causing confusion during the ./configure process?

relevant post:

gzbuffer was added to zlib in version 1.2.4. Your compile complains
about the missing gzbuffer function, but not, say gzopen, which is
called prior to gzbuffer. This would lead me to believe that you
potentially have a second zlib.h header on your system that is being
found during compile prior to the more recent version. However, the
configure script (which runs before the compile) seems to be finding
that a newer version is on the system, enabling the use of the gzbuffer
function, which otherwise would not be included in the compile.

Specifically, I ended up fixing my problem by listing a specific zlib > 1.2.3 in easyconfig.builddependencies

...
builddependencies = [('zlib', '1.2.7'), ('SAMtools', '1.1'), ('google-sparsehash', '2.0.2')]
...

Hope this saves someone else some time or helps inform the discussion.

Gus

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We have had this zlib issue here at JSC as well, mainly stemming from the fact that compilers and linkers are picking up a (very old version of a) system-installed zlib when they are built.

This "no version information available" error seems to show up when a user tries to compile or link a program with a compiler/linker that uses the old system version, while one of the dependencies is the newer EasyBuild-installed newer version

We are dealing with it by moving zlib in the dummy/dummy toolchain as a Core package and making it a (hidden) dependency of binutils, and therefore of the compilers and linkers that are build on top of it.

-Eric

From: Augustine (Gus) Dunn [[email protected]]
Sent: Thursday, January 22, 2015 10:53 PM
To: hpcugent/easybuild-framework
Subject: Re: [easybuild-framework] zlib built with EasyBuild yields "no version information available" error message when it's being used (#108)

OK I am adding some further information on possible zlib problems. According to this threadhttps://groups.google.com/forum/#!msg/stacks-users/DJuEmm9e08k/Elm4RotNCQoJ on the Stackshttp://creskolab.uoregon.edu/stacks/ user mail list, the base system's zlib seems to be causing confusion during the ./configure process?

relevant post:

gzbuffer was added to zlib in version 1.2.4. Your compile complains
about the missing gzbuffer function, but not, say gzopen, which is
called prior to gzbuffer. This would lead me to believe that you
potentially have a second zlib.h header on your system that is being
found during compile prior to the more recent version. However, the
configure script (which runs before the compile) seems to be finding
that a newer version is on the system, enabling the use of the gzbuffer
function, which otherwise would not be included in the compile.

Specifically, I ended up fixing my problem by listing a specific zlib > 1.2.3 in easyconfig.builddependencies

...
builddependencies = [('zlib', '1.2.7'), ('SAMtools', '1.1'), ('google-sparsehash', '2.0.2')]
...

Hope this saves someone else some time or helps inform the discussion.

Gus

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Reply to this email directly or view it on GitHubhttps://github.com//issues/108#issuecomment-71106614.

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Prof. Dr. Sebastian M. Schmidt

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Potential fix is in easybuilders/easybuild-easyconfigs#1350

It would be great if somebody could test it.

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fixed by easybuilders/easybuild-easyconfigs#1350

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