[gmx-users] gromacs-5.1.1 installation error: libxml2 problem
Irina Kosheleva
ikoshelev at cars.uchicago.edu
Mon Feb 15 16:23:37 CET 2016
Hi Mark,
I implemented your suggestions.
It looks like gromacs can find zlib (through CMAKE_PREFIX_PATH I presume) but have errors in libxml2.a , which are related to zlib functions.
Please see below.
Irina.
I have configure $PATH, LD_LIBRARY_PATH and CMAKE_PREFIX_PATH to point to my directories also:
echo $PATH
/home/ikosh/programs/autotools-bin/bin:....
echo $LD_LIBRARY_PATH
/home/ikosh/programs/autotools-bin/lib:....
echo $CMAKE_PREFIX_PATH
/home/ikosh/programs/autotools-bin:....
For libxml2-2.9.3 in my dir:
./configure --prefix=/home/ikosh/programs/autotools-bin --with-python-install-dir=/home/ikosh/programs/autotools-bin
Otherwise it tries to install python in top directories
It found zlib just OK:
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
Checking zlib
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for gzread in -lz... yes
NOW for gromacs compilation:
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-5.1.1/install
---
-- Checking for MPI_IN_PLACE - yes
-- Looking for zlibVersion in /home/ikosh/programs/autotools-bin/lib/libz.a
-- 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 "2.9.3")
-- 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
-- Looking for include file pthread.h
--
TAIL CMakeFiles/CMakeError.log
Determining if the function xmlTextWriterEndAttribute exists in the /home/ikosh/programs/autotools-bin/lib/libxml2.a failed with the following output:
Change Dir: /home/ikosh/gromacs-5.1.1/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_9d85a/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_9d85a.dir/build.make CMakeFiles/cmTC_9d85a.dir/build
gmake[1]: Entering directory `/gpfs/vesta-home/ikosh/gromacs-5.1.1/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_9d85a.dir/CheckFunctionExists.c.o
/soft/compilers/wrappers/xl/mpixlc_r -I/bgsys/drivers/ppcfloor/comm/sys/include -I/bgsys/drivers/ppcfloor/ -I/bgsys/drivers/ppcfloor/spi/include -I/bgsys/drivers/ppcfloor/spi/include/kernel/cnk -I/bgsys/drivers/ppcfloor/comm/xl/include -O3 -qsmp=omp -qarch=qp -qtune=qp -qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-030 -qlanglvl=extc99 -qarch=auto -qtune=auto -DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute -o CMakeFiles/cmTC_9d85a.dir/CheckFunctionExists.c.o -c /soft/buildtools/cmake/3.3.0/share/cmake-3.3/Modules/CheckFunctionExists.c
Linking C executable cmTC_9d85a
/soft/buildtools/cmake/3.3.0/bin/cmake -E cmake_link_script CMakeFiles/cmTC_9d85a.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=1500-030 -qlanglvl=extc99 -qarch=auto -qtune=auto -DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute CMakeFiles/cmTC_9d85a.dir/CheckFunctionExists.c.o -o cmTC_9d85a /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 `gzopen'
/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 `gzopen'
/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_9d85a] Error 1
gmake[1]: Leaving directory `/gpfs/vesta-home/ikosh/gromacs-5.1.1/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_9d85a/fast] Error 2
-----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.
> > >
> > >
> > > --
> > > 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-request at gromacs.org.
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > >
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> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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> > posting!
> >
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> > posting!
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