compile zephyr on windows

OpenMM Zephyr provides a visual application for running GPU-accelerated molecular simulations.
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Jack Shultz
Posts: 77
Joined: Thu May 28, 2009 6:49 pm

compile zephyr on windows

Post by Jack Shultz » Fri Jul 17, 2009 5:26 am

I am trying to compile on windows but I get trouble linking to libraries when I run cmake. I tried to install the binnary release of libxml2 and fftw3

C:\Users\jshultz\Documents\Visual Studio 2008\Projects\Gromacs-4.0.5-for-OpenMMZ
ephyr-0.8-Source>cmake . -G "Visual Studio 9 2008"
-- Could NOT find LibXml2 (missing: LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR)
CMake Error at CMakeLists.txt:302 (MESSAGE):
Cannot find fftw3 (with correct precision). Fix it, choose another FFT
library, or use the Gromacs built-in fftpack (slower)!


-- Configuring incomplete, errors occurred!

C:\Users\jshultz\Documents\Visual Studio 2008\Projects\Gromacs-4.0.5-for-OpenMMZ
ephyr-0.8-Source>
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Jack Shultz
Posts: 77
Joined: Thu May 28, 2009 6:49 pm

RE: compile zephyr on windows

Post by Jack Shultz » Fri Jul 17, 2009 12:50 pm

I put the Libxml2 libraries in the lib folder.
Now I need to resolve this FFT issue

C:\Users\jshultz\Documents\Visual Studio 2008\Projects\Gromacs-4.0.5-for-OpenMMZ
ephyr-0.8-Source>cmake G "Visual Studio 9 2008" -D "LIBXML2_INCLUDE_DIR:PATH=C:/
Users/jshultz/Documents/Visual Studio 2008/Projects/Gromacs-4.0.5-for-OpenMMZeph
yr-0.8-Source/lib/include" -D "FFT:PATH=C:/Users/jshultz/Documents/Visual Studio
2008/Projects/Gromacs-4.0.5-for-OpenMMZephyr-0.8-Source/lib" .
CMake Error at CMakeLists.txt:302 (MESSAGE):
Cannot find fftw3 (with correct precision). Fix it, choose another FFT
library, or use the Gromacs built-in fftpack (slower)!


-- Configuring incomplete, errors occurred!

C:\Users\jshultz\Documents\Visual Studio 2008\Projects\Gromacs-4.0.5-for-OpenMMZ
ephyr-0.8-Source>
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Jack Shultz
Posts: 77
Joined: Thu May 28, 2009 6:49 pm

RE: compile zephyr on windows

Post by Jack Shultz » Fri Jul 17, 2009 1:33 pm

update, I switched to the cmake gui. When I had errors the first couple attempts it highlighted the paths it could not find. I added the missing libraries and headers and then I was able to generate Visual Studio project files.
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Jack Shultz
Posts: 77
Joined: Thu May 28, 2009 6:49 pm

RE: compile zephyr on windows

Post by Jack Shultz » Fri Jul 17, 2009 3:37 pm

When I build this in Visual studio 2008, I get stuck on the gmx project. LIBXML2_LIBRARIES is not pointing to the correct directoy. I set it to
C:\Users\jshultz\Documents\Visual Studio 2008\Projects\libxml\lib

but visual studio is doing something unexpect :-(

1>------ Build started: Project: gmx, Configuration: Debug Win32 ------
1>Linking...
1>LINK : fatal error LNK1104: cannot open file 'LIBXML2_LIBRARIES-C:\Users\jshultz\Documents\Visual.obj'
1>Build log was saved at "file://c:\Users\jshultz\Documents\Visual Studio 2008\Projects\Gromacs-4.0.5-for-OpenMMZephyr-0.8-Source\src\gmxlib\gmx.dir\Debug\BuildLog.htm"
1>gmx - 1 error(s), 0 warning(s)
========== Build: 0 succeeded, 1 failed, 3 up-to-date, 0 skipped ==========
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Jack Shultz
Posts: 77
Joined: Thu May 28, 2009 6:49 pm

RE: compile zephyr on windows

Post by Jack Shultz » Sun Jul 19, 2009 8:45 am

Resolved some of the linking issues by changing directories to one closer to the root of the file system and paths that don't have space. I am also using some of the pre-compiled libraries available in the 3.3.1 windows release of gromacs.

I got most of the projects to compile except mdrun_openmm, genion, grompp and a few others

1>------ Build started: Project: mdrun_openmm, Configuration: Debug Win32 ------
1>Linking...
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static void __cdecl OpenMM::Platform::loadPluginLibrary(class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >)" (__imp_?loadPluginLibrary@Platform@OpenMM@@SAXV?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@@Z) referenced in function _load_plugins
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::OpenMMContext::setVelocities(class std::vector<class OpenMM::Vec3,class std::allocator<class OpenMM::Vec3> > const &)" (__imp_?setVelocities@OpenMMContext@OpenMM@@QAEXABV?$vector@VVec3@OpenMM@@V?$allocator@VVec3@OpenMM@@@std@@@std@@@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::OpenMMContext::setPositions(class std::vector<class OpenMM::Vec3,class std::allocator<class OpenMM::Vec3> > const &)" (__imp_?setPositions@OpenMMContext@OpenMM@@QAEXABV?$vector@VVec3@OpenMM@@V?$allocator@VVec3@OpenMM@@@std@@@std@@@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: class OpenMM::Platform & __thiscall OpenMM::OpenMMContext::getPlatform(void)" (__imp_?getPlatform@OpenMMContext@OpenMM@@QAEAAVPlatform@2@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::OpenMMContext::OpenMMContext(class OpenMM::System &,class OpenMM::Integrator &)" (__imp_??0OpenMMContext@OpenMM@@QAE@AAVSystem@1@AAVIntegrator@1@@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::Integrator::setConstraintTolerance(double)" (__imp_?setConstraintTolerance@Integrator@OpenMM@@QAEXN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::LangevinIntegrator::LangevinIntegrator(double,double,double)" (__imp_??0LangevinIntegrator@OpenMM@@QAE@NNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::BrownianIntegrator::BrownianIntegrator(double,double,double)" (__imp_??0BrownianIntegrator@OpenMM@@QAE@NNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::VerletIntegrator::VerletIntegrator(double)" (__imp_??0VerletIntegrator@OpenMM@@QAE@N@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::System::addConstraint(int,int,double)" (__imp_?addConstraint@System@OpenMM@@QAEHHHN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::GBSAOBCForce::addParticle(double,double,double)" (__imp_?addParticle@GBSAOBCForce@OpenMM@@QAEHNNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::GBSAOBCForce::setSolventDielectric(double)" (__imp_?setSolventDielectric@GBSAOBCForce@OpenMM@@QAEXN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::GBSAOBCForce::setSoluteDielectric(double)" (__imp_?setSoluteDielectric@GBSAOBCForce@OpenMM@@QAEXN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::GBSAOBCForce::GBSAOBCForce(void)" (__imp_??0GBSAOBCForce@OpenMM@@QAE@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::NonbondedForce::addException(int,int,double,double,double)" (__imp_?addException@NonbondedForce@OpenMM@@QAEHHHNNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::System::addParticle(double)" (__imp_?addParticle@System@OpenMM@@QAEHN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::NonbondedForce::addParticle(double,double,double)" (__imp_?addParticle@NonbondedForce@OpenMM@@QAEHNNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::NonbondedForce::setCutoffDistance(double)" (__imp_?setCutoffDistance@NonbondedForce@OpenMM@@QAEXN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::NonbondedForce::setPeriodicBoxVectors(class OpenMM::Vec3,class OpenMM::Vec3,class OpenMM::Vec3)" (__imp_?setPeriodicBoxVectors@NonbondedForce@OpenMM@@QAEXVVec3@2@00@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::NonbondedForce::setNonbondedMethod(enum OpenMM::NonbondedForce::NonbondedMethod)" (__imp_?setNonbondedMethod@NonbondedForce@OpenMM@@QAEXW4NonbondedMethod@12@@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::NonbondedForce::NonbondedForce(void)" (__imp_??0NonbondedForce@OpenMM@@QAE@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::RBTorsionForce::addTorsion(int,int,int,int,double,double,double,double,double,double)" (__imp_?addTorsion@RBTorsionForce@OpenMM@@QAEHHHHHNNNNNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::RBTorsionForce::RBTorsionForce(void)" (__imp_??0RBTorsionForce@OpenMM@@QAE@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::PeriodicTorsionForce::addTorsion(int,int,int,int,int,double,double)" (__imp_?addTorsion@PeriodicTorsionForce@OpenMM@@QAEHHHHHHNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::PeriodicTorsionForce::PeriodicTorsionForce(void)" (__imp_??0PeriodicTorsionForce@OpenMM@@QAE@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::HarmonicAngleForce::addAngle(int,int,int,double,double)" (__imp_?addAngle@HarmonicAngleForce@OpenMM@@QAEHHHHNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::HarmonicAngleForce::HarmonicAngleForce(void)" (__imp_??0HarmonicAngleForce@OpenMM@@QAE@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::HarmonicBondForce::addBond(int,int,double,double)" (__imp_?addBond@HarmonicBondForce@OpenMM@@QAEHHHNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::HarmonicBondForce::HarmonicBondForce(void)" (__imp_??0HarmonicBondForce@OpenMM@@QAE@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::System::addForce(class OpenMM::Force *)" (__imp_?addForce@System@OpenMM@@QAEXPAVForce@2@@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::CMMotionRemover::CMMotionRemover(int)" (__imp_??0CMMotionRemover@OpenMM@@QAE@H@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::System::System(void)" (__imp_??0System@OpenMM@@QAE@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class std::vector<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >,class std::allocator<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > > > __cdecl OpenMM::Platform::loadPluginsFromDirectory(class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >)" (__imp_?loadPluginsFromDirectory@Platform@OpenMM@@SA?AV?$vector@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@V?$allocator@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@@2@@std@@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@4@@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > __cdecl OpenMM::Platform::getDefaultPluginsDirectory(void)" (__imp_?getDefaultPluginsDirectory@Platform@OpenMM@@SA?AV?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class OpenMM::ForceImpl * __thiscall OpenMM::CMMotionRemover::createImpl(void)" (?createImpl@CMMotionRemover@OpenMM@@MAEPAVForceImpl@2@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class OpenMM::ForceImpl * __thiscall OpenMM::HarmonicBondForce::createImpl(void)" (?createImpl@HarmonicBondForce@OpenMM@@MAEPAVForceImpl@2@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class OpenMM::ForceImpl * __thiscall OpenMM::HarmonicAngleForce::createImpl(void)" (?createImpl@HarmonicAngleForce@OpenMM@@MAEPAVForceImpl@2@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class OpenMM::ForceImpl * __thiscall OpenMM::PeriodicTorsionForce::createImpl(void)" (?createImpl@PeriodicTorsionForce@OpenMM@@MAEPAVForceImpl@2@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class OpenMM::ForceImpl * __thiscall OpenMM::RBTorsionForce::createImpl(void)" (?createImpl@RBTorsionForce@OpenMM@@MAEPAVForceImpl@2@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class OpenMM::ForceImpl * __thiscall OpenMM::NonbondedForce::createImpl(void)" (?createImpl@NonbondedForce@OpenMM@@MAEPAVForceImpl@2@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class OpenMM::ForceImpl * __thiscall OpenMM::GBSAOBCForce::createImpl(void)" (?createImpl@GBSAOBCForce@OpenMM@@MAEPAVForceImpl@2@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "public: virtual void __thiscall OpenMM::VerletIntegrator::step(int)" (?step@VerletIntegrator@OpenMM@@UAEXH@Z)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual void __thiscall OpenMM::VerletIntegrator::initialize(class OpenMM::OpenMMContextImpl &)" (?initialize@VerletIntegrator@OpenMM@@MAEXAAVOpenMMContextImpl@2@@Z)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class std::vector<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >,class std::allocator<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > > > __thiscall OpenMM::VerletIntegrator::getKernelNames(void)" (?getKernelNames@VerletIntegrator@OpenMM@@MAE?AV?$vector@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@V?$allocator@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@@2@@std@@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "public: virtual void __thiscall OpenMM::BrownianIntegrator::step(int)" (?step@BrownianIntegrator@OpenMM@@UAEXH@Z)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual void __thiscall OpenMM::BrownianIntegrator::initialize(class OpenMM::OpenMMContextImpl &)" (?initialize@BrownianIntegrator@OpenMM@@MAEXAAVOpenMMContextImpl@2@@Z)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class std::vector<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >,class std::allocator<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > > > __thiscall OpenMM::BrownianIntegrator::getKernelNames(void)" (?getKernelNames@BrownianIntegrator@OpenMM@@MAE?AV?$vector@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@V?$allocator@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@@2@@std@@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "public: virtual void __thiscall OpenMM::LangevinIntegrator::step(int)" (?step@LangevinIntegrator@OpenMM@@UAEXH@Z)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual void __thiscall OpenMM::LangevinIntegrator::initialize(class OpenMM::OpenMMContextImpl &)" (?initialize@LangevinIntegrator@OpenMM@@MAEXAAVOpenMMContextImpl@2@@Z)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class std::vector<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >,class std::allocator<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > > > __thiscall OpenMM::LangevinIntegrator::getKernelNames(void)" (?getKernelNames@LangevinIntegrator@OpenMM@@MAE?AV?$vector@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@V?$allocator@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@@2@@std@@XZ)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::CMMotionRemover::~CMMotionRemover(void)" (__imp_??1CMMotionRemover@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::CMMotionRemover::`scalar deleting destructor'(unsigned int)" (??_GCMMotionRemover@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::HarmonicBondForce::~HarmonicBondForce(void)" (__imp_??1HarmonicBondForce@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::HarmonicBondForce::`scalar deleting destructor'(unsigned int)" (??_GHarmonicBondForce@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::HarmonicAngleForce::~HarmonicAngleForce(void)" (__imp_??1HarmonicAngleForce@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::HarmonicAngleForce::`scalar deleting destructor'(unsigned int)" (??_GHarmonicAngleForce@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::PeriodicTorsionForce::~PeriodicTorsionForce(void)" (__imp_??1PeriodicTorsionForce@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::PeriodicTorsionForce::`scalar deleting destructor'(unsigned int)" (??_GPeriodicTorsionForce@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::RBTorsionForce::~RBTorsionForce(void)" (__imp_??1RBTorsionForce@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::RBTorsionForce::`scalar deleting destructor'(unsigned int)" (??_GRBTorsionForce@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::NonbondedForce::~NonbondedForce(void)" (__imp_??1NonbondedForce@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::NonbondedForce::`scalar deleting destructor'(unsigned int)" (??_GNonbondedForce@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::GBSAOBCForce::~GBSAOBCForce(void)" (__imp_??1GBSAOBCForce@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::GBSAOBCForce::`scalar deleting destructor'(unsigned int)" (??_GGBSAOBCForce@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::VerletIntegrator::~VerletIntegrator(void)" (__imp_??1VerletIntegrator@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::VerletIntegrator::`scalar deleting destructor'(unsigned int)" (??_GVerletIntegrator@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::BrownianIntegrator::~BrownianIntegrator(void)" (__imp_??1BrownianIntegrator@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::BrownianIntegrator::`scalar deleting destructor'(unsigned int)" (??_GBrownianIntegrator@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::LangevinIntegrator::~LangevinIntegrator(void)" (__imp_??1LangevinIntegrator@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::LangevinIntegrator::`scalar deleting destructor'(unsigned int)" (??_GLangevinIntegrator@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::System::~System(void)" (__imp_??1System@OpenMM@@QAE@XZ) referenced in function "public: void * __thiscall OpenMM::System::`scalar deleting destructor'(unsigned int)" (??_GSystem@OpenMM@@QAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::OpenMMContext::~OpenMMContext(void)" (__imp_??1OpenMMContext@OpenMM@@QAE@XZ) referenced in function "public: void * __thiscall OpenMM::OpenMMContext::`scalar deleting destructor'(unsigned int)" (??_GOpenMMContext@OpenMM@@QAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::State::~State(void)" (__imp_??1State@OpenMM@@QAE@XZ) referenced in function _openmm_copy_state
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: double __thiscall OpenMM::State::getTime(void)const " (__imp_?getTime@State@OpenMM@@QBENXZ) referenced in function _openmm_copy_state
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: class std::vector<class OpenMM::Vec3,class std::allocator<class OpenMM::Vec3> > const & __thiscall OpenMM::State::getForces(void)const " (__imp_?getForces@State@OpenMM@@QBEABV?$vector@VVec3@OpenMM@@V?$allocator@VVec3@OpenMM@@@std@@@std@@XZ) referenced in function _openmm_copy_state
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: class std::vector<class OpenMM::Vec3,class std::allocator<class OpenMM::Vec3> > const & __thiscall OpenMM::State::getVelocities(void)const " (__imp_?getVelocities@State@OpenMM@@QBEABV?$vector@VVec3@OpenMM@@V?$allocator@VVec3@OpenMM@@@std@@@std@@XZ) referenced in function _openmm_copy_state
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: class std::vector<class OpenMM::Vec3,class std::allocator<class OpenMM::Vec3> > const & __thiscall OpenMM::State::getPositions(void)const " (__imp_?getPositions@State@OpenMM@@QBEABV?$vector@VVec3@OpenMM@@V?$allocator@VVec3@OpenMM@@@std@@@std@@XZ) referenced in function _openmm_copy_state
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::System::getNumParticles(void)const " (__imp_?getNumParticles@System@OpenMM@@QBEHXZ) referenced in function _openmm_copy_state
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: class OpenMM::State __thiscall OpenMM::OpenMMContext::getState(int)const " (__imp_?getState@OpenMMContext@OpenMM@@QBE?AVState@2@H@Z) referenced in function _openmm_copy_state
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_1d referenced in function _gmx_fft_init_1d
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_free referenced in function _gmx_fft_init_1d
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_malloc referenced in function _gmx_fft_init_1d
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_r2c_1d referenced in function _gmx_fft_init_1d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_c2r_1d referenced in function _gmx_fft_init_1d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_2d referenced in function _gmx_fft_init_2d
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_r2c_2d referenced in function _gmx_fft_init_2d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_c2r_2d referenced in function _gmx_fft_init_2d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_3d referenced in function _gmx_fft_init_3d
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_r2c_3d referenced in function _gmx_fft_init_3d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_c2r_3d referenced in function _gmx_fft_init_3d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_execute_dft referenced in function _gmx_fft_1d
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_execute_dft_c2r referenced in function _gmx_fft_1d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_execute_dft_r2c referenced in function _gmx_fft_1d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_destroy_plan referenced in function _gmx_fft_destroy
1>C:\Zephyr0.5\src\win\src\kernel\Debug\mdrun_openmm.exe : fatal error LNK1120: 84 unresolved externals
1>Build log was saved at "file://c:\Zephyr0.5\src\win\src\kernel\mdrun_openmm.dir\Debug\BuildLog.htm"
1>mdrun_openmm - 85 error(s), 0 warning(s)
========== Build: 0 succeeded, 1 failed, 6 up-to-date, 0 skipped ==========
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User avatar
Jack Shultz
Posts: 77
Joined: Thu May 28, 2009 6:49 pm

RE: compile zephyr on windows

Post by Jack Shultz » Sun Jul 19, 2009 9:57 am

Resolved some of the linking issues by changing directories to one closer to
the root of the file system and paths that don't have space. I am also using
some of the pre-compiled libraries available in the 3.3.1 windows release of
gromacs.

I got most of the projects to compile except mdrun_openmm, genion, grompp and
a few others

1>------ Build started: Project: mdrun_openmm, Configuration: Debug Win32 ------
1>Linking...
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static void __cdecl OpenMM::Platform::loadPluginLibrary(class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >)" (__imp_?loadPluginLibrary@Platform@OpenMM@@SAXV?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@@Z) referenced in function _load_plugins
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::OpenMMContext::setVelocities(class std::vector<class OpenMM::Vec3,class std::allocator<class OpenMM::Vec3> > const &)" (__imp_?setVelocities@OpenMMContext@OpenMM@@QAEXABV?$vector@VVec3@OpenMM@@V?$allocator@VVec3@OpenMM@@@std@@@std@@@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::OpenMMContext::setPositions(class std::vector<class OpenMM::Vec3,class std::allocator<class OpenMM::Vec3> > const &)" (__imp_?setPositions@OpenMMContext@OpenMM@@QAEXABV?$vector@VVec3@OpenMM@@V?$allocator@VVec3@OpenMM@@@std@@@std@@@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: class OpenMM::Platform & __thiscall OpenMM::OpenMMContext::getPlatform(void)" (__imp_?getPlatform@OpenMMContext@OpenMM@@QAEAAVPlatform@2@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::OpenMMContext::OpenMMContext(class OpenMM::System &,class OpenMM::Integrator &)" (__imp_??0OpenMMContext@OpenMM@@QAE@AAVSystem@1@AAVIntegrator@1@@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::Integrator::setConstraintTolerance(double)" (__imp_?setConstraintTolerance@Integrator@OpenMM@@QAEXN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::LangevinIntegrator::LangevinIntegrator(double,double,double)" (__imp_??0LangevinIntegrator@OpenMM@@QAE@NNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::BrownianIntegrator::BrownianIntegrator(double,double,double)" (__imp_??0BrownianIntegrator@OpenMM@@QAE@NNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::VerletIntegrator::VerletIntegrator(double)" (__imp_??0VerletIntegrator@OpenMM@@QAE@N@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::System::addConstraint(int,int,double)" (__imp_?addConstraint@System@OpenMM@@QAEHHHN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::GBSAOBCForce::addParticle(double,double,double)" (__imp_?addParticle@GBSAOBCForce@OpenMM@@QAEHNNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::GBSAOBCForce::setSolventDielectric(double)" (__imp_?setSolventDielectric@GBSAOBCForce@OpenMM@@QAEXN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::GBSAOBCForce::setSoluteDielectric(double)" (__imp_?setSoluteDielectric@GBSAOBCForce@OpenMM@@QAEXN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::GBSAOBCForce::GBSAOBCForce(void)" (__imp_??0GBSAOBCForce@OpenMM@@QAE@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::NonbondedForce::addException(int,int,double,double,double)" (__imp_?addException@NonbondedForce@OpenMM@@QAEHHHNNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::System::addParticle(double)" (__imp_?addParticle@System@OpenMM@@QAEHN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::NonbondedForce::addParticle(double,double,double)" (__imp_?addParticle@NonbondedForce@OpenMM@@QAEHNNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::NonbondedForce::setCutoffDistance(double)" (__imp_?setCutoffDistance@NonbondedForce@OpenMM@@QAEXN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::NonbondedForce::setPeriodicBoxVectors(class OpenMM::Vec3,class OpenMM::Vec3,class OpenMM::Vec3)" (__imp_?setPeriodicBoxVectors@NonbondedForce@OpenMM@@QAEXVVec3@2@00@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::NonbondedForce::setNonbondedMethod(enum OpenMM::NonbondedForce::NonbondedMethod)" (__imp_?setNonbondedMethod@NonbondedForce@OpenMM@@QAEXW4NonbondedMethod@12@@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::NonbondedForce::NonbondedForce(void)" (__imp_??0NonbondedForce@OpenMM@@QAE@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::RBTorsionForce::addTorsion(int,int,int,int,double,double,double,double,double,double)" (__imp_?addTorsion@RBTorsionForce@OpenMM@@QAEHHHHHNNNNNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::RBTorsionForce::RBTorsionForce(void)" (__imp_??0RBTorsionForce@OpenMM@@QAE@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::PeriodicTorsionForce::addTorsion(int,int,int,int,int,double,double)" (__imp_?addTorsion@PeriodicTorsionForce@OpenMM@@QAEHHHHHHNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::PeriodicTorsionForce::PeriodicTorsionForce(void)" (__imp_??0PeriodicTorsionForce@OpenMM@@QAE@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::HarmonicAngleForce::addAngle(int,int,int,double,double)" (__imp_?addAngle@HarmonicAngleForce@OpenMM@@QAEHHHHNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::HarmonicAngleForce::HarmonicAngleForce(void)" (__imp_??0HarmonicAngleForce@OpenMM@@QAE@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::HarmonicBondForce::addBond(int,int,double,double)" (__imp_?addBond@HarmonicBondForce@OpenMM@@QAEHHHNN@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::HarmonicBondForce::HarmonicBondForce(void)" (__imp_??0HarmonicBondForce@OpenMM@@QAE@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall OpenMM::System::addForce(class OpenMM::Force *)" (__imp_?addForce@System@OpenMM@@QAEXPAVForce@2@@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::CMMotionRemover::CMMotionRemover(int)" (__imp_??0CMMotionRemover@OpenMM@@QAE@H@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::System::System(void)" (__imp_??0System@OpenMM@@QAE@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class std::vector<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >,class std::allocator<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > > > __cdecl OpenMM::Platform::loadPluginsFromDirectory(class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >)" (__imp_?loadPluginsFromDirectory@Platform@OpenMM@@SA?AV?$vector@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@V?$allocator@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@@2@@std@@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@4@@Z) referenced in function _openmm_init
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: static class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > __cdecl OpenMM::Platform::getDefaultPluginsDirectory(void)" (__imp_?getDefaultPluginsDirectory@Platform@OpenMM@@SA?AV?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@XZ) referenced in function _openmm_init
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class OpenMM::ForceImpl * __thiscall OpenMM::CMMotionRemover::createImpl(void)" (?createImpl@CMMotionRemover@OpenMM@@MAEPAVForceImpl@2@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class OpenMM::ForceImpl * __thiscall OpenMM::HarmonicBondForce::createImpl(void)" (?createImpl@HarmonicBondForce@OpenMM@@MAEPAVForceImpl@2@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class OpenMM::ForceImpl * __thiscall OpenMM::HarmonicAngleForce::createImpl(void)" (?createImpl@HarmonicAngleForce@OpenMM@@MAEPAVForceImpl@2@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class OpenMM::ForceImpl * __thiscall OpenMM::PeriodicTorsionForce::createImpl(void)" (?createImpl@PeriodicTorsionForce@OpenMM@@MAEPAVForceImpl@2@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class OpenMM::ForceImpl * __thiscall OpenMM::RBTorsionForce::createImpl(void)" (?createImpl@RBTorsionForce@OpenMM@@MAEPAVForceImpl@2@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class OpenMM::ForceImpl * __thiscall OpenMM::NonbondedForce::createImpl(void)" (?createImpl@NonbondedForce@OpenMM@@MAEPAVForceImpl@2@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class OpenMM::ForceImpl * __thiscall OpenMM::GBSAOBCForce::createImpl(void)" (?createImpl@GBSAOBCForce@OpenMM@@MAEPAVForceImpl@2@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "public: virtual void __thiscall OpenMM::VerletIntegrator::step(int)" (?step@VerletIntegrator@OpenMM@@UAEXH@Z)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual void __thiscall OpenMM::VerletIntegrator::initialize(class OpenMM::OpenMMContextImpl &)" (?initialize@VerletIntegrator@OpenMM@@MAEXAAVOpenMMContextImpl@2@@Z)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class std::vector<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >,class std::allocator<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > > > __thiscall OpenMM::VerletIntegrator::getKernelNames(void)" (?getKernelNames@VerletIntegrator@OpenMM@@MAE?AV?$vector@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@V?$allocator@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@@2@@std@@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "public: virtual void __thiscall OpenMM::BrownianIntegrator::step(int)" (?step@BrownianIntegrator@OpenMM@@UAEXH@Z)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual void __thiscall OpenMM::BrownianIntegrator::initialize(class OpenMM::OpenMMContextImpl &)" (?initialize@BrownianIntegrator@OpenMM@@MAEXAAVOpenMMContextImpl@2@@Z)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class std::vector<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >,class std::allocator<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > > > __thiscall OpenMM::BrownianIntegrator::getKernelNames(void)" (?getKernelNames@BrownianIntegrator@OpenMM@@MAE?AV?$vector@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@V?$allocator@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@@2@@std@@XZ)
1>md_openmm.obj : error LNK2001: unresolved external symbol "public: virtual void __thiscall OpenMM::LangevinIntegrator::step(int)" (?step@LangevinIntegrator@OpenMM@@UAEXH@Z)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual void __thiscall OpenMM::LangevinIntegrator::initialize(class OpenMM::OpenMMContextImpl &)" (?initialize@LangevinIntegrator@OpenMM@@MAEXAAVOpenMMContextImpl@2@@Z)
1>md_openmm.obj : error LNK2001: unresolved external symbol "protected: virtual class std::vector<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >,class std::allocator<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > > > __thiscall OpenMM::LangevinIntegrator::getKernelNames(void)" (?getKernelNames@LangevinIntegrator@OpenMM@@MAE?AV?$vector@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@V?$allocator@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@@2@@std@@XZ)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::CMMotionRemover::~CMMotionRemover(void)" (__imp_??1CMMotionRemover@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::CMMotionRemover::`scalar deleting destructor'(unsigned int)" (??_GCMMotionRemover@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::HarmonicBondForce::~HarmonicBondForce(void)" (__imp_??1HarmonicBondForce@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::HarmonicBondForce::`scalar deleting destructor'(unsigned int)" (??_GHarmonicBondForce@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::HarmonicAngleForce::~HarmonicAngleForce(void)" (__imp_??1HarmonicAngleForce@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::HarmonicAngleForce::`scalar deleting destructor'(unsigned int)" (??_GHarmonicAngleForce@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::PeriodicTorsionForce::~PeriodicTorsionForce(void)" (__imp_??1PeriodicTorsionForce@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::PeriodicTorsionForce::`scalar deleting destructor'(unsigned int)" (??_GPeriodicTorsionForce@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::RBTorsionForce::~RBTorsionForce(void)" (__imp_??1RBTorsionForce@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::RBTorsionForce::`scalar deleting destructor'(unsigned int)" (??_GRBTorsionForce@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::NonbondedForce::~NonbondedForce(void)" (__imp_??1NonbondedForce@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::NonbondedForce::`scalar deleting destructor'(unsigned int)" (??_GNonbondedForce@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::GBSAOBCForce::~GBSAOBCForce(void)" (__imp_??1GBSAOBCForce@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::GBSAOBCForce::`scalar deleting destructor'(unsigned int)" (??_GGBSAOBCForce@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::VerletIntegrator::~VerletIntegrator(void)" (__imp_??1VerletIntegrator@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::VerletIntegrator::`scalar deleting destructor'(unsigned int)" (??_GVerletIntegrator@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::BrownianIntegrator::~BrownianIntegrator(void)" (__imp_??1BrownianIntegrator@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::BrownianIntegrator::`scalar deleting destructor'(unsigned int)" (??_GBrownianIntegrator@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: virtual __thiscall OpenMM::LangevinIntegrator::~LangevinIntegrator(void)" (__imp_??1LangevinIntegrator@OpenMM@@UAE@XZ) referenced in function "public: virtual void * __thiscall OpenMM::LangevinIntegrator::`scalar deleting destructor'(unsigned int)" (??_GLangevinIntegrator@OpenMM@@UAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::System::~System(void)" (__imp_??1System@OpenMM@@QAE@XZ) referenced in function "public: void * __thiscall OpenMM::System::`scalar deleting destructor'(unsigned int)" (??_GSystem@OpenMM@@QAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::OpenMMContext::~OpenMMContext(void)" (__imp_??1OpenMMContext@OpenMM@@QAE@XZ) referenced in function "public: void * __thiscall OpenMM::OpenMMContext::`scalar deleting destructor'(unsigned int)" (??_GOpenMMContext@OpenMM@@QAEPAXI@Z)
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __thiscall OpenMM::State::~State(void)" (__imp_??1State@OpenMM@@QAE@XZ) referenced in function _openmm_copy_state
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: double __thiscall OpenMM::State::getTime(void)const " (__imp_?getTime@State@OpenMM@@QBENXZ) referenced in function _openmm_copy_state
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: class std::vector<class OpenMM::Vec3,class std::allocator<class OpenMM::Vec3> > const & __thiscall OpenMM::State::getForces(void)const " (__imp_?getForces@State@OpenMM@@QBEABV?$vector@VVec3@OpenMM@@V?$allocator@VVec3@OpenMM@@@std@@@std@@XZ) referenced in function _openmm_copy_state
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: class std::vector<class OpenMM::Vec3,class std::allocator<class OpenMM::Vec3> > const & __thiscall OpenMM::State::getVelocities(void)const " (__imp_?getVelocities@State@OpenMM@@QBEABV?$vector@VVec3@OpenMM@@V?$allocator@VVec3@OpenMM@@@std@@@std@@XZ) referenced in function _openmm_copy_state
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: class std::vector<class OpenMM::Vec3,class std::allocator<class OpenMM::Vec3> > const & __thiscall OpenMM::State::getPositions(void)const " (__imp_?getPositions@State@OpenMM@@QBEABV?$vector@VVec3@OpenMM@@V?$allocator@VVec3@OpenMM@@@std@@@std@@XZ) referenced in function _openmm_copy_state
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: int __thiscall OpenMM::System::getNumParticles(void)const " (__imp_?getNumParticles@System@OpenMM@@QBEHXZ) referenced in function _openmm_copy_state
1>md_openmm.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: class OpenMM::State __thiscall OpenMM::OpenMMContext::getState(int)const " (__imp_?getState@OpenMMContext@OpenMM@@QBE?AVState@2@H@Z) referenced in function _openmm_copy_state
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_1d referenced in function _gmx_fft_init_1d
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_free referenced in function _gmx_fft_init_1d
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_malloc referenced in function _gmx_fft_init_1d
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_r2c_1d referenced in function _gmx_fft_init_1d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_c2r_1d referenced in function _gmx_fft_init_1d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_2d referenced in function _gmx_fft_init_2d
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_r2c_2d referenced in function _gmx_fft_init_2d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_c2r_2d referenced in function _gmx_fft_init_2d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_3d referenced in function _gmx_fft_init_3d
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_r2c_3d referenced in function _gmx_fft_init_3d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_plan_dft_c2r_3d referenced in function _gmx_fft_init_3d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_execute_dft referenced in function _gmx_fft_1d
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_execute_dft_c2r referenced in function _gmx_fft_1d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_execute_dft_r2c referenced in function _gmx_fft_1d_real
1>md.lib(gmx_fft_fftw3.obj) : error LNK2019: unresolved external symbol __imp__fftwf_destroy_plan referenced in function _gmx_fft_destroy
1>C:\Zephyr0.5\src\win\src\kernel\Debug\mdrun_openmm.exe : fatal error LNK1120: 84 unresolved externals
1>Build log was saved at "file://c:\Zephyr0.5\src\win\src\kernel\mdrun_openmm.dir\Debug\BuildLog.htm"
1>mdrun_openmm - 85 error(s), 0 warning(s)
========== Build: 0 succeeded, 1 failed, 6 up-to-date, 0 skipped ==========
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User avatar
Christopher Bruns
Posts: 32
Joined: Thu Apr 07, 2005 1:10 pm

RE: compile zephyr on windows

Post by Christopher Bruns » Mon Jul 20, 2009 4:55 pm

I am not sure why your posts from the 19th do not show up on the forums. Perhaps the web server does not like some of the characters in the post. (I don't mean you (: )

From your email, it seems that the compiler is finding the header files for OpenMM and FFTW OK, but the linker is not finding the OpenMM and FFTW library files (.lib and/or .dll files). Are these libraries on your Windows PATH?
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Joy Ku
Posts: 80
Joined: Tue Oct 02, 2007 5:22 pm

RE: compile zephyr on windows

Post by Joy Ku » Tue Jul 21, 2009 9:57 am

The web server does not always handle ampersands (&) properly and so sometimes posts with these characters do not appear. We are working on a solution to this.

Joy
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Jack Shultz
Posts: 77
Joined: Thu May 28, 2009 6:49 pm

RE: compile zephyr on windows

Post by Jack Shultz » Wed Jul 22, 2009 8:30 am

Thanks Chris and Joy.

I went back and added the libraries for fftw and OpenMM to my windows path. I also made sure there was a reference in visuals studio C++ Directories for these libraries.
I also set these library directories using the additional libraries option in the mdrun_openmm project

I'm using pre-compile windows versions of fftw and openmm.
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User avatar
Jack Shultz
Posts: 77
Joined: Thu May 28, 2009 6:49 pm

RE: compile zephyr on windows

Post by Jack Shultz » Wed Jul 22, 2009 9:01 am

I tried two pre-compiled version of fftw
First I tried precompiled DLL files for FFTW 3.2.2 in single/double/long-double precision

Then I tried, Alessio Massaro contributed Windows binaries of fftw-3.0.1, compiled with the Intel C Compiler version 7.1.

Note here is the command line listed for the linkers. It produced the same error message.
/OUT:"C:\Zephyr0.5\src\win\src\kernel\Release\mdrun_openmm.exe" /VERSION:0.0 /INCREMENTAL:NO /NOLOGO /LIBPATH:"C:\Zephyr0.5\src\OpenMMPreview3-WindowsVC9\lib" /LIBPATH:"C:\Zephyr0.5\src\fftw-3.0.1" /MANIFEST /MANIFESTFILE:"mdrun_openmm.dir\Release\mdrun_openmm.exe.intermediate.manifest" /MANIFESTUAC:"level='asInvoker' uiAccess='false'" /PDB:"C:/Zephyr0.5/src/win/src/kernel/Release/mdrun_openmm.pdb" /SUBSYSTEM:CONSOLE /DYNAMICBASE /NXCOMPAT /IMPLIB:"C:\Zephyr0.5\src\win\src\kernel\Release\mdrun_openmm.lib" /ERRORREPORT:PROMPT kernel32.lib user32.lib gdi32.lib winspool.lib shell32.lib ole32.lib oleaut32.lib uuid.lib comdlg32.lib advapi32.lib ws2_32.lib Release\gmxpreprocess.lib ..\mdlib\Release\md.lib ..\gmxlib\Release\gmx.lib ..\gmxlib\nonbonded\nb_kernel\Release\nb_kernel.lib
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