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Hi,
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.
Regarding gromacs-2016 not using libxml2, running "ldd gmx"
gives:
linux-vdso.so.1 => (0x00007fffa35ff000)
libhwloc.so.5 => /opt/pkg/2015Q2/lib/libhwloc.so.5
(0x00007f6604273000)
libz.so.1 => /opt/pkg/2015Q2/lib/libz.so.1
(0x00007f660405e000)
librt.so.1 => /lib64/librt.so.1 (0x00007f6603e42000)
libblas.so.4 => /opt/pkg/2015Q2/lib/libblas.so.4
(0x00007f6603bf2000)
liblapack.so.4 => /opt/pkg/2015Q2/lib/liblapack.so.4
(0x00007f6603390000)
libpthread.so.0 => /lib64/libpthread.so.0
(0x00007f6603173000)
libstdc++.so.6 =>
/opt/pkg/2015Q2/gcc49/x86_64-redhat-linux/lib/../lib64/libstdc++.so.6
(0x00007f6602e60000)
libm.so.6 => /lib64/libm.so.6 (0x00007f6602bdc000)
libgomp.so.1 =>
/opt/pkg/2015Q2/gcc49/x86_64-redhat-linux/lib/../lib64/libgomp.so.1
(0x00007f66029c6000)
libgcc_s.so.1 =>
/opt/pkg/2015Q2/gcc49/x86_64-redhat-linux/lib/../lib64/libgcc_s.so.1
(0x00007f66027af000)
libc.so.6 => /lib64/libc.so.6 (0x00007f660241b000)
libxml2.so.2 => /opt/pkg/2015Q2/lib/libxml2.so.2
(0x00007f66020be000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f6601eb9000)
liblzma.so.5 => /opt/pkg/2015Q2/lib/liblzma.so.5
(0x00007f6601c94000)
/lib64/ld-linux-x86-64.so.2 (0x00007f66044a0000)
libgfortran.so.3 =>
/opt/pkg/2015Q2/gcc49/x86_64-redhat-linux/lib/../lib64/libgfortran.so.3
(0x00007f6601977000)
libquadmath.so.0 =>
/opt/pkg/2015Q2/gcc49/lib/../lib64/libquadmath.so.0
(0x00007f6601739000)
Note the reference to libxml2.so.2.
Quentin
On 19/08/16 21:45, Justin Lemkul wrote:
On 8/18/16 8:44 PM, Victor Rosas Garcia wrote:
I thought
the "build" directory had to be *outside* the gromacs source
directory. Don't know for sure if that makes a difference.
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.
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.
-Justin
2016-08-18
18:20 GMT-05:00 Quentin Kaas <[email protected]>:
Hi Mark,
Thank you for your answer. I just have redone again everything
but I get
the same problem. I am not even compiling with MPI or GPU
support and I
have the same.
Hereis my procedure:
"""
tar xzvf gromacs-2016.tar.gz
cd gromacs-2016
mkdir build
cd build/
cmake -DGMX_GPU=OFF -DGMX_MPI=OFF
-DCMAKE_INSTALL_PREFIX=/home/
q.kaas/share/gromacs-2016_nompi/ -DGMX_BUILD_OWN_FFTW=ON
-DBUILD_SHARED_LIBS=OFF -DGMX_SIMD=AVX_256 ..
nice -20 make -j 2
"""
And the answer is the same:
"""
(...)
[100%] Built target libgromacs
Linking CXX executable ../../bin/template
/opt/pkg/2015Q2/lib/libxml2.so.2: undefined reference to
`gzopen64'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all]
Error 2
make: *** [all] Error
"""
What is this "template" doing? Could that be coming from this
binary?
There is no such thing in 5.1.3.
Thank you
Quentin
On 18/08/16 22:17, Mark Abraham wrote:
Hi,
GROMACS 2016 doesn't use libxml2 at all, so it looks like
there's something
strange going on with how you've done that build, because
there's no way
the template can have such a linking dependency.
Mark
On Thu, Aug 18, 2016 at 2:43 AM Quentin Kaas
<[email protected]> <[email protected]>
wrote:
Hello,
I just tried building Gromacs2016. The build went fine until
it reached
the linking stage:
linking CXX executable ../../bin/template
/opt/pkg/2015Q2/lib/libxml2.so.2: undefined reference to
`gzopen64'
collect2: error: ld returned 1 exit status
make[1]: *** [bin/template] Error 1
make: *** [share/template/CMakeFiles/template.dir/all] Error 2
Could someone help me tell cmake to tell ld where the zlib
library is?
I compiled Gromacs-5.1.3 about 10 min before trying the new
2016 version
and it went without any complaint. There might be something to
fix in the
2016 version?
Best wishes
Quentin
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Level 2 North, Building 80, The University of Queensland,
Brisbane QLD
4072, Australia
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http://researchers.uq.edu.au/researcher/1804
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