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<p>Hi,</p>
<p>I finally succeeded to build gromacs 2016, there was indeed an
issue with two zlib libraries installed in at different folder. I
had to modify the link.txt to add a path to the more recent
libraries (the path was set in environment variable but for some
reason was not considered by cmake). Once again, when I compile
5.1.3 (or previous versions) I never encountered this issue.<br>
</p>
<p>Regarding gromacs-2016 not using libxml2, running "ldd gmx"
gives:</p>
<p> linux-vdso.so.1 => (0x00007fffa35ff000)<br>
libhwloc.so.5 => /opt/pkg/2015Q2/lib/libhwloc.so.5
(0x00007f6604273000)<br>
libz.so.1 => /opt/pkg/2015Q2/lib/libz.so.1
(0x00007f660405e000)<br>
librt.so.1 => /lib64/librt.so.1 (0x00007f6603e42000)<br>
libblas.so.4 => /opt/pkg/2015Q2/lib/libblas.so.4
(0x00007f6603bf2000)<br>
liblapack.so.4 => /opt/pkg/2015Q2/lib/liblapack.so.4
(0x00007f6603390000)<br>
libpthread.so.0 => /lib64/libpthread.so.0
(0x00007f6603173000)<br>
libstdc++.so.6 =>
/opt/pkg/2015Q2/gcc49/x86_64-redhat-linux/lib/../lib64/libstdc++.so.6
(0x00007f6602e60000)<br>
libm.so.6 => /lib64/libm.so.6 (0x00007f6602bdc000)<br>
libgomp.so.1 =>
/opt/pkg/2015Q2/gcc49/x86_64-redhat-linux/lib/../lib64/libgomp.so.1
(0x00007f66029c6000)<br>
libgcc_s.so.1 =>
/opt/pkg/2015Q2/gcc49/x86_64-redhat-linux/lib/../lib64/libgcc_s.so.1
(0x00007f66027af000)<br>
libc.so.6 => /lib64/libc.so.6 (0x00007f660241b000)<br>
libxml2.so.2 => /opt/pkg/2015Q2/lib/libxml2.so.2
(0x00007f66020be000)<br>
libdl.so.2 => /lib64/libdl.so.2 (0x00007f6601eb9000)<br>
liblzma.so.5 => /opt/pkg/2015Q2/lib/liblzma.so.5
(0x00007f6601c94000)<br>
/lib64/ld-linux-x86-64.so.2 (0x00007f66044a0000)<br>
libgfortran.so.3 =>
/opt/pkg/2015Q2/gcc49/x86_64-redhat-linux/lib/../lib64/libgfortran.so.3
(0x00007f6601977000)<br>
libquadmath.so.0 =>
/opt/pkg/2015Q2/gcc49/lib/../lib64/libquadmath.so.0
(0x00007f6601739000)<br>
</p>
<br>
Note the reference to libxml2.so.2.<br>
<br>
Quentin<br>
<br>
<div class="moz-cite-prefix">On 19/08/16 21:45, Justin Lemkul wrote:<br>
</div>
<blockquote class=" cite"
id="mid_8a9af04b_4fe8_86ac_deb5_bbffa42403ff_vt_edu"
cite="mid:8a9af04b-4fe8-86ac-deb5-bbffa42403ff@vt.edu" type="cite">
<br>
<br>
On 8/18/16 8:44 PM, Victor Rosas Garcia wrote:
<br>
<blockquote class=" cite" id="Cite_3091238" type="cite">I thought
the "build" directory had to be *outside* the gromacs source
<br>
directory. Don't know for sure if that makes a difference.
<br>
<br>
</blockquote>
<br>
No, the build directory can be wherever you like, and building
within source is fine (and recommended in the install guide). One
should not *install* within the source as that generates problems.
<br>
<br>
The full CMake output would be helpful here, as clearly the build
process is doing something it shouldn't, but that is probably
specific to the system in question, because as Mark said, it is
not anticipated that GROMACS should be throwing this sort of
error.
<br>
<br>
-Justin
<br>
<br>
<blockquote class=" cite" id="Cite_6272208" type="cite">2016-08-18
18:20 GMT-05:00 Quentin Kaas <a class="moz-txt-link-rfc2396E" href="mailto:q.kaas@imb.uq.edu.au"><q.kaas@imb.uq.edu.au></a>:
<br>
<br>
<blockquote class=" cite" id="Cite_6490626" type="cite">Hi Mark,
<br>
<br>
Thank you for your answer. I just have redone again everything
but I get
<br>
the same problem. I am not even compiling with MPI or GPU
support and I
<br>
have the same.
<br>
<br>
Hereis my procedure:
<br>
"""
<br>
tar xzvf gromacs-2016.tar.gz
<br>
cd gromacs-2016
<br>
mkdir build
<br>
cd build/
<br>
cmake -DGMX_GPU=OFF -DGMX_MPI=OFF
-DCMAKE_INSTALL_PREFIX=/home/
<br>
q.kaas/share/gromacs-2016_nompi/ -DGMX_BUILD_OWN_FFTW=ON
<br>
-DBUILD_SHARED_LIBS=OFF -DGMX_SIMD=AVX_256 ..
<br>
nice -20 make -j 2
<br>
"""
<br>
<br>
And the answer is the same:
<br>
<br>
"""
<br>
(...)
<br>
[100%] Built target libgromacs
<br>
Linking CXX executable ../../bin/template
<br>
/opt/pkg/2015Q2/lib/libxml2.so.2: undefined reference to
`gzopen64'
<br>
collect2: error: ld returned 1 exit status
<br>
make[2]: *** [bin/template] Error 1
<br>
make[1]: *** [share/template/CMakeFiles/template.dir/all]
Error 2
<br>
make: *** [all] Error
<br>
"""
<br>
<br>
What is this "template" doing? Could that be coming from this
binary?
<br>
There is no such thing in 5.1.3.
<br>
<br>
Thank you
<br>
Quentin
<br>
<br>
<br>
<br>
On 18/08/16 22:17, Mark Abraham wrote:
<br>
<br>
Hi,
<br>
<br>
GROMACS 2016 doesn't use libxml2 at all, so it looks like
there's something
<br>
strange going on with how you've done that build, because
there's no way
<br>
the template can have such a linking dependency.
<br>
<br>
Mark
<br>
<br>
On Thu, Aug 18, 2016 at 2:43 AM Quentin Kaas
<a class="moz-txt-link-rfc2396E" href="mailto:q.kaas@imb.uq.edu.au"><q.kaas@imb.uq.edu.au></a> <a class="moz-txt-link-rfc2396E" href="mailto:q.kaas@imb.uq.edu.au"><q.kaas@imb.uq.edu.au></a>
wrote:
<br>
<br>
<br>
Hello,
<br>
<br>
I just tried building Gromacs2016. The build went fine until
it reached
<br>
the linking stage:
<br>
<br>
linking CXX executable ../../bin/template
<br>
/opt/pkg/2015Q2/lib/libxml2.so.2: undefined reference to
`gzopen64'
<br>
collect2: error: ld returned 1 exit status
<br>
make[1]: *** [bin/template] Error 1
<br>
make: *** [share/template/CMakeFiles/template.dir/all] Error 2
<br>
<br>
Could someone help me tell cmake to tell ld where the zlib
library is?
<br>
<br>
I compiled Gromacs-5.1.3 about 10 min before trying the new
2016 version
<br>
and it went without any complaint. There might be something to
fix in the
<br>
2016 version?
<br>
<br>
Best wishes
<br>
<br>
Quentin
<br>
--
<br>
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--
<br>
*Dr Quentin Kaas*
<br>
<br>
Institute for Molecular Bioscience (IMB)
<br>
Level 2 North, Building 80, The University of Queensland,
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<br>
4072, Australia
<br>
F: +61 7 3346 2021
<br>
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</blockquote>
</blockquote>
<br>
</blockquote>
<br>
<div class="moz-signature">-- <br>
<small>
<font color="#000099"><b>Dr Quentin Kaas</b></font><br>
<br>
<font color="#6633ff">Institute for Molecular Bioscience (IMB)</font><br>
<font color="#9999ff">
Level 2 North, Building 80, The University of Queensland,
Brisbane QLD 4072, Australia<br>
F: +61 7 3346 2021<br>
</font>
<br>
<font color="#3333ff">
<a href="http://researchers.uq.edu.au/researcher/1804">http://researchers.uq.edu.au/researcher/1804</a><br>
<a href="http://www.conoserver.org/">http://www.conoserver.org/</a><br>
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