[gmx-users] gromacs-5.1.1 installation error: libxml2 problem

Thu Feb 11 18:52:31 CET 2016

No, I'm not sure. As a matter of fact I was not able to  find source of libxml2-devel  (+xz-devel, +zlib-devel)  (tar.gz)  for this arch to install it as a user. You might be right on this comment.
Thank you.

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Smith, Micholas D.
Sent: Thursday, February 11, 2016 11:33 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

Quick clarifying question, are you sure you have the development version of the libxml2 package (the source with the headers and everything)?

Also this might be a good time to complain to your sys-admin to install the libxml2-dev library, as it is used in a lot of other programs too, and you would just be saving everyone a headache.

===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Irina Kosheleva <ikoshelev at cars.uchicago.edu>
Sent: Thursday, February 11, 2016 12:08 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] gromacs-5.1.1 installation error:  libxml2 problem

Dear gmx-users.
I would like to install gromacs-5.1.1 on a cluster where I have only user privileges. The machine has arch linux-rhel_6-ppc64.
I would like to install it with unittest support thus I need libxml2.a compiled library.
The cluster does not have this library installed so I have downloaded libxml2-2.9.2 and compiled it with zlib support:
 ./configure --prefix=/home/ikosh/programs/autotools-bin --with-python-install-dir=/home/ikosh/programs/autotools-bin --with-zlib=/soft/libraries/alcf/current/xl/ZLIB

Now, I would like to use this static libxml2.a library to compile gromacs-5.1.1:
cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX -DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/include -DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfftw3f.a -DLIBXML2_INCLUDE_DIR=/gpfs/vesta-home/ikosh/programs/autotools-bin/include  -DLIBXML2_LIBRARIES=/gpfs/vesta-home/ikosh/programs/autotools-bin/lib/libxml2.a -DZLIB_INCLUDE_DIR=/soft/libraries/soft/libraries/alcf/current/xl/ZLIB/include -DZLIB=/soft/libraries/alcf/current/xl/ZLIB/lib/libz.a    -DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON  -DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp" -DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install

--output  just the error:
-- Looking for xmlTextWriterEndAttribute in /home/ikosh/programs/autotools-bin/lib/libxml2.a
-- Looking for xmlTextWriterEndAttribute in /home/ikosh/programs/autotools-bin/lib/libxml2.a - not found
CMake Warning at CMakeLists.txt:543 (message):
  libxml2 not found.  Will build GROMACS without unit-tests.  This is not
  recommended, because the unit-tests help to verify that GROMACS functions
  correctly.  Most likely you are missing the libxml2-dev(el) package.  After
  you installed it, set GMX_BUILD_UNITTESTS=ON.

Looking at the CMakeError.log in CMakeFiles:
/soft/buildtools/cmake/3.3.0/bin/cmake -E cmake_link_script CMakeFiles/cmTC_09bc5.dir/link.txt --verbose=1
/soft/compilers/wrappers/xl/mpixlc_r  -Wl,-relax -O3 -qsmp=omp -qarch=qp -qtune=qp -qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-03
0 -qlanglvl=extc99 -qarch=auto -qtune=auto  -DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute    CMakeFiles/cmTC_09bc5.dir/CheckFunctionExist
s.c.o  -o cmTC_09bc5  /home/ikosh/programs/autotools-bin/lib/libxml2.a
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function `xmlGzfileOpenW':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1275: undefined reference to `gzopen64'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1246: undefined reference to `gzdopen'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function `__xmlParserInputBufferCreateFilename':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:2670: undefined reference to `gzdirect'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function `xmlFreeZMemBuff':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1556: undefined reference to `deflateEnd'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function `xmlGzfileOpen_real':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1167: undefined reference to `gzdopen'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1198: undefined reference to `gzopen64'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function `xmlGzfileClose':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1331: undefined reference to `gzclose'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function `xmlGzfileWrite':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1315: undefined reference to `gzwrite'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function `xmlZMemBuffGetContent':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1758: undefined reference to `deflate'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function `xmlZMemBuffAppend':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1717: undefined reference to `deflate'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1729: undefined reference to `crc32'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function `xmlGzfileRead':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1295: undefined reference to `gzread'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function `xmlCreateZMemBuff':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1600: undefined reference to `deflateInit2_'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1615: undefined reference to `crc32'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(nanohttp.o): In function `xmlNanoHTTPFreeCtxt':
/home/ikosh/programs/libxml2-2.9.3/nanohttp.c:432: undefined reference to `inflateEnd'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(nanohttp.o): In function `xmlNanoHTTPRead':
/home/ikosh/programs/libxml2-2.9.3/nanohttp.c:1292: undefined reference to `inflate'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(nanohttp.o): In function `xmlNanoHTTPScanAnswer':
/home/ikosh/programs/libxml2-2.9.3/nanohttp.c:829: undefined reference to `inflateInit2_'
gmake[1]: *** [cmTC_09bc5] Error 1
gmake[1]: Leaving directory `/gpfs/vesta-home/ikosh/gromacs-5.1.1/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_09bc5/fast] Error 2

SO OBVIOUSLY A COMPILATION PROBLEM when libxml2.a can not find some links.

Do you have any suggestions how I can fix it?
Thank you,
Irina.

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