Hello, Using the flag -DGMX_USE_TNG=off does not help. Scanning dependencies of target gmx [ 98%] Building CXX object share/template/CMakeFiles/template.dir/template.cpp.o [100%] Building CXX object src/programs/CMakeFiles/gmx.dir/gmx.cpp.o [100%] Building CXX object src/programs/CMakeFiles/gmx.dir/legacymodules.cpp.o [100%] Linking CXX executable ../../bin/gmx_mpi [100%] Linking CXX executable ../../bin/template /bgsys/drivers/ppcfloor/gnu-linux/powerpc64-bgq-linux/bin/ld: cannot find -lz /bgsys/drivers/ppcfloor/gnu-linux/powerpc64-bgq-linux/bin/ld: cannot find -lz make[2]: *** [bin/gmx_mpi] Error 1 make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs.... make[2]: *** [bin/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2
Anything else I may try? I am using xl IBM compiler. Do you think that switching to another compiler like gcc or clang may help? Irina. -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: Tuesday, February 16, 2016 6:16 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem 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 < ikoshe...@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-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: Friday, February 12, 2016 5:04 PM > To: gmx-us...@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 > <ikoshe...@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/in > clude > > > -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-boun...@maillist.sys.kth.se [mailto: > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > > Abraham > > Sent: Friday, February 12, 2016 3:47 PM > > To: gmx-us...@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 > > <ikoshe...@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-boun...@maillist.sys.kth.se [mailto: > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > > > Mark Abraham > > > Sent: Thursday, February 11, 2016 11:47 AM > > > To: gmx-us...@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. <smit...@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-boun...@maillist.sys.kth.se < > > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > Irina > > > > Kosheleva <ikoshe...@cars.uchicago.edu> > > > > Sent: Thursday, February 11, 2016 12:08 PM > > > > To: gromacs.org_gmx-users@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/includ > > > > e > > > > -DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfft > > > > w3f.a > > > > > > > > > > -DLIBXML2_INCLUDE_DIR=/gpfs/vesta-home/ikosh/programs/autotools-bin/in > clude > > > > > > > > > > -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/inst > > > > all > > > > > > > > --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-use > > > > rs > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > -- > > > > 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-use > > > > rs > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > 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 gmx-users-requ...@gromacs.org. > > > -- > > > 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 gmx-users-requ...@gromacs.org. > > > > > -- > > 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 gmx-users-requ...@gromacs.org. > > -- > > 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 gmx-users-requ...@gromacs.org. > > > -- > 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 gmx-users-requ...@gromacs.org. > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org. -- 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 gmx-users-requ...@gromacs.org.
