Compiling VOTCA on cluster
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Clement Koh
Aug 31, 2020, 7:11:04 PM8/31/20
to votca
Hi,
I'm trying to compile votca on my local cluster and I'm facing an error at the make step. Does anyone have any idea what the issue could be? The make step output is below:
Scanning dependencies of target votca_tools_manpages
[ 0%] Built target votca_tools_manpages
Scanning dependencies of target gitversion
Current git revision is 521998a
[ 0%] Built target gitversion
Scanning dependencies of target votca_tools
[ 1%] Building CXX object tools/src/libtools/CMakeFiles/votca_tools.dir/akimaspline.cc.o
[ 2%] Building CXX object tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o
In file included from /moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:23:0,
from /moto/home/cfk2120/packages/votca/tools/include/votca/tools/application.h:21,
from /moto/home/cfk2120/packages/votca/tools/src/libtools/application.cc:19:
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/tokenizer.h: In constructor ‘votca::tools::Tokenizer::Tokenizer(const string&, const char*)’:
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/tokenizer.h:50:11: error: ‘make_unique’ is not a member of ‘std’
tok = std::make_unique<boost::tokenizer<boost::char_separator<char>>>(_str,
^
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/tokenizer.h:50:73: error: expected primary-expression before ‘>’ token
tok = std::make_unique<boost::tokenizer<boost::char_separator<char>>>(_str,
^
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/tokenizer.h:51:75: warning: left operand of comma operator has no effect [-Wunused-value]
sep);
^
In file included from /moto/home/cfk2120/packages/votca/tools/include/votca/tools/application.h:21:0,
from /moto/home/cfk2120/packages/votca/tools/src/libtools/application.cc:19:
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h: In constructor ‘votca::tools::Property::Property(const string&, const string&, const string&)’:
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:59:7: warning: declaration of ‘path’ shadows a member of 'this' [-Wshadow]
: _name(name), _value(value), _path(path) {}
^
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:59:7: warning: declaration of ‘value’ shadows a member of 'this' [-Wshadow]
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:59:7: warning: declaration of ‘name’ shadows a member of 'this' [-Wshadow]
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h: In member function ‘votca::tools::Property& votca::tools::Property::set(const string&, const string&)’:
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:248:56: warning: declaration of ‘value’ shadows a member of 'this' [-Wshadow]
const std::string &value) {
^
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h: In member function ‘votca::tools::Property& votca::tools::Property::add(const string&, const string&)’:
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:255:56: warning: declaration of ‘value’ shadows a member of 'this' [-Wshadow]
const std::string &value) {
^
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:256:15: warning: declaration of ‘path’ shadows a member of 'this' [-Wshadow]
std::string path = _path;
^
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h: In member function ‘void votca::tools::Property::setAttribute(const string&, const T&)’:
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:420:50: warning: declaration of ‘value’ shadows a member of 'this' [-Wshadow]
const T &value) {
^
make[2]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o] Error 1
make[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2
make: *** [all] Error 2
I followed the general installation instructions listed online, with my cmake step being:
cmake -DBUILD_CSAPPS=ON -DCMAKE_INSTALL_PREFIX=/moto/home/cfk2120/packages/votca_build -DGROMACS_INCLUDE_DIR=/moto/kumar/users/cfk2120/serial_gromacs/include -DGROMACS_LIBRARY=/moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so -DLIBXC_LIBRARY=/moto/home/cfk2120/packages/libxc/lib -DLIBXC_INCLUDE_DIR=/moto/home/cfk2120/packages/libxc/include ..
The output of cmake is the following:
-- 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
-- Performing Test COMPILER_SUPPORTS-Wall
-- Performing Test COMPILER_SUPPORTS-Wall - Success
-- Performing Test COMPILER_SUPPORTS-Wextra
-- Performing Test COMPILER_SUPPORTS-Wextra - Success
-- Performing Test COMPILER_SUPPORTS-Wpedantic
-- Performing Test COMPILER_SUPPORTS-Wpedantic - Success
-- Performing Test COMPILER_SUPPORTS-Wshadow
-- Performing Test COMPILER_SUPPORTS-Wshadow - Success
-- Performing Test COMPILER_SUPPORTS-Wconversion
-- Performing Test COMPILER_SUPPORTS-Wconversion - Success
-- Found Git: /usr/bin/git (found version "1.8.3.1")
-- 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: 1.53.0
-- Found the following Boost libraries:
-- program_options
-- filesystem
-- system
-- Check size of int
-- Check size of int - done
-- Could NOT find MKL (missing: MKL_INCLUDE_DIR MKL_Core_LINK_LIBRARY)
-- Found Eigen3: /moto/kumar/users/cfk2120/eigen_build
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1")
-- Checking for module 'fftw3'
-- No package 'fftw3' found
-- Could NOT find FFTW3 (missing: FFTW3_LIBRARY FFTW3_INCLUDE_DIR)
-- 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")
-- Performing Test HAVE_AIX
-- Performing Test HAVE_AIX - Failed
-- Could NOT find TXT2TAGS (missing: TXT2TAGS_EXECUTABLE)
txt2tags not found, help cmake to find it by setting TXT2TAGS_EXECUTABLE
-- Found UnixCommands: /usr/bin/bash
-- Boost version: 1.53.0
-- Found the following Boost libraries:
-- program_options
-- filesystem
-- system
-- Found Eigen3: /moto/kumar/users/cfk2120/eigen_build
-- Found 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 /moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so
-- Looking for c++ gmx_version in /moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so - found
-- Looking for c++ gmx_is_single_precision in /moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so
-- Looking for c++ gmx_is_single_precision in /moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so - found
-- Looking for c++ gmx_is_double_precision in /moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so
-- Looking for c++ gmx_is_double_precision in /moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so - not found
-- Found GROMACS: /moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so (found suitable version "2018.7", minimum required is "2018")
-- Could NOT find GMX (missing: GMX_EXECUTABLE)
-- 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
-- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (found version "")
-- Could NOT find LMP (missing: LMP_EXECUTABLE)
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Could NOT find CLANG_FORMAT: Found unsuitable version "0.0", but required is at least "10" (found CLANG_FORMAT_EXECUTABLE-NOTFOUND)
-- The following OPTIONAL packages have been found:
* Git
* UnixCommands
* PkgConfig
-- The following REQUIRED packages have been found:
* EXPAT
* Threads
* Boost (required version >= 1.53.0)
* Eigen3 (required version >= 3.3.0)
* GROMACS (required version >= 2018)
-- The following OPTIONAL packages have not been found:
* MKL
* FFTW3
* TXT2TAGS
* HDF5
* Doxygen
* CLANG_FORMAT (required version >= 10)
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
BUILD_CSAPPS
LIBXC_INCLUDE_DIR
LIBXC_LIBRARY
I'm trying to compile votca on my local cluster and I'm facing an error at the make step. Does anyone have any idea what the issue could be? The make step output is below:
Scanning dependencies of target votca_tools_manpages
[ 0%] Built target votca_tools_manpages
Scanning dependencies of target gitversion
Current git revision is 521998a
[ 0%] Built target gitversion
Scanning dependencies of target votca_tools
[ 1%] Building CXX object tools/src/libtools/CMakeFiles/votca_tools.dir/akimaspline.cc.o
[ 2%] Building CXX object tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o
In file included from /moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:23:0,
from /moto/home/cfk2120/packages/votca/tools/include/votca/tools/application.h:21,
from /moto/home/cfk2120/packages/votca/tools/src/libtools/application.cc:19:
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/tokenizer.h: In constructor ‘votca::tools::Tokenizer::Tokenizer(const string&, const char*)’:
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/tokenizer.h:50:11: error: ‘make_unique’ is not a member of ‘std’
tok = std::make_unique<boost::tokenizer<boost::char_separator<char>>>(_str,
^
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/tokenizer.h:50:73: error: expected primary-expression before ‘>’ token
tok = std::make_unique<boost::tokenizer<boost::char_separator<char>>>(_str,
^
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/tokenizer.h:51:75: warning: left operand of comma operator has no effect [-Wunused-value]
sep);
^
In file included from /moto/home/cfk2120/packages/votca/tools/include/votca/tools/application.h:21:0,
from /moto/home/cfk2120/packages/votca/tools/src/libtools/application.cc:19:
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h: In constructor ‘votca::tools::Property::Property(const string&, const string&, const string&)’:
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:59:7: warning: declaration of ‘path’ shadows a member of 'this' [-Wshadow]
: _name(name), _value(value), _path(path) {}
^
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:59:7: warning: declaration of ‘value’ shadows a member of 'this' [-Wshadow]
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:59:7: warning: declaration of ‘name’ shadows a member of 'this' [-Wshadow]
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h: In member function ‘votca::tools::Property& votca::tools::Property::set(const string&, const string&)’:
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:248:56: warning: declaration of ‘value’ shadows a member of 'this' [-Wshadow]
const std::string &value) {
^
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h: In member function ‘votca::tools::Property& votca::tools::Property::add(const string&, const string&)’:
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:255:56: warning: declaration of ‘value’ shadows a member of 'this' [-Wshadow]
const std::string &value) {
^
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:256:15: warning: declaration of ‘path’ shadows a member of 'this' [-Wshadow]
std::string path = _path;
^
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h: In member function ‘void votca::tools::Property::setAttribute(const string&, const T&)’:
/moto/home/cfk2120/packages/votca/tools/include/votca/tools/property.h:420:50: warning: declaration of ‘value’ shadows a member of 'this' [-Wshadow]
const T &value) {
^
make[2]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o] Error 1
make[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2
make: *** [all] Error 2
I followed the general installation instructions listed online, with my cmake step being:
cmake -DBUILD_CSAPPS=ON -DCMAKE_INSTALL_PREFIX=/moto/home/cfk2120/packages/votca_build -DGROMACS_INCLUDE_DIR=/moto/kumar/users/cfk2120/serial_gromacs/include -DGROMACS_LIBRARY=/moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so -DLIBXC_LIBRARY=/moto/home/cfk2120/packages/libxc/lib -DLIBXC_INCLUDE_DIR=/moto/home/cfk2120/packages/libxc/include ..
The output of cmake is the following:
-- 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
-- Performing Test COMPILER_SUPPORTS-Wall
-- Performing Test COMPILER_SUPPORTS-Wall - Success
-- Performing Test COMPILER_SUPPORTS-Wextra
-- Performing Test COMPILER_SUPPORTS-Wextra - Success
-- Performing Test COMPILER_SUPPORTS-Wpedantic
-- Performing Test COMPILER_SUPPORTS-Wpedantic - Success
-- Performing Test COMPILER_SUPPORTS-Wshadow
-- Performing Test COMPILER_SUPPORTS-Wshadow - Success
-- Performing Test COMPILER_SUPPORTS-Wconversion
-- Performing Test COMPILER_SUPPORTS-Wconversion - Success
-- Found Git: /usr/bin/git (found version "1.8.3.1")
-- 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: 1.53.0
-- Found the following Boost libraries:
-- program_options
-- filesystem
-- system
-- Check size of int
-- Check size of int - done
-- Could NOT find MKL (missing: MKL_INCLUDE_DIR MKL_Core_LINK_LIBRARY)
-- Found Eigen3: /moto/kumar/users/cfk2120/eigen_build
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1")
-- Checking for module 'fftw3'
-- No package 'fftw3' found
-- Could NOT find FFTW3 (missing: FFTW3_LIBRARY FFTW3_INCLUDE_DIR)
-- 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")
-- Performing Test HAVE_AIX
-- Performing Test HAVE_AIX - Failed
-- Could NOT find TXT2TAGS (missing: TXT2TAGS_EXECUTABLE)
txt2tags not found, help cmake to find it by setting TXT2TAGS_EXECUTABLE
-- Found UnixCommands: /usr/bin/bash
-- Boost version: 1.53.0
-- Found the following Boost libraries:
-- program_options
-- filesystem
-- system
-- Found Eigen3: /moto/kumar/users/cfk2120/eigen_build
-- Found 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 /moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so
-- Looking for c++ gmx_version in /moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so - found
-- Looking for c++ gmx_is_single_precision in /moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so
-- Looking for c++ gmx_is_single_precision in /moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so - found
-- Looking for c++ gmx_is_double_precision in /moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so
-- Looking for c++ gmx_is_double_precision in /moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so - not found
-- Found GROMACS: /moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so (found suitable version "2018.7", minimum required is "2018")
-- Could NOT find GMX (missing: GMX_EXECUTABLE)
-- 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
-- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (found version "")
-- Could NOT find LMP (missing: LMP_EXECUTABLE)
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Could NOT find CLANG_FORMAT: Found unsuitable version "0.0", but required is at least "10" (found CLANG_FORMAT_EXECUTABLE-NOTFOUND)
-- The following OPTIONAL packages have been found:
* Git
* UnixCommands
* PkgConfig
-- The following REQUIRED packages have been found:
* EXPAT
* Threads
* Boost (required version >= 1.53.0)
* Eigen3 (required version >= 3.3.0)
* GROMACS (required version >= 2018)
-- The following OPTIONAL packages have not been found:
* MKL
* FFTW3
* TXT2TAGS
* HDF5
* Doxygen
* CLANG_FORMAT (required version >= 10)
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
BUILD_CSAPPS
LIBXC_INCLUDE_DIR
LIBXC_LIBRARY
Christoph Junghans
Aug 31, 2020, 7:44:54 PM8/31/20
to vo...@googlegroups.com
make_unique is a C++-14 feature, looking at
https://gcc.gnu.org/projects/cxx-status.html#cxx14 it seems gcc 4.8.5
isn't fully supporting that standard.
Just use a newer compiler.
Christoph
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
> You received this message because you are subscribed to the Google Groups "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/ce8d422f-b3a8-4bfa-9fb4-da92af09fd72n%40googlegroups.com.
--
Christoph Junghans
Web: http://www.compphys.de
https://gcc.gnu.org/projects/cxx-status.html#cxx14 it seems gcc 4.8.5
isn't fully supporting that standard.
Just use a newer compiler.
Christoph
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
> You received this message because you are subscribed to the Google Groups "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/ce8d422f-b3a8-4bfa-9fb4-da92af09fd72n%40googlegroups.com.
--
Christoph Junghans
Web: http://www.compphys.de
Clement Koh
Aug 31, 2020, 8:23:09 PM8/31/20
to votca
Thanks for the quick reply. I used gcc 7.2.0 instead and now I'm stuck on the following error:
Scanning dependencies of target votca_tools_manpages
[ 0%] Built target votca_tools_manpages
Scanning dependencies of target gitversion
Current git revision is 521998a
[ 0%] Built target gitversion
Scanning dependencies of target votca_tools
[ 1%] Building CXX object tools/src/libtools/CMakeFiles/votca_tools.dir/akimaspline.cc.o
[ 2%] Building CXX object tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o
[ 2%] Building CXX object tools/src/libtools/CMakeFiles/votca_tools.dir/calculator.cc.o
[ 3%] Building CXX object tools/src/libtools/CMakeFiles/votca_tools.dir/colors.cc.o
[ 4%] Building CXX object tools/src/libtools/CMakeFiles/votca_tools.dir/correlate.cc.o
[ 5%] Building CXX object tools/src/libtools/CMakeFiles/votca_tools.dir/crosscorrelate.cc.o
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Scanning dependencies of target votca_property
[ 30%] Building CXX object tools/src/tools/CMakeFiles/votca_property.dir/votca_property.cc.o
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CMakeFiles/votca_property.dir/votca_property.cc.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
votca_property.cc:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE]+0x76): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
CMakeFiles/votca_property.dir/votca_property.cc.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() const':
votca_property.cc:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv]+0x20): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/votca_property.dir/votca_property.cc.o: In function `boost::program_options::typed_value<long, char>::name[abi:cxx11]() const':
votca_property.cc:(.text._ZNK5boost15program_options11typed_valueIlcE4nameB5cxx11Ev[_ZNK5boost15program_options11typed_valueIlcE4nameB5cxx11Ev]+0x20): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/votca_property.dir/votca_property.cc.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)':
votca_property.cc:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x21): undefined reference to `boost::program_options::validation_error::get_template[abi:cxx11](boost::program_options::validation_error::kind_t)'
votca_property.cc:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x39): undefined reference to `boost::program_options::error_with_option_name::error_with_option_name(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
CMakeFiles/votca_property.dir/votca_property.cc.o: In function `VotcaProperty::Run()':
votca_property.cc:(.text._ZN13VotcaProperty3RunEv[_ZN13VotcaProperty3RunEv]+0x58): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
votca_property.cc:(.text._ZN13VotcaProperty3RunEv[_ZN13VotcaProperty3RunEv]+0x247): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
votca_property.cc:(.text._ZN13VotcaProperty3RunEv[_ZN13VotcaProperty3RunEv]+0x3e7): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/votca_property.dir/votca_property.cc.o: In function `void boost::program_options::validate<long, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, long*, long)':
votca_property.cc:(.text._ZN5boost15program_options8validateIlcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIlcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x4f8): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x30): more undefined references to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' follow
CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE[_ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE]+0x38): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._ZTVN5boost15program_options11typed_valueIlcEE[_ZTVN5boost15program_options11typed_valueIlcEE]+0x38): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
../libtools/libvotca_tools.so.6: undefined reference to `boost::program_options::option_description::description[abi:cxx11]() const'
../libtools/libvotca_tools.so.6: undefined reference to `boost::program_options::option_description::format_parameter[abi:cxx11]() const'
../libtools/libvotca_tools.so.6: undefined reference to `boost::program_options::option_description::format_name[abi:cxx11]() const'
../libtools/libvotca_tools.so.6: undefined reference to `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
../libtools/libvotca_tools.so.6: undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
../libtools/libvotca_tools.so.6: undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
../libtools/libvotca_tools.so.6: undefined reference to `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)'
collect2: error: ld returned 1 exit status
make[2]: *** [tools/src/tools/votca_property] Error 1
make[1]: *** [tools/src/tools/CMakeFiles/votca_property.dir/all] Error 2
make: *** [all] Error 2
Christoph Junghans
Aug 31, 2020, 8:27:45 PM8/31/20
to vo...@googlegroups.com
On Mon, Aug 31, 2020 at 6:23 PM Clement Koh <kfjcl...@gmail.com> wrote:
>
> Thanks for the quick reply. I used gcc 7.2.0 instead and now I'm stuck on the following error:
The error below looks like the boost has been compiled with an older compiler.
>
> Thanks for the quick reply. I used gcc 7.2.0 instead and now I'm stuck on the following error:
I recommend building votca with Spack, see
https://github.com/votca/votca/blob/master/share/doc/INSTALL.rst#spack
that will build all the dependencies as well.
Christoph
Clement Koh
Sep 1, 2020, 12:40:42 AM9/1/20
to votca
Thanks! I tried Spack but it faced errors compiling boost.
I ended up compiling my own boost using gcc 7.2.0. And then I had to make cmake refer to the new boost directory.
This ended up being my command for cmake:
BOOST_ROOT=/moto/kumar/users/cfk2120/boost CC=/cm/local/apps/gcc/7.2.0/bin/gcc CXX=/cm/local/apps/gcc/7.2.0/bin/g++ ../../my_cmake/bin/cmake -DBUILD_CSAPPS=ON -DCMAKE_INSTALL_PREFIX=/moto/home/cfk2120/packages/votca_build -DGROMACS_INCLUDE_DIR=/moto/kumar/users/cfk2120/serial_gromacs/include -DGROMACS_LIBRARY=/moto/kumar/users/cfk2120/serial_gromacs/lib64/libgromacs.so ..
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