[gmx-users] Installing mdrun-gpu Using Gromacs-4.5.3
Solomon Berman
smberman at bu.edu
Tue Nov 16 00:01:06 CET 2010
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-request at gromacs.org wrote:
> From: Rossen Apostolov <rossen at kth.se>
> Date: November 15, 2010 5:13:06 PM EST
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Installing mdrun-gpu Using Gromacs-4.5.3
> Reply-To: Discussion list for GROMACS users <gmx-users at 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 at 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-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101115/9a39a1f5/attachment.html>
More information about the gromacs.org_gmx-users
mailing list