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: [email protected] [mailto:[email protected]] On Behalf Of Mark Abraham Sent: Thursday, February 11, 2016 11:47 AM To: [email protected] 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. <[email protected]> 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: [email protected] < > [email protected]> on behalf of Irina > Kosheleva <[email protected]> > Sent: Thursday, February 11, 2016 12:08 PM > To: [email protected] > 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. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
