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Instrumenting CXX Applications
Kevin Huck edited this page Oct 28, 2019
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This page is an overview of how to use TAU to instrument a C++ application that uses CMake as a configuration/build tool. THe application shown in this example is OpenMM, an open-source molecular dynamics application.
The most important thing to understand about instrumenting C++ applications is that without some selective instrumentation and/or filtering of timers, the application can quickly be overwhelmed with timer calls due to the high number of getter/setter methods that are common in C++ applications. When blindly instrumenting an entire application (especially with compiler-based instrumentation), all of the member functions and template expansions of some standard library objects will also be instrumented, introducing several orders of magnitude of overhead. To prevent that, we use selective instrumentation and the PDT infrastructure for source-to-source instrumentation.
More detailed instructions for installing TAU are located here.
We will configure PDT with:
wget http://tau.uoregon.edu/pdt.tgz
tar -xzf pdt.tgz
cd pdtoolkit-3.25.1
# Perform in-place installation
./configure -GNU
make -j installOne particular problem with OpenMM is it's use of transient threads. The source code will detect the number of cores on the node, and launch that many pthreads (despite what the documentation says about the OPENMM_CPU_THREADS variable).
We will configure TAU with thread recycling (an experimental feature), because for some applciations OpenMM will launch N threads, destroy them, and re-launch them (possibly many times). Currently, TAU has a hard-coded thread count limit of 128-512 (depending on the platform). In this particular example, we will configure TAU with (your path to PDT may vary):
./configure -useropt=-DTAU_RECYCLE_THREADS#-O2#-g -pdt=/home/users/khuck/src/pdtoolkit-3.25.1 -pthread -bfd=download -unwind=download -otf=downloadThe -useropt=-DTAU_RECYCLE_THREADS#-O2#-g argument will replace the default -O2 -g compiler arguments to build TAU (the # character is used to represent white space, and will be converted by the configuration process).
As mentioned earlier, for this example we are building OpenMM. To get the source:
git clone https://github.com/openmm/openmm.git
cd openmmOn this example test system, we are building on an IBM POWER9 node with 40 cores (160 HW threads) and NVIDIA V100 GPUs. These are the modules and environment settings required to build (OpenMM dependencies):
module purge
module load cuda/9.2
module load fftw/3.3.8-openmpi4-gcc6.3
module load openmpi/4.0.1-gcc6.3
module load gcc/6.3
module load cmake/3.15.4
module list
# Add Swig 4 to the path
PATH=/usr/local/packages/swig/4.0.1/bin:$PATH
# Set the TAU settings
export TAU_MAKEFILE=/home/users/khuck/src/tau2/ibm64linux/lib/Makefile.tau-gnu-pthread-pdt
export TAU_OPTIONS="-optQuiet -optRevert -optNoCompInst -optShared -optSelectFile=/home/users/khuck/src/openmm/select.tau"The meanings of the TAU options are:
- -optQuiet - parse/instrument/compile silently
- -optRevert - if the parser fails, try other options, then just compile if all fail
- -optNoCompInst - don't use compiler-based instrumentation if PDT instrumentation fails
- -optShared - link with the libTAUsh.so shared library, not libTAU.a
- -optSelectFile - use this select file to specify which files/functions to instrument
The contents of select.tau are (to instrument only the main function and any functions in the OpenMM namespace):
BEGIN_INCLUDE_LIST
"int main#"
"#OpenMM#"
END_INCLUDE_LISTThese are the settings required to build. However, the CMake configuration for OpenMM uses the compiler to auto-detect hardware and OS configuration settings - including some tests designed to fail. Because we are using the TAU compiler wrappers to instrument the application, we need to tell CMake about the compiler wrapper but disable TAU instrumentation - otherwise the TAU error output will interfere with the auto-detection process. To do that we change the TAU_OPTIONS environment variable for cmake, then change it back:
mkdir build-tau
cd build-tau
# save the TAU options
OLD_TAU_OPTIONS=${TAU_OPTIONS}
TAU_OPTIONS="-optQuiet -optLinkOnly -optRevert -optNoCompInst"
cmake -G "Unix Makefiles" .. \
-DCMAKE_C_COMPILER=`which tau_cc.sh` \
-DCMAKE_CXX_COMPILER=`which tau_cxx.sh` \
-DCMAKE_BUILD_TYPE=RelWithDebInfo
# Restore the TAU options for building
TAU_OPTIONS=${OLD_TAU_OPTIONS}
make -j40The current (as of October 24, 2019) C++ parser used by PDT cannot support some language features, so several compiler errors will be seen when building, but the -optRevert option will tell tau_cxx.sh to fall back to different settings until either one source parser succeeds or the file is left uninstrumented.
After building, you can validate the build with make test in the build-tau directory (although some tests take a long time to run).
Running an individual test (for example, ./TestReferenceCustomIntegrator in the build directory will write a bunch of profile.* files (one per concurrent thread & process), and they can be summarized on the command line with the pprof TAU program:
$ pprof .
FUNCTION SUMMARY (mean):
---------------------------------------------------------------------------------------
%Time Exclusive Inclusive #Call #Subrs Inclusive Name
msec total msec usec/call
---------------------------------------------------------------------------------------
68.9 0.00273 74 1.98758 1.98758 37424 OpenMM::threadBody(void*)
68.9 0.00761 74 1.98758 4.19876 37422 void *OpenMM::threadBody(void *)
68.9 74 74 3.97516 0 18709 void OpenMM::ThreadPool::syncThreads()
54.4 18 58 1 9466.81 58735 .TAU application
8.8 8 9 499.932 5198.64 19 double OpenMM::NonbondedForceImpl::calcForcesAndEnergy(OpenMM::ContextImpl &, bool, bool, int)
1.9 1 2 621.124 2981.39 3 double OpenMM::HarmonicBondForceImpl::calcForcesAndEnergy(OpenMM::ContextImpl &, bool, bool, int) [THROTTLED]
1.2 0.00284 1 0.136646 4.40373 9748 void OpenMM::ReferenceConstraints::ReferenceConstraints(const OpenMM::System &)
0.9 0.425 0.966 0.0124224 1.98758 77779 void OpenMM::ThreadPool::ThreadPool(int)
0.5 0.592 0.592 372.671 0.00621118 2 void OpenMM::ReferenceAndersenThermostat::applyThermostat(const std::vector<std::vector<int, std::allocator<int>>, std::allocator<std::vector<int, std::allocator<int>>>> &, std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &, std::vector<double, std::allocator<double>> &, double, double, double) const
0.5 0.541 0.541 1.98758 0 272 pthread_create
0.5 0.0738 0.5 0.310559 5.42236 1611 void OpenMM::MonteCarloBarostatImpl::updateContextState(OpenMM::ContextImpl &, bool &)
0.3 0.272 0.35 621.124 347.329 1 double OpenMM::SimTKOpenMMUtilities::getNormallyDistributedRandomNumber() [THROTTLED]
0.3 0.225 0.286 621.124 273.658 0 double OpenMM::SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() [THROTTLED]
0.2 0.187 0.253 621.124 186.335 0 void OpenMM::ReferenceBondForce::calculateForce(int, std::vector<std::vector<int, std::allocator<int>>, std::allocator<std::vector<int, std::allocator<int>>>> &, std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &, std::vector<std::vector<double, std::allocator<double>>, std::allocator<std::vector<double, std::allocator<double>>>> &, std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &, double *, OpenMM::ReferenceBondIxn &) [THROTTLED]
0.2 0.00131 0.206 0.0124224 1.98758 16583 void OpenMM::ThreadPool::~ThreadPool()
0.2 0.205 0.205 1.98758 0 103 pthread_join
0.2 0.2 0.203 621.124 12.4224 0 void OpenMM::ReferenceHarmonicBondIxn::calculateBondIxn(std::vector<int, std::allocator<int>> &, std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &, std::vector<double, std::allocator<double>> &, std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &, double *, double *) [THROTTLED]
0.2 0.172 0.172 621.124 0 0 void OpenMM::ReferenceVirtualSites::computePositions(const OpenMM::System &, std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &) [THROTTLED]
0.1 0.161 0.161 621.124 0 0 void OpenMM::ReferenceForce::getDeltaRPeriodic(const OpenMM::Vec3 &, const OpenMM::Vec3 &, const OpenMM::Vec3 *, double *) [THROTTLED]
0.1 0.159 0.159 621.124 0 0 void OpenMM::ReferenceForce::ReferenceForce() [THROTTLED]
0.1 0.158 0.158 621.124 0 0 double OpenMM::Integrator::getStepSize() const [THROTTLED]
0.1 0.155 0.155 621.124 0 0 void OpenMM::ReferenceHarmonicBondIxn::ReferenceHarmonicBondIxn() [THROTTLED]
0.1 0.155 0.155 0.0124224 0 12506 void OpenMM::ThreadPool::waitForThreads()
0.1 0.151 0.151 621.124 0 0 void OpenMM::ReferenceDynamics::setReferenceConstraintAlgorithm(OpenMM::ReferenceConstraintAlgorithm *) [THROTTLED]
0.1 0.149 0.149 621.124 0 0 void OpenMM::Integrator::setStepSize(double) [THROTTLED]
0.1 0.143 0.143 621.124 0 0 void OpenMM::ReferenceBondForce::~ReferenceBondForce() [THROTTLED]
0.1 0.142 0.142 621.124 0 0 int OpenMM::ReferenceDynamics::incrementTimeStep() [THROTTLED]
0.1 0.141 0.141 621.124 0 0 void OpenMM::ReferenceBondIxn::~ReferenceBondIxn() [THROTTLED]
0.1 0.14 0.14 621.124 0 0 void OpenMM::ReferenceForce::getDeltaR(const OpenMM::Vec3 &, const OpenMM::Vec3 &, double *) [THROTTLED]
0.1 0.14 0.14 621.124 0 0 double OpenMM::Integrator::getConstraintTolerance() const [THROTTLED]
0.1 0.138 0.138 621.124 0 0 uint32_t OpenMM_SFMT::gen_rand32(OpenMM_SFMT::SFMT &) [THROTTLED]
0.1 0.138 0.138 621.124 0 0 void OpenMM::ReferenceBondForce::ReferenceBondForce() [THROTTLED]
0.1 0.138 0.138 621.124 0 0 const std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &OpenMM::State::getPositions() const [THROTTLED]
0.1 0.137 0.137 621.124 0 0 double OpenMM::ReferenceDynamics::getDeltaT() const [THROTTLED]
0.1 0.137 0.137 621.124 0 0 void OpenMM::ReferenceForce::~ReferenceForce() [THROTTLED]
0.1 0.137 0.137 621.124 0 0 void OpenMM::ReferenceHarmonicBondIxn::~ReferenceHarmonicBondIxn() [THROTTLED]
0.1 0.136 0.136 621.124 0 0 void OpenMM::ReferenceBondIxn::ReferenceBondIxn() [THROTTLED]
0.1 0.122 0.122 512.255 0 0 void OpenMM::ReferenceVirtualSites::distributeForces(const OpenMM::System &, const std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &, std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &)
0.1 0.114 0.114 509.224 0 0 const std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &OpenMM::State::getVelocities() const
0.1 0.104 0.104 462.646 0 0 void OpenMM::ReferenceLJCoulomb14::ReferenceLJCoulomb14()
0.1 0.103 0.103 462.646 0 0 void OpenMM::ReferenceLJCoulomb14::~ReferenceLJCoulomb14()
0.1 0.0422 0.0627 89.6087 89.6087 1 void OpenMM::State::StateBuilder::setPeriodicBoxVectors(const OpenMM::Vec3 &, const OpenMM::Vec3 &, const OpenMM::Vec3 &)
0.0 0.0276 0.0424 57.2857 57.2857 1 void OpenMM::State::StateBuilder::setEnergy(double, double)
0.0 0.0244 0.0409 50.3168 50.3168 1 void OpenMM::State::StateBuilder::setPositions(const std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &)
0.0 0.0265 0.0265 89.6087 0 0 OpenMM::State OpenMM::State::StateBuilder::getState()
0.0 0.0208 0.0249 12.4348 12.4224 2 void OpenMM::ReferenceConstraints::applyToVelocities(std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &, std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &, std::vector<double, std::allocator<double>> &, double)
0.0 0.0217 0.0217 89.6087 0 0 void OpenMM::State::State(double)
0.0 0.016 0.0215 18.7019 12.4224 1 void OpenMM::ReferenceConstraints::apply(std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &, std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &, std::vector<double, std::allocator<double>> &, double)
0.0 0.0205 0.0205 89.6087 0 0 void OpenMM::State::setPeriodicBoxVectors(const OpenMM::Vec3 &, const OpenMM::Vec3 &, const OpenMM::Vec3 &)
0.0 0.0204 0.0204 93.3727 0 0 void OpenMM::System::getConstraintParameters(int, int &, int &, double &) const
0.0 0.0201 0.0201 89.6087 0 0 void OpenMM::State::StateBuilder::StateBuilder(double)
0.0 0.0165 0.0165 50.3168 0 0 void OpenMM::State::setPositions(const std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &)
0.0 0.0147 0.0147 57.2857 0 0 void OpenMM::State::setEnergy(double, double)
0.0 0.0131 0.0131 57.677 0 0 double OpenMM::State::getKineticEnergy() const
0.0 0.00654 0.0114 13.0497 13.0497 1 void OpenMM::State::StateBuilder::setVelocities(const std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &)
0.0 0.00804 0.00804 31.1242 0 0 OpenMM::ReferenceConstraintAlgorithm *OpenMM::ReferenceDynamics::getReferenceConstraintAlgorithm() const
0.0 0.00565 0.00565 25.6398 0 0 double OpenMM::State::getPotentialEnergy() const
0.0 0.00546 0.00546 12.4224 0 0 void OpenMM::ReferenceSETTLEAlgorithm::apply(std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &, std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &, std::vector<double, std::allocator<double>> &, double)
0.0 0.00486 0.00486 13.0497 0 0 void OpenMM::State::setVelocities(const std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &)
0.0 0.00472 0.00476 0.00621118 0.0807453 767 void OpenMM::CustomBondForceImpl::initialize(OpenMM::ContextImpl &)
0.0 0.00468 0.00472 0.00621118 0.0807453 760 void OpenMM::CustomAngleForceImpl::initialize(OpenMM::ContextImpl &)
0.0 0.00436 0.0044 1.49068 0.136646 3 OpenMM::Kernel &OpenMM::Kernel::operator=(const OpenMM::Kernel &)
0.0 0.00405 0.00405 12.4224 0 0 void OpenMM::ReferenceSETTLEAlgorithm::applyToVelocities(std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &, std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &, std::vector<double, std::allocator<double>> &, double)
0.0 0.00285 0.00285 12.8137 0 0 double OpenMM::System::getParticleMass(int) const
0.0 0.0016 0.0016 0.310559 0 5 void OpenMM::ReferenceMonteCarloBarostat::applyBarostat(std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &, const OpenMM::Vec3 *, double, double, double)
0.0 0.00155 0.00155 0.149068 0 10 void OpenMM::SimTKOpenMMUtilities::setRandomNumberSeed(uint32_t)
0.0 0.000981 0.00129 0.0559006 0.298137 23 void OpenMM::NonbondedForceImpl::initialize(OpenMM::ContextImpl &)
0.0 0.00126 0.00127 2.32298 0.0186335 1 void OpenMM::Kernel::~Kernel()
0.0 0.00127 0.00127 6.21118 0 0 double OpenMM::State::getTime() const
0.0 0.00111 0.00117 0.0124224 0.236025 94 void OpenMM::CustomExternalForceImpl::initialize(OpenMM::ContextImpl &)
0.0 0.00111 0.00115 0.198758 0.198758 6 void OpenMM_SFMT::init_gen_rand(uint32_t, OpenMM_SFMT::SFMT &)
0.0 0.000863 0.00111 0.248447 0.745342 4 void OpenMM::SerializationProxy::registerProxy(const std::type_info &, const OpenMM::SerializationProxy *)
0.0 0.000155 0.00054 0.00621118 0.00621118 87 Lepton::CustomFunction *createReferenceTabulatedFunction(const OpenMM::TabulatedFunction &) C
0.0 0.00046 0.000516 0.0248447 0.180124 21 void OpenMM::HarmonicBondForceImpl::initialize(OpenMM::ContextImpl &)
0.0 0.000242 0.000466 0.223602 0.223602 2 Lepton::CustomFunction *OpenMM::ReferenceContinuous1DFunction::clone() const
0.0 0.00018 0.000447 0.0124224 0.0124224 36 void OpenMM::ThreadPool::execute(std::function<void (OpenMM::ThreadPool &, int)>)
0.0 0.000255 0.000385 0.00621118 0.0124224 62 void OpenMM::ReferenceContinuous1DFunction::ReferenceContinuous1DFunction(const OpenMM::Continuous1DFunction &)
0.0 0.000342 0.000342 1.51553 0 0 void OpenMM::Kernel::Kernel()
0.0 0.000248 0.000286 0.00621118 0.0372671 46 void OpenMM::MonteCarloBarostatImpl::initialize(OpenMM::ContextImpl &)
0.0 0.00028 0.00028 0.807453 0 0 void OpenMM::KernelImpl::KernelImpl(std::string, const OpenMM::Platform &)
0.0 0.000255 0.000267 0.136646 0.0372671 2 void OpenMM::ReferenceConstraints::~ReferenceConstraints()
0.0 0.000267 0.000267 0.0124224 0 22 void OpenMM::ThreadPool::resumeThreads()
0.0 0.000217 0.000236 0.0124224 0.0745342 19 int QUERN_compute_qr(int, int, const int *, const int *, const double *, const int *, int **, int **, double **, int **, int **, double **) C
0.0 0.000224 0.00023 0.0186335 0.0372671 12 double OpenMM::CustomAngleForceImpl::calcForcesAndEnergy(OpenMM::ContextImpl &, bool, bool, int)
0.0 0.000143 0.000224 0.223602 0.223602 1 void OpenMM::ReferenceContinuous1DFunction::ReferenceContinuous1DFunction(const OpenMM::ReferenceContinuous1DFunction &)
0.0 0.000186 0.000211 0.0248447 0.149068 9 double OpenMM::CustomExternalForceImpl::calcForcesAndEnergy(OpenMM::ContextImpl &, bool, bool, int)
0.0 0.00018 0.000193 0.0248447 0.0496894 8 OpenMM::ForceImpl *OpenMM::HarmonicBondForce::createImpl() const
0.0 0.000174 0.000193 0.0124224 0.0745342 16 std::map<std::string, double, std::less<std::string>, std::allocator<std::pair<const std::string, double>>> OpenMM::CustomAngleForceImpl::getDefaultParameters()
0.0 0.000186 0.000186 0.807453 0 0 void OpenMM::Kernel::Kernel(OpenMM::KernelImpl *)
0.0 0.000168 0.00018 0.0124224 0.0745342 15 std::map<std::string, double, std::less<std::string>, std::allocator<std::pair<const std::string, double>>> OpenMM::CustomBondForceImpl::getDefaultParameters()
0.0 0.000155 0.000161 0.00621118 0.0248447 26 void OpenMM::NonbondedForceImpl::calcEwaldParameters(const OpenMM::System &, const OpenMM::NonbondedForce &, double &, int &, int &, int &)
0.0 0.000143 0.000155 0.0372671 0.0372671 4 void OpenMM::State::StateBuilder::setForces(const std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &)
0.0 0.00013 0.000137 0.00621118 0.0124224 22 OpenMM::ForceImpl *OpenMM::CustomAngleForce::createImpl() const
0.0 0.000124 0.000137 0.00621118 0.0186335 22 OpenMM::ForceImpl *OpenMM::MonteCarloBarostat::createImpl() const
0.0 0.000124 0.00013 0.0124224 0.0248447 10 OpenMM::ForceImpl *OpenMM::CustomExternalForce::createImpl() const
0.0 0.00013 0.00013 0.0745342 0 2 OpenMM_SFMT::SFMTData *OpenMM_SFMT::createSFMTData()
0.0 0.000118 0.00013 0.0248447 0.0248447 5 double OpenMM::ReferenceContinuous1DFunction::evaluate(const double *) const
0.0 0.000124 0.00013 0.00621118 0.00621118 21 void OpenMM::SplineFitter::createNaturalSpline(const std::vector<double, std::allocator<double>> &, const std::vector<double, std::allocator<double>> &, std::vector<double, std::allocator<double>> &)
0.0 0.000118 0.000124 0.00621118 0.0124224 20 OpenMM::ForceImpl *OpenMM::CustomBondForce::createImpl() const
0.0 0.000106 0.000106 0.621118 0 0 double OpenMM::State::getPeriodicBoxVolume() const
0.0 9.94E-05 9.94E-05 0.0186335 0 5 double OpenMM::CustomBondForceImpl::calcForcesAndEnergy(OpenMM::ContextImpl &, bool, bool, int)
0.0 9.32E-05 9.32E-05 0.248447 0 0 const std::string &OpenMM::SerializationProxy::getTypeName() const
0.0 8.07E-05 8.07E-05 0.248447 0 0 std::map<const std::string, const OpenMM::SerializationProxy *, std::less<const std::string>, std::allocator<std::pair<const std::string, const OpenMM::SerializationProxy *>>> &OpenMM::SerializationProxy::getProxiesByName()
0.0 8.07E-05 8.07E-05 0.229814 0 0 void OpenMM::Continuous1DFunction::getFunctionParameters(std::vector<double, std::allocator<double>> &, double &, double &) const
0.0 8.07E-05 8.07E-05 0.136646 0 1 void OpenMM::ReferenceMonteCarloBarostat::restorePositions(std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &)
0.0 7.45E-05 7.45E-05 0.248447 0 0 std::map<const std::string, const OpenMM::SerializationProxy *, std::less<const std::string>, std::allocator<std::pair<const std::string, const OpenMM::SerializationProxy *>>> &OpenMM::SerializationProxy::getProxiesByType()
0.0 6.83E-05 6.83E-05 0.0559006 0 1 double OpenMM::NonbondedForceImpl::calcDispersionCorrection(const OpenMM::System &, const OpenMM::NonbondedForce &)
0.0 6.21E-05 6.21E-05 0.310559 0 0 int OpenMM::ReferenceContinuous1DFunction::getNumArguments() const
0.0 6.21E-05 6.21E-05 0.136646 0 0 void OpenMM::System::~System()
0.0 5.59E-05 5.59E-05 0.0993789 0 1 int OpenMM::System::addConstraint(int, int, double)
0.0 5.59E-05 5.59E-05 0.0745342 0 1 int QUERN_multiply_with_q_transpose(int, const int *, const int *, const double *, double *) C
0.0 4.97E-05 4.97E-05 0.136646 0 0 const OpenMM::Force &OpenMM::System::getForce(int) const
0.0 4.97E-05 4.97E-05 0.111801 0 0 std::map<std::string, double, std::less<std::string>, std::allocator<std::pair<const std::string, double>>> OpenMM::NonbondedForceImpl::getDefaultParameters()
0.0 4.97E-05 4.97E-05 0.136646 0 0 void OpenMM::System::System()
0.0 4.97E-05 4.97E-05 0.15528 0 0 void OpenMM::System::getDefaultPeriodicBoxVectors(OpenMM::Vec3 &, OpenMM::Vec3 &, OpenMM::Vec3 &) const
0.0 4.35E-05 4.35E-05 0.0745342 0 1 int QUERN_solve_with_r(int, const int *, const int *, const double *, const double *, double *) C
0.0 4.35E-05 4.35E-05 0.149068 0 0 void OpenMM::Integrator::setConstraintTolerance(double)
0.0 4.35E-05 4.35E-05 0.136646 0 0 void OpenMM::ReferenceDynamics::ReferenceDynamics(int, double, double)
0.0 4.35E-05 4.35E-05 0.136646 0 0 void OpenMM::ReferenceDynamics::~ReferenceDynamics()
0.0 3.73E-05 3.73E-05 0.0559006 0 1 int OpenMM::HarmonicBondForce::addBond(int, int, double, double)
0.0 3.73E-05 3.73E-05 0.136646 0 0 void OpenMM::Integrator::Integrator()
0.0 3.73E-05 3.73E-05 0.248447 0 0 void OpenMM::SerializationProxy::SerializationProxy(const std::string &)
0.0 3.73E-05 3.73E-05 0.198758 0 0 void OpenMM_SFMT::period_certification(OpenMM_SFMT::SFMT &)
0.0 3.11E-05 3.11E-05 0.149068 0 0 double *OpenMM::ReferenceForce::getVariablePointer(Lepton::CompiledExpression &, const std::string &)
0.0 3.11E-05 3.11E-05 0.0745342 0 0 int OpenMM::ThreadPool::getNumThreads() const
0.0 3.11E-05 3.11E-05 0.0559006 0 1 std::vector<std::string, std::allocator<std::string>> OpenMM::NonbondedForceImpl::getKernelNames()
0.0 3.11E-05 3.11E-05 0.068323 0 0 void OpenMM_SFMT::deleteSFMTData(OpenMM_SFMT::SFMTData *)
0.0 2.48E-05 2.48E-05 0.0559006 0 0 const std::string &OpenMM::CustomAngleForce::getGlobalParameterName(int) const
0.0 2.48E-05 2.48E-05 0.0559006 0 0 void OpenMM::NonbondedForceImpl::~NonbondedForceImpl()
0.0 2.48E-05 2.48E-05 0.149068 0 0 void OpenMM::ReferenceForce::setVariable(double *, double)
0.0 6.21E-06 1.86E-05 0.0124224 0.0124224 2 OpenMM::ForceImpl *OpenMM::AndersenThermostat::createImpl() const
0.0 1.86E-05 1.86E-05 0.0745342 0 0 bool copy_row(int, const int *, const double *, SparseVector &)
0.0 1.86E-05 1.86E-05 0.0372671 0 0 double *OpenMM::SimTKOpenMMUtilities::allocateOneDRealOpenMMArray(int, double *, int, double, const std::string &)
0.0 1.86E-05 1.86E-05 0.0124224 0 2 int OpenMM::CustomExternalForce::addParticle(int, const std::vector<double, std::allocator<double>> &)
0.0 1.86E-05 1.86E-05 0.0124224 0 2 std::map<std::string, double, std::less<std::string>, std::allocator<std::pair<const std::string, double>>> OpenMM::MonteCarloBarostatImpl::getDefaultParameters()
0.0 1.86E-05 1.86E-05 0.0248447 0 1 void QUERN_free_result(int *, int *, double *) C
0.0 1.24E-05 1.24E-05 0.0248447 0 0 bool OpenMM::HarmonicBondForce::usesPeriodicBoundaryConditions() const
0.0 1.24E-05 1.24E-05 0.0372671 0 0 double OpenMM::CustomBondForce::getGlobalParameterDefaultValue(int) const
0.0 1.24E-05 1.24E-05 0.0248447 0 0 double OpenMM::SplineFitter::evaluateSpline(const std::vector<double, std::allocator<double>> &, const std::vector<double, std::allocator<double>> &, const std::vector<double, std::allocator<double>> &, double)
0.0 1.24E-05 1.24E-05 0.0186335 0 1 int OpenMM::CustomAngleForce::addGlobalParameter(const std::string &, double)
0.0 1.24E-05 1.24E-05 0.00621118 0 2 int OpenMM::CustomBondForce::addBond(int, int, const std::vector<double, std::allocator<double>> &)
0.0 1.24E-05 1.24E-05 0.0186335 0 1 int OpenMM::CustomBondForce::addGlobalParameter(const std::string &, double)
0.0 1.24E-05 1.24E-05 0.0248447 0 0 std::map<std::string, double, std::less<std::string>, std::allocator<std::pair<const std::string, double>>> OpenMM::CustomExternalForceImpl::getDefaultParameters()
0.0 1.24E-05 1.24E-05 0.0248447 0 0 std::vector<std::string, std::allocator<std::string>> OpenMM::HarmonicBondForceImpl::getKernelNames()
0.0 1.24E-05 1.24E-05 0.0559006 0 0 void OpenMM::HarmonicBondForce::getBondParameters(int, int &, int &, double &, double &) const
0.0 1.24E-05 1.24E-05 0.136646 0 0 void OpenMM::Integrator::~Integrator()
0.0 1.24E-05 1.24E-05 0.0372671 0 0 void OpenMM::SimTKOpenMMUtilities::freeOneDRealOpenMMArray(double *, const std::string &)
0.0 1.24E-05 1.24E-05 0.0372671 0 0 void OpenMM::State::setForces(const std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &)
0.0 6.21E-06 6.21E-06 0.00621118 0 1 bool OpenMM::CustomBondForce::usesPeriodicBoundaryConditions() const
0.0 6.21E-06 6.21E-06 0.00621118 0 1 bool OpenMM::System::usesPeriodicBoundaryConditions() const
0.0 6.21E-06 6.21E-06 0.0124224 0 0 const std::string &OpenMM::CustomAngleForce::getEnergyParameterDerivativeName(int) const
0.0 6.21E-06 6.21E-06 0.0124224 0 0 const std::string &OpenMM::CustomBondForce::getEnergyParameterDerivativeName(int) const
0.0 6.21E-06 6.21E-06 0.0559006 0 0 const std::string &OpenMM::CustomBondForce::getGlobalParameterName(int) const
0.0 6.21E-06 6.21E-06 0.0124224 0 0 const std::string &OpenMM::CustomExternalForce::getEnergyFunction() const
0.0 6.21E-06 6.21E-06 0.0372671 0 0 double OpenMM::CustomAngleForce::getGlobalParameterDefaultValue(int) const
0.0 6.21E-06 6.21E-06 0.00621118 0 1 int OpenMM::CustomAngleForce::addAngle(int, int, int, const std::vector<double, std::allocator<double>> &)
0.0 6.21E-06 6.21E-06 0.0186335 0 0 int OpenMM::NonbondedForceImpl::findZero(const OpenMM::NonbondedForceImpl::ErrorFunction &, int)
0.0 6.21E-06 6.21E-06 0.00621118 0 1 std::vector<std::string, std::allocator<std::string>> OpenMM::CustomAngleForceImpl::getKernelNames()
0.0 6.21E-06 6.21E-06 0.00621118 0 1 std::vector<std::string, std::allocator<std::string>> OpenMM::CustomBondForceImpl::getKernelNames()
0.0 6.21E-06 6.21E-06 0.00621118 0 1 std::vector<std::string, std::allocator<std::string>> OpenMM::MonteCarloBarostatImpl::getKernelNames()
0.0 6.21E-06 6.21E-06 0.0124224 0 0 void OpenMM::AndersenThermostat::AndersenThermostat(double, double)
0.0 6.21E-06 6.21E-06 0.00621118 0 1 void OpenMM::AndersenThermostatProxy::AndersenThermostatProxy()
0.0 6.21E-06 6.21E-06 0.00621118 0 1 void OpenMM::Continuous1DFunction::Continuous1DFunction(const std::vector<double, std::allocator<double>> &, double, double)
0.0 6.21E-06 6.21E-06 0.00621118 0 1 void OpenMM::CustomAngleForce::CustomAngleForce(const std::string &)
0.0 6.21E-06 6.21E-06 0.0124224 0 0 void OpenMM::CustomAngleForce::getAngleParameters(int, int &, int &, int &, std::vector<double, std::allocator<double>> &) const
0.0 6.21E-06 6.21E-06 0.00621118 0 1 void OpenMM::CustomAngleForceImpl::CustomAngleForceImpl(const OpenMM::CustomAngleForce &)
0.0 6.21E-06 6.21E-06 0.0124224 0 0 void OpenMM::CustomBondForce::getBondParameters(int, int &, int &, std::vector<double, std::allocator<double>> &) const
0.0 6.21E-06 6.21E-06 0.00621118 0 1 void OpenMM::CustomBondForceImpl::CustomBondForceImpl(const OpenMM::CustomBondForce &)
0.0 6.21E-06 6.21E-06 0.00621118 0 1 void OpenMM::CustomBondForceImpl::~CustomBondForceImpl()
0.0 6.21E-06 6.21E-06 0.0248447 0 0 void OpenMM::HarmonicBondForce::HarmonicBondForce()
0.0 6.21E-06 6.21E-06 0.0248447 0 0 void OpenMM::HarmonicBondForceImpl::HarmonicBondForceImpl(const OpenMM::HarmonicBondForce &)
0.0 6.21E-06 6.21E-06 0.0248447 0 0 void OpenMM::HarmonicBondForceImpl::~HarmonicBondForceImpl()
0.0 6.21E-06 6.21E-06 0.00621118 0 1 void OpenMM::MonteCarloAnisotropicBarostatProxy::MonteCarloAnisotropicBarostatProxy()
0.0 6.21E-06 6.21E-06 0.00621118 0 1 void OpenMM::MonteCarloBarostatImpl::MonteCarloBarostatImpl(const OpenMM::MonteCarloBarostat &)
0.0 6.21E-06 6.21E-06 0.0124224 0 0 void OpenMM::ReferenceAndersenThermostat::~ReferenceAndersenThermostat()
0.0 6.21E-06 6.21E-06 0.00621118 0 1 void OpenMM::ReferenceMonteCarloBarostat::ReferenceMonteCarloBarostat(int, const std::vector<std::vector<int, std::allocator<int>>, std::allocator<std::vector<int, std::allocator<int>>>> &)
0.0 6.21E-06 6.21E-06 0.00621118 0 1 void OpenMM::ReferenceMonteCarloBarostat::~ReferenceMonteCarloBarostat()
0.0 6.21E-06 6.21E-06 0.00621118 0 1 void OpenMM::ReferenceSETTLEAlgorithm::ReferenceSETTLEAlgorithm(const std::vector<int, std::allocator<int>> &, const std::vector<int, std::allocator<int>> &, const std::vector<int, std::allocator<int>> &, const std::vector<double, std::allocator<double>> &, const std::vector<double, std::allocator<double>> &, std::vector<double, std::allocator<double>> &)
0.0 6.21E-06 6.21E-06 0.0372671 0 0 void OpenMM::SimTKOpenMMUtilities::crossProductVector3(double *, double *, double *)
0.0 6.21E-06 6.21E-06 0.00621118 0 1 void OpenMM::SplineFitter::solveTridiagonalMatrix(const std::vector<double, std::allocator<double>> &, const std::vector<double, std::allocator<double>> &, const std::vector<double, std::allocator<double>> &, const std::vector<double, std::allocator<double>> &, std::vector<double, std::allocator<double>> &)
0.0 6.21E-06 6.21E-06 0.00621118 0 1 void runPlatformTests()
0.0 0 0 0.00621118 0 0 bool OpenMM::CustomAngleForce::usesPeriodicBoundaryConditions() const
0.0 0 0 0.00621118 0 0 const std::string &OpenMM::CustomAngleForce::getEnergyFunction() const
0.0 0 0 0.00621118 0 0 const std::string &OpenMM::CustomBondForce::getEnergyFunction() const
0.0 0 0 0.0186335 0 0 const std::vector<OpenMM::Vec3, std::allocator<OpenMM::Vec3>> &OpenMM::State::getForces() const
0.0 0 0 0.0124224 0 0 std::vector<std::string, std::allocator<std::string>> OpenMM::CustomExternalForceImpl::getKernelNames()
0.0 0 0 0.00621118 0 0 void OpenMM::CMMotionRemoverProxy::CMMotionRemoverProxy()
0.0 0 0 0.0124224 0 0 void OpenMM::CustomAngleForce::addEnergyParameterDerivative(const std::string &)
0.0 0 0 0.00621118 0 0 void OpenMM::CustomAngleForceImpl::~CustomAngleForceImpl()
0.0 0 0 0.00621118 0 0 void OpenMM::CustomBondForce::CustomBondForce(const std::string &)
0.0 0 0 0.0124224 0 0 void OpenMM::CustomBondForce::addEnergyParameterDerivative(const std::string &)
0.0 0 0 0.0124224 0 0 void OpenMM::CustomExternalForce::CustomExternalForce(const std::string &)
0.0 0 0 0.0248447 0 0 void OpenMM::CustomExternalForce::getParticleParameters(int, int &, std::vector<double, std::allocator<double>> &) const
0.0 0 0 0.0124224 0 0 void OpenMM::CustomExternalForceImpl::CustomExternalForceImpl(const OpenMM::CustomExternalForce &)
0.0 0 0 0.0124224 0 0 void OpenMM::CustomExternalForceImpl::~CustomExternalForceImpl()
0.0 0 0 0.00621118 0 0 void OpenMM::MonteCarloBarostat::MonteCarloBarostat(double, double, int)
0.0 0 0 0.00621118 0 0 void OpenMM::MonteCarloBarostatProxy::MonteCarloBarostatProxy()
0.0 0 0 0.00621118 0 0 void OpenMM::MonteCarloMembraneBarostatProxy::MonteCarloMembraneBarostatProxy()
0.0 0 0 0.0559006 0 0 void OpenMM::NonbondedForceImpl::NonbondedForceImpl(const OpenMM::NonbondedForce &)
0.0 0 0 0.0124224 0 0 void OpenMM::ReferenceAndersenThermostat::ReferenceAndersenThermostat()
0.0 0 0 0.0248447 0 0 void OpenMM::System::setDefaultPeriodicBoxVectors(const OpenMM::Vec3 &, const OpenMM::Vec3 &, const OpenMM::Vec3 &)
0.0 0 0 0.00621118 0 0 void OpenMM::System::setParticleMass(int, double) Still have questions? Check out the official documentation or contact tau-bugs@cs.uoregon.edu for help.
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