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

[Mark Abraham]

Hi,

IIRC ALCF does make available libxml2 with headers for bgq on Vesta, so I'm
sure the have/will on Mira too! Ask them.

Mark

On Thu, 11 Feb 2016 18:33 Smith, Micholas D. <smithmd at ornl.gov> wrote:

> 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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