Dear all,
I am trying to install the newest version of VOTCA on cluster, the error
comes at the make step:
Scanning dependencies of target votca_tools_manpages
[ 0%] Built target votca_tools_manpages
Scanning dependencies of target gitversion
Current git revision is f00d0dd
[ 0%] Built target gitversion
Scanning dependencies of target votca_tools
[ 1%] Building CXX object
tools/src/libtools/CMakeFiles/votca_tools.dir/akimaspline.cc.o
[ 1%] Building CXX object
tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o
[ 2%] Building CXX object
tools/src/libtools/CMakeFiles/votca_tools.dir/colors.cc.o
[ 3%] Building CXX object
tools/src/libtools/CMakeFiles/votca_tools.dir/correlate.cc.o
[ 3%] Building CXX object
tools/src/libtools/CMakeFiles/votca_tools.dir/crosscorrelate.cc.o
[ 4%] Building CXX object
tools/src/libtools/CMakeFiles/votca_tools.dir/cubicspline.cc.o
[ 5%] Building CXX object
tools/src/libtools/CMakeFiles/votca_tools.dir/datacollection.cc.o
[ 5%] Building CXX object
tools/src/libtools/CMakeFiles/votca_tools.dir/edge.cc.o
[ 6%] Building CXX object
tools/src/libtools/CMakeFiles/votca_tools.dir/edgecontainer.cc.o
[ 7%] Building CXX object
tools/src/libtools/CMakeFiles/votca_tools.dir/elements.cc.o
[ 7%] Building CXX object
tools/src/libtools/CMakeFiles/votca_tools.dir/globals.cc.o
[ 8%] Building CXX object
tools/src/libtools/CMakeFiles/votca_tools.dir/graph.cc.o
In file included from /usr/include/c++/4.8/algorithm:62:0,
from
/work/06148/vsc31483/software/votca_src/tools/src/libtools/graph.cc:20:
/usr/include/c++/4.8/bits/stl_algo.h: In instantiation of
‘_RandomAccessIterator std::__unguarded_partition(_RandomAccessIterator,
_RandomAccessIterator, const _Tp&, _Compare) [with _RandomAccessIterator =
__gnu_cxx::__normal_iterator<std::pair<int, votca::tools::GraphNode>*,
std::vector<std::pair<int, votca::tools::GraphNode> > >; _Tp =
std::pair<int, votca::tools::GraphNode>; _Compare = bool (*)(std::pair<int,
votca::tools::GraphNode>&, std::pair<int, votca::tools::GraphNode>&)]’:
/usr/include/c++/4.8/bits/stl_algo.h:2296:78: required from
‘_RandomAccessIterator
std::__unguarded_partition_pivot(_RandomAccessIterator,
_RandomAccessIterator, _Compare) [with _RandomAccessIterator =
__gnu_cxx::__normal_iterator<std::pair<int, votca::tools::GraphNode>*,
std::vector<std::pair<int, votca::tools::GraphNode> > >; _Compare = bool
(*)(std::pair<int, votca::tools::GraphNode>&, std::pair<int,
votca::tools::GraphNode>&)]’
/usr/include/c++/4.8/bits/stl_algo.h:2337:62: required from ‘void
std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size,
_Compare) [with _RandomAccessIterator =
__gnu_cxx::__normal_iterator<std::pair<int, votca::tools::GraphNode>*,
std::vector<std::pair<int, votca::tools::GraphNode> > >; _Size = long int;
_Compare = bool (*)(std::pair<int, votca::tools::GraphNode>&,
std::pair<int, votca::tools::GraphNode>&)]’
/usr/include/c++/4.8/bits/stl_algo.h:5499:44: required from ‘void
std::sort(_RAIter, _RAIter, _Compare) [with _RAIter =
__gnu_cxx::__normal_iterator<std::pair<int, votca::tools::GraphNode>*,
std::vector<std::pair<int, votca::tools::GraphNode> > >; _Compare = bool
(*)(std::pair<int, votca::tools::GraphNode>&, std::pair<int,
votca::tools::GraphNode>&)]’
/work/06148/vsc31483/software/votca_src/tools/src/libtools/graph.cc:127:51:
required from here
/usr/include/c++/4.8/bits/stl_algo.h:2263:35: error: invalid initialization
of reference of type ‘std::pair<int, votca::tools::GraphNode>&’ from
expression of type ‘const std::pair<int, votca::tools::GraphNode>’
while (__comp(*__first, __pivot))
^
/usr/include/c++/4.8/bits/stl_algo.h:2266:34: error: invalid initialization
of reference of type ‘std::pair<int, votca::tools::GraphNode>&’ from
expression of type ‘const std::pair<int, votca::tools::GraphNode>’
while (__comp(__pivot, *__last))
^
tools/src/libtools/CMakeFiles/votca_tools.dir/build.make:205: recipe for
target 'tools/src/libtools/CMakeFiles/votca_tools.dir/graph.cc.o' failed
make[2]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/graph.cc.o]
Error 1
CMakeFiles/Makefile2:217: recipe for target
'tools/src/libtools/CMakeFiles/votca_tools.dir/all' failed
make[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2
Please let me know how I can fix it. Thanks in advance!
Best regards,
Zidan
The installation procedure is shown as following:
git clone -b master --recursive https://github.com/votca/votca.git
I passed through the cmake procedure with:
cmake -DBUILD_CSGAPPS=ON -DCMAKE_INSTALL_PREFIX=/work/software/votca -
DWITH_GMX=ON -DGROMACS_INCLUDE_DIR=/work/software/gromacs/include -
DGROMACS_LIBRARY=/work/software/gromacs/lib64/libgromacs_mpi.so -
DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DEIGEN3_INCLUDE_DIR=/opt/apps/intel18/
eigen/3.3.4/include/eigen3 -DBOOST_ROOT=/opt/apps/intel18/boost/1.64 ..
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Git: /opt/apps/git/2.19.1/bin/git (found version "2.19.1")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Boost version: 1.64.0
-- Found the following Boost libraries:
-- program_options
-- filesystem
-- system
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.28")
-- Checking for module 'fftw3'
-- Found fftw3, version 3.3.8
-- Found FFTW3: /opt/apps/intel18/cray_mpich_7_7/fftw3/3.3.8/lib/libfftw3.so
-- Looking for fftw_plan_r2r_1d in
/opt/apps/intel18/cray_mpich_7_7/fftw3/3.3.8/lib/libfftw3.so;
-- Looking for fftw_plan_r2r_1d in
/opt/apps/intel18/cray_mpich_7_7/fftw3/3.3.8/lib/libfftw3.so; - found
-- Looking for assert.h
-- Looking for assert.h - found
-- Looking for math.h
-- Looking for math.h - found
-- Looking for stdio.h
-- Looking for stdio.h - found
-- Looking for stdlib.h
-- Looking for stdlib.h - found
-- Looking for string.h
-- Looking for string.h - found
-- Looking for C++ include cmath
-- Looking for C++ include cmath - found
-- Looking for C++ include fstream
-- Looking for C++ include fstream - found
-- Looking for C++ include functional
-- Looking for C++ include functional - found
-- Looking for C++ include iostream
-- Looking for C++ include iostream - found
-- Looking for C++ include limits
-- Looking for C++ include limits - found
-- Looking for C++ include list
-- Looking for C++ include list - found
-- Looking for C++ include map
-- Looking for C++ include map - found
-- Looking for C++ include ostream
-- Looking for C++ include ostream - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for C++ include stack
-- Looking for C++ include stack - found
-- Looking for C++ include stdexcept
-- Looking for C++ include stdexcept - found
-- Looking for C++ include string
-- Looking for C++ include string - found
-- Looking for C++ include vector
-- Looking for C++ include vector - found
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- Found EXPAT: /usr/lib64/libexpat.so (found version "2.1.0")
-- Checking for module 'sqlite3'
-- Found sqlite3, version 3.8.10.2
-- Found SQLITE3: /usr/lib64/libsqlite3.so
-- Performing Test HAVE_AIX
-- Performing Test HAVE_AIX - Failed
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.6") found
components: doxygen dot
-- Could NOT find TXT2TAGS (missing: TXT2TAGS_EXECUTABLE)
txt2tags not found, help cmake to find it by setting TXT2TAGS_EXECUTABLE
-- Found UnixCommands: /bin/bash
-- Boost version: 1.64.0
-- Found the following Boost libraries:
-- program_options
-- filesystem
-- system
-- Checking for module 'libvotca_tools'
-- No package 'libvotca_tools' found
-- Found VOTCA_TOOLS: votca_tools
-- Checking for module 'libgromacs_d'
-- No package 'libgromacs_d' found
-- Checking for module 'libgromacs'
-- No package 'libgromacs' found
-- Looking for c++ gmx_version in
/work/06148/vsc31483/software/gromacs/lib64/libgromacs_mpi.so
-- Looking for c++ gmx_version in
/work/06148/vsc31483/software/gromacs/lib64/libgromacs_mpi.so - found
-- Looking for c++ gmx_is_single_precision in
/work/06148/vsc31483/software/gromacs/lib64/libgromacs_mpi.so
-- Looking for c++ gmx_is_single_precision in
/work/06148/vsc31483/software/gromacs/lib64/libgromacs_mpi.so - found
-- Looking for c++ gmx_is_double_precision in
/work/06148/vsc31483/software/gromacs/lib64/libgromacs_mpi.so
-- Looking for c++ gmx_is_double_precision in
/work/06148/vsc31483/software/gromacs/lib64/libgromacs_mpi.so - not found
-- Found GROMACS:
/work/06148/vsc31483/software/gromacs/lib64/libgromacs_mpi.so (found
suitable version "20180004", minimum required is "20160000")
-- Looking for C++ include algorithm
-- Looking for C++ include algorithm - found
-- Looking for C++ include iomanip
-- Looking for C++ include iomanip - found
-- Looking for C++ include numeric
-- Looking for C++ include numeric - found
-- Looking for C++ include cstdlib
-- Looking for C++ include cstdlib - found
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5:
/opt/apps/intel18/hdf5/1.8.21/x86_64/lib/libhdf5.so;/opt/apps/intel18/hdf5/1.8.21/x86_64/lib/libsz.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so
(found version "1.8.21") found components: C
-- Could NOT find GMX (missing: GMX_EXECUTABLE)
-- Boost version: 1.64.0
-- Found the following Boost libraries:
-- program_options
-- Checking for module 'libvotca_tools'
-- No package 'libvotca_tools' found
-- Checking for module 'libvotca_csg'
-- No package 'libvotca_csg' found
-- Found VOTCA_CSG: votca_csg
-- Could NOT find CLANG_FORMAT (missing: CLANG_FORMAT_EXECUTABLE)
-- The following OPTIONAL packages have been found:
* Git
* FFTW3
* EXPAT
* UnixCommands
* HDF5
* PkgConfig
* Doxygen
-- The following REQUIRED packages have been found:
* Threads
* GROMACS (required version >= 20160000)
* Boost (required version >= 1.57.0)
* Eigen3 (required version >= 3.3.0)
* SQLITE3
* VOTCA_TOOLS
* VOTCA_CSG
-- The following OPTIONAL packages have not been found:
* TXT2TAGS
-- Configuring done
-- Generating done
-- Build files have been written to:
/work/06148/vsc31483/software/votca_src/build
--
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