[gmx-users] gromacs-5.1.1 installation error: libxml2 problem
Mark Abraham
mark.j.abraham at gmail.com
Wed Feb 17 01:15:59 CET 2016
Hi,
That commit's based off a development version of GROMACS, which naturally
isn't as reliable as the released versions (or supported). I don't know why
this wasn't working properly then, but probably cmake -DGMX_USE_TNG=off is
enough to hack off the attempt to link zlib.
Mark
On Wed, Feb 17, 2016 at 12:29 AM Irina Kosheleva <
ikoshelev at cars.uchicago.edu> wrote:
> Hello Mark.
> Your suggestions let me
> make and make install without errors gromacs-5.1.1.
> For libxml2:
> ./configure --prefix=/home/ikosh/programs/autotools-bin --without-python
> --without-zlib --without-lzma
>
> cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r
> -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX
> -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_rc/install
>
> My goal however build waxsdebye module of a development version available
> on
> git fetch https://gerrit.gromacs.org/gromacs refs/changes/59/2659/131
> cmake configuration can recognize
> -- Looking for zlibVersion in
> /home/ikosh/programs/autotools-bin/lib/libz.a - found
> -- Found LibXml2: /home/ikosh/programs/autotools-bin/lib/libxml2.a (found
> version "2.7.6")
> -- Looking for xmlTextWriterEndAttribute in
> /home/ikosh/programs/autotools-bin/lib/libxml2.a
> -- Looking for xmlTextWriterEndAttribute in
> /home/ikosh/programs/autotools-bin/lib/libxml2.a - found
> -- Looking for fftwf_plan_r2r_1d in
> /home/ikosh/programs/autotools-bin/lib/libfftw3f.a
> -- Looking for fftwf_plan_r2r_1d in
> /home/ikosh/programs/autotools-bin/lib/libfftw3f.a - found
>
> However at the end of the build there is an error:
> [100%] Built target libgromacs
> Scanning dependencies of target template
> [100%] Building CXX object
> share/template/CMakeFiles/template.dir/template.cpp.o
> [100%] Linking CXX executable ../../bin/template
> /bgsys/drivers/ppcfloor/gnu-linux/powerpc64-bgq-linux/bin/ld: cannot find
> -lz
> make[2]: *** [bin/template] Error 1
>
> Is it a problem on gmx side? What library it is linking to?
> 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 5:04 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem
>
> Hi,
>
> I configure libxml2 without python or threads or anything except zlib,
> since we use none of that. You have enabled python, which is probably not
> fatal, but has caused problems some other time.
>
> More importantly is that you are trying to specify everything to cmake, and
> not handling zlib correctly. Instead of -DZLIB=whatever,
> -DZLIB_LIBRARIES=whatever will probably work, but I find it less
> problematic to put the search paths into CMAKE_PREFIX_PATH and let the
> cmake package do the work, to help avoid mistakes. Libxml2 needs both parts
> of zlib to be found for our cmake test to pass, so that the test code will
> build later on.
>
> Mark
>
> On Fri, 12 Feb 2016 23:14 Irina Kosheleva <ikoshelev at cars.uchicago.edu>
> wrote:
>
> > 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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