[gmx-developers] issues with libxml detection issues with GMX_BUILD_UNITTESTS=ON

[Szilárd Páll]

On Thu, Feb 18, 2016 at 3:46 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> Hi,
>
> On Thu, Feb 18, 2016 at 3:28 PM Szilárd Páll <pall.szilard at gmail.com> wrote:
>>
>> Hi,
>>
>> Thanks for looking into this!
>>
>> I was not aware that zlib is only required if libxml2 was configured
>> with it. Unless there is an easy way to check for the libxml2
>> dependencies before the xmlTextWriterEndAttribute test is performed, I
>> have no better suggestion. Aren't there some symbols or exported
>> functions only present when libxml2 is configured with zlib?
>
>
> We could probably do that. If we adopt the tinyxml2 route, then I'd suggest
> we leave such libxml2 management issues as TODOs for if/when we add other
> code that requires functionality from libxml2.
>
>> Replacing libxml2 external dependency for this particular use-case
>> sounds useful, although it does add some code complexity and
>> maintenenace burden. However, I'm not sure the alternative requires
>> less code (especially if the BG/Q issue is a very different one than
>> what I ran into).
>
>
> If we don't end up needing libxml2 for anything else, then a bunch of code
> that we apparently don't maintain well enough currently gets to disappear,
> which is something.

If you're referring tot he CMake code that's going to disappear,
similar code (though perhaps more simple) will have to replace if we
want to be distro-friendly.

> Mark
>
>> --
>> Szilárd
>>
>>
>> On Thu, Feb 18, 2016 at 2:39 PM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>> > Hi,
>> >
>> > Yes, perhaps that call to check_library_exists can be improved, e.g. by
>> > setting CMAKE_REQUIRED_LIBRARIES for the check (see
>> > https://cmake.org/cmake/help/v3.0/module/CheckLibraryExists.html).
>> > However,
>> > it is awkward to do a good job here, because libxml2 only requires zlib
>> > if
>> > the former was configured that way, so we have a fairly large number of
>> > conditions to handle in constructing our handling (shared/static,
>> > whether
>> > either was found, whether libxml2 needs zlib or not, whether test
>> > binaries
>> > need to be built, etc.).
>> >
>> > Roland suggested https://gerrit.gromacs.org/#/c/5630/2 but I am not sure
>> > if
>> > it is related.
>> >
>> > Alternatively/also, since currently the only use for XML handling in
>> > master
>> > branch is for test reference data, I have uploaded
>> > https://gerrit.gromacs.org/#/c/5653/ to replace this use of libxml2 with
>> > a
>> > bundled copy of tinyxml2, as part of
>> > http://redmine.gromacs.org/issues/1908
>> > so that we get rid of such problematic external dependencies. These have
>> > been causing grief lately for users on BG/Q machines. I suggest we keep
>> > libxml2 detection and handling present but inactive while the future of
>> > various patches in Gerrit gets resolved.
>> >
>> > Mark
>> >
>> > On Wed, Feb 10, 2016 at 4:37 PM Szilárd Páll <pall.szilard at gmail.com>
>> > wrote:
>> >>
>> >> Hi,
>> >>
>> >> $ cmake -DGMX_PREFER_STATIC_LIBS=ON -DGMX_BUILD_UNITTESTS=ON
>> >>
>> >> [...]
>> >> -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.a
>> >> -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.a - found
>> >> -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.a (found version
>> >> "2.9.1")
>> >> -- Looking for xmlTextWriterEndAttribute in
>> >> /usr/lib/x86_64-linux-gnu/libxml2.a
>> >> -- Looking for xmlTextWriterEndAttribute in
>> >> /usr/lib/x86_64-linux-gnu/libxml2.a - not found
>> >> [...]
>> >> CMake Error at CMakeLists.txt:562 (message):
>> >>   Cannot build unit tests without libxml2.  Either set
>> >>   GMX_BUILD_UNITTESTS=OFF or tell CMake how to find a working version
>> >> of
>> >>   libxml2.
>> >>
>> >> Even though both libz and libxml are detected, the
>> >> xmlTextWriterEndAttribute lib test fails to link as the
>> >> check_library_exists() does not pass -lz.
>> >>
>> >> I vaguely remember some discussion around it so I thought I'd ask
>> >> whether this is a known issue before filing a report.
>> >>
>> >> Are there any simple workarounds for this? (I tried passing -lz in the
>> >> linker flags, but that does not help).
>> >> Could we provide a better hint in the error?
>> >>
>> >> Cheers,
>> >> --
>> >> Szilárd
>> >> --
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>> >
>> >
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>
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