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

Fri Feb 12 23:13:55 CET 2016

Hi,
I have compiled my own libxlm2-2.9.3 (this is not a devel from what I know)
Using:
./configure CC=mpixlcxx_r --prefix=/home/ikosh/programs/autotools-bin --with-python-install-dir=/home/ikosh/programs/autotools-bin --with
-zlib=/soft/libraries/alcf/current/xl/ZLIB --enable-static --disable-shared
This did not produce errors in config.log

Cmake:
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=/home/ikosh/programs/autotools-bin/include -DFFTWF_LIBRARY=/home/ikosh/programs/autotools-bin/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

The compiler flags are static. There is no static libxml2.a installed on vesta as far as I know, however there are dynamic libxml2.so libraries which I did not use because CMAKE_TOOLCHAIN_FILE is static and I use all flags for static libraries.
Does  this approach pose a problem?
I am really interested in the way you have used libxml2 for the compilation on vesta.
Irina.

-----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 Mark Abraham
Sent: Friday, February 12, 2016 3:47 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

Hi,

What command did you use to use their libxml2? Things work for me, but that
doesn't mean there isn't a problem :-)

Mark

On Fri, 12 Feb 2016 20:41 Irina Kosheleva <ikoshelev at cars.uchicago.edu>
wrote:

> Hello Mark,
> This is the response I'm getting
> Please send your problem to gmx user forum
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List). Your
> problem seems come from Gromacs cmake command parsing. The related source
> code is pretty convoluted.  Relevant Gromacs developer may answer your
> question.
> Irina
>
> -----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 Mark
> Abraham
> Sent: Thursday, February 11, 2016 11:47 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem
>
> 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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