Thank you very much for writing! I have tried what was suggested, and the following errors were produced follow the use of the make mdrun command:
[100%] Building C object src/kernel/CMakeFiles/mdrun.dir/md_openmm.c.o Linking CXX executable mdrun-gpu ld: warning: in /usr/local/openmm/lib/libOpenMM.dylib, file was built for i386 which is not the architecture being linked (x86_64) Undefined symbols: "OpenMM::Context::~Context()", referenced from: _openmm_cleanup in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::Platform::getDefaultPluginsDirectory()", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::Context::getState(int) const", referenced from: _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::MonteCarloBarostat::MonteCarloBarostat(double, double, int)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::NonbondedForce::getNonbondedMethod() const", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::Context::setVelocities(std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3> > const&)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::CustomTorsionForce::CustomTorsionForce(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::NonbondedForce::getCutoffDistance() const", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::NonbondedForce::setCutoffDistance(double)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::Platform::getPlatform(int)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::NonbondedForce::addException(int, int, double, double, double, bool)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::AndersenThermostat::AndersenThermostat(double, double)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::Platform::setPropertyDefaultValue(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::HarmonicBondForce::addBond(int, int, double, double)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::State::getPotentialEnergy() const", referenced from: _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::GBSAOBCForce::setNonbondedMethod(OpenMM::GBSAOBCForce::NonbondedMethod)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::CustomTorsionForce::addPerTorsionParameter(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::VerletIntegrator::VerletIntegrator(double)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::Platform::getPropertyNames()", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::NonbondedForce::NonbondedForce()", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::GBSAOBCForce::GBSAOBCForce()", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::NonbondedForce::setEwaldErrorTolerance(double)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::CustomTorsionForce::addTorsion(int, int, int, int, std::vector<double, std::allocator<double> > const&)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::System::System()", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::Platform::getNumPlatforms()", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::PeriodicTorsionForce::PeriodicTorsionForce()", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::GBSAOBCForce::addParticle(double, double, double)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::State::getKineticEnergy() const", referenced from: _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::System::~System()", referenced from: _openmm_cleanup in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::Context::getPlatform()", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::PeriodicTorsionForce::addTorsion(int, int, int, int, int, double, double)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::State::getTime() const", referenced from: _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::NonbondedForce::addParticle(double, double, double)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::HarmonicBondForce::HarmonicBondForce()", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::State::getVelocities() const", referenced from: _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::Context::setPositions(std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3> > const&)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::CMMotionRemover::CMMotionRemover(int)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::BrownianIntegrator::BrownianIntegrator(double, double, double)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::Platform::loadPluginsFromDirectory(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::HarmonicAngleForce::HarmonicAngleForce()", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::GBSAOBCForce::setCutoffDistance(double)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::System::addConstraint(int, int, double)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::System::setDefaultPeriodicBoxVectors(OpenMM::Vec3 const&, OpenMM::Vec3 const&, OpenMM::Vec3 const&)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::RBTorsionForce::RBTorsionForce()", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::NonbondedForce::setNonbondedMethod(OpenMM::NonbondedForce::NonbondedMethod)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::HarmonicAngleForce::addAngle(int, int, int, double, double)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::LangevinIntegrator::LangevinIntegrator(double, double, double)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::State::getForces() const", referenced from: _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::Context::Context(OpenMM::System&, OpenMM::Integrator&, OpenMM::Platform&)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::State::getPositions() const", referenced from: _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) "OpenMM::RBTorsionForce::addTorsion(int, int, int, int, double, double, double, double, double, double)", referenced from: _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) _openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o) ld: symbol(s) not found collect2: ld returned 1 exit status make[3]: *** [src/kernel/mdrun-gpu] Error 1 make[2]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2 make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 make: *** [mdrun] Error 2 I did use the OpenMM software provided on their website for Mac. Is there a workaround for this issue? Thanks again for the help! Best, Solomon Berman Department of Chemistry Boston University On Nov 15, 2010, at 5:44 PM, gmx-users-requ...@gromacs.org wrote: > From: Rossen Apostolov <ros...@kth.se> > Date: November 15, 2010 5:13:06 PM EST > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Installing mdrun-gpu Using Gromacs-4.5.3 > Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > Hi, > > Did you run CMake in a fresh directory? If not try > > $ rm CMakeCache.txt > $ cmake -DGMX_OPENMM=ON > $ make mdrun > > Cheers, > Rossen > > On 11/14/10 5:58 PM, Solomon Berman wrote: >> Good day friends, >> >> I am trying to install mdrun-gpu on my MacBook Pro, using Mac OS X Snow >> Leopard v. 10.6.5. >> >> I typed the following commands into the terminal screen while in the >> gromacs-4.5.3 source directory. >> >> cmake -DGMX_OPENMM=ON >> make mdrun >> >> The following error messages are produced: >> >> [ 63%] Building C object >> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o >> /gromacs-4.5.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c: >> In function ‘nb_kernel400nf_x86_64_sse’: >> /gromacs-4.5.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: >> error: ‘gmx_invsqrt_exptab’ undeclared (first use in this function) >> /gromacs-4.5.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: >> error: (Each undeclared identifier is reported only once >> /gromacs-4.5.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: >> error: for each function it appears in.) >> /gromacs-4.5.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: >> error: ‘gmx_invsqrt_fracttab’ undeclared (first use in this function) >> make[3]: *** >> [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o] >> Error 1 >> make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 >> make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 >> make: *** [mdrun] Error 2 >> >> >> I am not sure how to troubleshoot these error messages. I know this is a >> new implementation, where we were originally given precompiled binaries for >> download, so this may or may not be unique to the switch over. >> >> Any help anyone would be willing to provide, I would be greatly >> appreciative. Thank you! >> >> Best, >> >> Solomon Berman >> Department of Chemistry >> Boston University-- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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