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

[Mark Abraham]

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.

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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