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openmm / openmm-plumed

OpenMM plugin to interface with PLUMED
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Installation with openmm on anaconda 3 #18

Closed linusyukwong closed 6 years ago

linusyukwong commented 6 years ago

I installed both openmm 7.3.2 and plumed 2.3.3 with anaconda, but encountered the following when installing openmm-plumed from source: [ 3%] Building CXX object CMakeFiles/OpenMMPlumed.dir/openmmapi/src/PlumedForce.cpp.o [ 7%] Building CXX object CMakeFiles/OpenMMPlumed.dir/openmmapi/src/PlumedForceImpl.cpp.o [ 11%] Building CXX object CMakeFiles/OpenMMPlumed.dir/serialization/src/PlumedForceProxy.cpp.o [ 15%] Building CXX object CMakeFiles/OpenMMPlumed.dir/serialization/src/PlumedSerializationProxyRegistration.cpp.o [ 19%] Linking CXX shared library libOpenMMPlumed.so [ 19%] Built target OpenMMPlumed [ 23%] Building CXX object serialization/tests/CMakeFiles/TestSerializePlumedForce.dir/TestSerializePlumedForce.cpp.o [ 26%] Linking CXX executable TestSerializePlumedForce CMakeFiles/TestSerializePlumedForce.dir/TestSerializePlumedForce.cpp.o: In function testSerialization()': TestSerializePlumedForce.cpp:(.text+0x1f5): undefined reference toOpenMM::throwException(char const, int, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/TestSerializePlumedForce.dir/TestSerializePlumedForce.cpp.o: In function `void OpenMM::XmlSerializer::serialize(PlumedPlugin::PlumedForce const, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::ostream&)': TestSerializePlumedForce.cpp:(.text._ZN6OpenMM13XmlSerializer9serializeIN12PlumedPlugin11PlumedForceEEEvPKT_RKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSo[_ZN6OpenMM13XmlSerializer9serializeIN12PlumedPlugin11PlumedForceEEEvPKT_RKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSo]+0x72): undefined reference to `OpenMM::SerializationNode::setName(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' TestSerializePlumedForce.cpp:(.text._ZN6OpenMM13XmlSerializer9serializeIN12PlumedPlugin11PlumedForceEEEvPKT_RKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSo[_ZN6OpenMM13XmlSerializer9serializeIN12PlumedPlugin11PlumedForceEEEvPKT_RKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSo]+0xe1): undefined reference to OpenMM::SerializationNode::hasProperty(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' TestSerializePlumedForce.cpp:(.text._ZN6OpenMM13XmlSerializer9serializeIN12PlumedPlugin11PlumedForceEEEvPKT_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSo[_ZN6OpenMM13XmlSerializer9serializeIN12PlumedPlugin11PlumedForceEEEvPKT_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSo]+0x121): undefined reference toOpenMM::SerializationProxy::getTypeName[abi:cxx11]() const' TestSerializePlumedForce.cpp:(.text._ZN6OpenMM13XmlSerializer9serializeIN12PlumedPlugin11PlumedForceEEEvPKT_RKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSo[_ZN6OpenMM13XmlSerializer9serializeIN12PlumedPlugin11PlumedForceEEEvPKT_RKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSo]+0x17d): undefined reference to OpenMM::SerializationProxy::getTypeName[abi:cxx11]() const' TestSerializePlumedForce.cpp:(.text._ZN6OpenMM13XmlSerializer9serializeIN12PlumedPlugin11PlumedForceEEEvPKT_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSo[_ZN6OpenMM13XmlSerializer9serializeIN12PlumedPlugin11PlumedForceEEEvPKT_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSo]+0x1c3): undefined reference toOpenMM::SerializationNode::setStringProperty(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' ../../libOpenMMPlumed.so: undefined reference to OpenMM::Platform::createKernel(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, OpenMM::ContextImpl&) const' ../../libOpenMMPlumed.so: undefined reference toOpenMM::SerializationNode::getIntProperty(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' ../../libOpenMMPlumed.so: undefined reference to `OpenMM::SerializationNode::getStringProperty(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' ../../libOpenMMPlumed.so: undefined reference to OpenMM::SerializationNode::setIntProperty(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)' ../../libOpenMMPlumed.so: undefined reference toOpenMM::SerializationProxy::SerializationProxy(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)' collect2: error: ld returned 1 exit status serialization/tests/CMakeFiles/TestSerializePlumedForce.dir/build.make:84: recipe for target 'serialization/tests/TestSerializePlumedForce' failed make[2]: [serialization/tests/TestSerializePlumedForce] Error 1 CMakeFiles/Makefile2:122: recipe for target 'serialization/tests/CMakeFiles/TestSerializePlumedForce.dir/all' failed make[1]: [serialization/tests/CMakeFiles/TestSerializePlumedForce.dir/all] Error 2 Makefile:140: recipe for target 'all' failed make: *** [all] Error 2

linusyukwong commented 6 years ago

Solved by installing openmm and plumed from souce