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: [email protected] [mailto:[email protected]] On Behalf Of Mark Abraham Sent: Friday, February 12, 2016 3:47 PM To: [email protected] 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 <[email protected]> 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: [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]. > -- 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].
