Provided by: libhmsbeagle-dev_3.1.2+dfsg-13_amd64 
NAME
libhmsbeagle/beagle.h - This file documents the API as well as header for the Broad-
platform Evolutionary Analysis General Likelihood Evaluator.
SYNOPSIS
#include 'libhmsbeagle/platform.h'
Classes
struct BeagleInstanceDetails
Information about a specific instance.
struct BeagleResource
Description of a hardware resource.
struct BeagleResourceList
List of hardware resources.
struct BeagleBenchmarkedResource
Description of a benchmarked hardware resource.
struct BeagleBenchmarkedResourceList
Ordered list of benchmarked hardware resources, from fastest to slowest.
struct BeagleOperation
A list of integer indices which specify a partial likelihoods operation.
struct BeagleOperationByPartition
A list of integer indices which specify a partial likelihoods operation for a
partitioned analysis.
Enumerations
enum BeagleReturnCodes { BEAGLE_SUCCESS = 0, BEAGLE_ERROR_GENERAL = -1,
BEAGLE_ERROR_OUT_OF_MEMORY = -2, BEAGLE_ERROR_UNIDENTIFIED_EXCEPTION = -3,
BEAGLE_ERROR_UNINITIALIZED_INSTANCE = -4, BEAGLE_ERROR_OUT_OF_RANGE = -5,
BEAGLE_ERROR_NO_RESOURCE = -6, BEAGLE_ERROR_NO_IMPLEMENTATION = -7,
BEAGLE_ERROR_FLOATING_POINT = -8 }
Error return codes.
enum BeagleFlags { BEAGLE_FLAG_PRECISION_SINGLE = 1 << 0, BEAGLE_FLAG_PRECISION_DOUBLE = 1
<< 1, BEAGLE_FLAG_COMPUTATION_SYNCH = 1 << 2, BEAGLE_FLAG_COMPUTATION_ASYNCH = 1 << 3,
BEAGLE_FLAG_EIGEN_REAL = 1 << 4, BEAGLE_FLAG_EIGEN_COMPLEX = 1 << 5,
BEAGLE_FLAG_SCALING_MANUAL = 1 << 6, BEAGLE_FLAG_SCALING_AUTO = 1 << 7,
BEAGLE_FLAG_SCALING_ALWAYS = 1 << 8, BEAGLE_FLAG_SCALING_DYNAMIC = 1 << 25,
BEAGLE_FLAG_SCALERS_RAW = 1 << 9, BEAGLE_FLAG_SCALERS_LOG = 1 << 10,
BEAGLE_FLAG_INVEVEC_STANDARD = 1 << 20, BEAGLE_FLAG_INVEVEC_TRANSPOSED = 1 << 21,
BEAGLE_FLAG_VECTOR_SSE = 1 << 11, BEAGLE_FLAG_VECTOR_AVX = 1 << 24,
BEAGLE_FLAG_VECTOR_NONE = 1 << 12, BEAGLE_FLAG_THREADING_CPP = 1 << 30,
BEAGLE_FLAG_THREADING_OPENMP = 1 << 13, BEAGLE_FLAG_THREADING_NONE = 1 << 14,
BEAGLE_FLAG_PROCESSOR_CPU = 1 << 15, BEAGLE_FLAG_PROCESSOR_GPU = 1 << 16,
BEAGLE_FLAG_PROCESSOR_FPGA = 1 << 17, BEAGLE_FLAG_PROCESSOR_CELL = 1 << 18,
BEAGLE_FLAG_PROCESSOR_PHI = 1 << 19, BEAGLE_FLAG_PROCESSOR_OTHER = 1 << 26,
BEAGLE_FLAG_FRAMEWORK_CUDA = 1 << 22, BEAGLE_FLAG_FRAMEWORK_OPENCL = 1 << 23,
BEAGLE_FLAG_FRAMEWORK_CPU = 1 << 27, BEAGLE_FLAG_PARALLELOPS_STREAMS = 1 << 28,
BEAGLE_FLAG_PARALLELOPS_GRID = 1 << 29 }
Hardware and implementation capability flags.
enum BeagleBenchmarkFlags { BEAGLE_BENCHFLAG_SCALING_NONE = 1 << 0,
BEAGLE_BENCHFLAG_SCALING_ALWAYS = 1 << 1, BEAGLE_BENCHFLAG_SCALING_DYNAMIC = 1 << 2 }
Benchmarking mode flags for resource performance evaluation with
beagleGetOrderedResourceList.
enum BeagleOpCodes { BEAGLE_OP_COUNT = 7, BEAGLE_PARTITION_OP_COUNT = 9, BEAGLE_OP_NONE =
-1 }
Operation codes.
Functions
BEAGLE_DLLEXPORT const char * beagleGetVersion (void)
Get version.
BEAGLE_DLLEXPORT const char * beagleGetCitation (void)
Get citation.
BEAGLE_DLLEXPORT BeagleResourceList * beagleGetResourceList (void)
Get list of hardware resources.
BEAGLE_DLLEXPORT BeagleBenchmarkedResourceList * beagleGetBenchmarkedResourceList (int
tipCount, int compactBufferCount, int stateCount, int patternCount, int categoryCount,
int *resourceList, int resourceCount, long preferenceFlags, long requirementFlags, int
eigenModelCount, int partitionCount, int calculateDerivatives, long benchmarkFlags)
Get a benchmarked list of hardware resources for the given analysis parameters.
BEAGLE_DLLEXPORT int beagleCreateInstance (int tipCount, int partialsBufferCount, int
compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int
matrixBufferCount, int categoryCount, int scaleBufferCount, int *resourceList, int
resourceCount, long preferenceFlags, long requirementFlags, BeagleInstanceDetails
*returnInfo)
Create a single instance.
BEAGLE_DLLEXPORT int beagleFinalizeInstance (int instance)
Finalize this instance.
BEAGLE_DLLEXPORT int beagleFinalize (void)
Finalize the library.
BEAGLE_DLLEXPORT int beagleSetCPUThreadCount (int instance, int threadCount)
Set number of threads for native CPU implementation.
BEAGLE_DLLEXPORT int beagleSetTipStates (int instance, int tipIndex, const int *inStates)
Set the compact state representation for tip node.
BEAGLE_DLLEXPORT int beagleSetTipPartials (int instance, int tipIndex, const double
*inPartials)
Set an instance partials buffer for tip node.
BEAGLE_DLLEXPORT int beagleSetPartials (int instance, int bufferIndex, const double
*inPartials)
Set an instance partials buffer.
BEAGLE_DLLEXPORT int beagleGetPartials (int instance, int bufferIndex, int scaleIndex,
double *outPartials)
Get partials from an instance buffer.
BEAGLE_DLLEXPORT int beagleSetEigenDecomposition (int instance, int eigenIndex, const
double *inEigenVectors, const double *inInverseEigenVectors, const double
*inEigenValues)
Set an eigen-decomposition buffer.
BEAGLE_DLLEXPORT int beagleSetStateFrequencies (int instance, int stateFrequenciesIndex,
const double *inStateFrequencies)
Set a state frequency buffer.
BEAGLE_DLLEXPORT int beagleSetCategoryWeights (int instance, int categoryWeightsIndex,
const double *inCategoryWeights)
Set a category weights buffer.
BEAGLE_DLLEXPORT int beagleSetCategoryRates (int instance, const double *inCategoryRates)
Set the default category rates buffer.
BEAGLE_DLLEXPORT int beagleSetCategoryRatesWithIndex (int instance, int
categoryRatesIndex, const double *inCategoryRates)
Set a category rates buffer.
BEAGLE_DLLEXPORT int beagleSetPatternWeights (int instance, const double
*inPatternWeights)
Set pattern weights.
BEAGLE_DLLEXPORT int beagleSetPatternPartitions (int instance, int partitionCount, const
int *inPatternPartitions)
Set pattern partition assignments.
BEAGLE_DLLEXPORT int beagleConvolveTransitionMatrices (int instance, const int
*firstIndices, const int *secondIndices, const int *resultIndices, int matrixCount)
Set partitions by pattern weight.
BEAGLE_DLLEXPORT int beagleUpdateTransitionMatrices (int instance, int eigenIndex, const
int *probabilityIndices, const int *firstDerivativeIndices, const int
*secondDerivativeIndices, const double *edgeLengths, int count)
Calculate a list of transition probability matrices.
BEAGLE_DLLEXPORT int beagleUpdateTransitionMatricesWithMultipleModels (int instance, const
int *eigenIndices, const int *categoryRateIndices, const int *probabilityIndices,
const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double
*edgeLengths, int count)
Calculate a list of transition probability matrices with multiple models.
BEAGLE_DLLEXPORT int beagleSetTransitionMatrix (int instance, int matrixIndex, const
double *inMatrix, double paddedValue)
Set a finite-time transition probability matrix.
BEAGLE_DLLEXPORT int beagleGetTransitionMatrix (int instance, int matrixIndex, double
*outMatrix)
Get a finite-time transition probability matrix.
BEAGLE_DLLEXPORT int beagleSetTransitionMatrices (int instance, const int *matrixIndices,
const double *inMatrices, const double *paddedValues, int count)
Set multiple transition matrices.
BEAGLE_DLLEXPORT int beagleUpdatePartials (const int instance, const BeagleOperation
*operations, int operationCount, int cumulativeScaleIndex)
Calculate or queue for calculation partials using a list of operations.
BEAGLE_DLLEXPORT int beagleUpdatePartialsByPartition (const int instance, const
BeagleOperationByPartition *operations, int operationCount)
Calculate or queue for calculation partials using a list of partition operations.
BEAGLE_DLLEXPORT int beagleWaitForPartials (const int instance, const int
*destinationPartials, int destinationPartialsCount)
Block until all calculations that write to the specified partials have completed.
BEAGLE_DLLEXPORT int beagleAccumulateScaleFactors (int instance, const int *scaleIndices,
int count, int cumulativeScaleIndex)
Accumulate scale factors.
BEAGLE_DLLEXPORT int beagleAccumulateScaleFactorsByPartition (int instance, const int
*scaleIndices, int count, int cumulativeScaleIndex, int partitionIndex)
Accumulate scale factors by partition.
BEAGLE_DLLEXPORT int beagleRemoveScaleFactors (int instance, const int *scaleIndices, int
count, int cumulativeScaleIndex)
Remove scale factors.
BEAGLE_DLLEXPORT int beagleRemoveScaleFactorsByPartition (int instance, const int
*scaleIndices, int count, int cumulativeScaleIndex, int partitionIndex)
Remove scale factors by partition.
BEAGLE_DLLEXPORT int beagleResetScaleFactors (int instance, int cumulativeScaleIndex)
Reset scalefactors.
BEAGLE_DLLEXPORT int beagleResetScaleFactorsByPartition (int instance, int
cumulativeScaleIndex, int partitionIndex)
Reset scalefactors by partition.
BEAGLE_DLLEXPORT int beagleCopyScaleFactors (int instance, int destScalingIndex, int
srcScalingIndex)
Copy scale factors.
BEAGLE_DLLEXPORT int beagleGetScaleFactors (int instance, int srcScalingIndex, double
*outScaleFactors)
Get scale factors.
BEAGLE_DLLEXPORT int beagleCalculateRootLogLikelihoods (int instance, const int
*bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices,
const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood)
Calculate site log likelihoods at a root node.
BEAGLE_DLLEXPORT int beagleCalculateRootLogLikelihoodsByPartition (int instance, const int
*bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices,
const int *cumulativeScaleIndices, const int *partitionIndices, int partitionCount,
int count, double *outSumLogLikelihoodByPartition, double *outSumLogLikelihood)
Calculate site log likelihoods at a root node with per partition buffers.
BEAGLE_DLLEXPORT int beagleCalculateEdgeLogLikelihoods (int instance, const int
*parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices,
const int *firstDerivativeIndices, const int *secondDerivativeIndices, const int
*categoryWeightsIndices, const int *stateFrequenciesIndices, const int
*cumulativeScaleIndices, int count, double *outSumLogLikelihood, double
*outSumFirstDerivative, double *outSumSecondDerivative)
Calculate site log likelihoods and derivatives along an edge.
BEAGLE_DLLEXPORT int beagleCalculateEdgeLogLikelihoodsByPartition (int instance, const int
*parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices,
const int *firstDerivativeIndices, const int *secondDerivativeIndices, const int
*categoryWeightsIndices, const int *stateFrequenciesIndices, const int
*cumulativeScaleIndices, const int *partitionIndices, int partitionCount, int count,
double *outSumLogLikelihoodByPartition, double *outSumLogLikelihood, double
*outSumFirstDerivativeByPartition, double *outSumFirstDerivative, double
*outSumSecondDerivativeByPartition, double *outSumSecondDerivative)
Calculate multiple site log likelihoods and derivatives along an edge with per
partition buffers.
BEAGLE_DLLEXPORT int beagleGetLogLikelihood (int instance, double *outSumLogLikelihood)
Returns log likelihood sum and subsequent to an asynchronous integration call.
BEAGLE_DLLEXPORT int beagleGetDerivatives (int instance, double *outSumFirstDerivative,
double *outSumSecondDerivative)
Returns derivative sums subsequent to an asynchronous integration call.
BEAGLE_DLLEXPORT int beagleGetSiteLogLikelihoods (int instance, double *outLogLikelihoods)
Get site log likelihoods for last beagleCalculateRootLogLikelihoods or
beagleCalculateEdgeLogLikelihoods call.
BEAGLE_DLLEXPORT int beagleGetSiteDerivatives (int instance, double *outFirstDerivatives,
double *outSecondDerivatives)
Get site derivatives for last beagleCalculateEdgeLogLikelihoods call.
Detailed Description
This file documents the API as well as header for the Broad-platform Evolutionary Analysis
General Likelihood Evaluator.
Copyright 2009-2013 Phylogenetic Likelihood Working Group
This file is part of BEAGLE.
BEAGLE is free software: you can redistribute it and/or modify it under the terms of the
GNU Lesser General Public License as published by the Free Software Foundation, either
version 3 of the License, or (at your option) any later version.
BEAGLE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along with
BEAGLE. If not, see http://www.gnu.org/licenses/.
KEY CONCEPTS
The key to BEAGLE performance lies in delivering fine-scale parallelization while
minimizing data transfer and memory copy overhead. To accomplish this, the library lacks
the concept of data structure for a tree, in spite of the intended use for phylogenetic
analysis. Instead, BEAGLE acts directly on flexibly indexed data storage (called buffers)
for observed character states and partial likelihoods. The client program can set the
input buffers to reflect the data and can calculate the likelihood of a particular
phylogeny by invoking likelihood calculations on the appropriate input and output buffers
in the correct order. Because of this design simplicity, the library can support many
different tree inference algorithms and likelihood calculation on a variety of models.
Arbitrary numbers of states can be used, as can nonreversible substitution matrices via
complex eigen decompositions, and mixture models with multiple rate categories and/or
multiple eigen decompositions. Finally, BEAGLE application programming interface (API)
calls can be asynchronous, allowing the calling program to implement other coarse-scale
parallelization schemes such as evaluating independent genes or running concurrent Markov
chains.
USAGE
To use the library, a client program first creates an instance of BEAGLE by calling
beagleCreateInstance; multiple instances per client are possible and encouraged. All
additional functions are called with a reference to this instance. The client program can
optionally request that an instance run on certain hardware (e.g., a GPU) or have
particular features (e.g., double-precision math). Next, the client program must specify
the data dimensions and specify key aspects of the phylogenetic model. Character state
data are then loaded and can be in the form of discrete observed states or partial
likelihoods for ambiguous characters. The observed data are usually unchanging and loaded
only once at the start to minimize memory copy overhead. The character data can be
compressed into unique “site patterns” and associated weights for each. The parameters of
the substitution process can then be specified, including the equilibrium state
frequencies, the rates for one or more substitution rate categories and their weights, and
finally, the eigen decomposition for the substitution process.
In order to calculate the likelihood of a particular tree, the client program then
specifies a series of integration operations that correspond to steps in Felsenstein’s
algorithm. Finite-time transition probabilities for each edge are loaded directly if
considering a nondiagonalizable model or calculated in parallel from the eigen
decomposition and edge lengths specified. This is performed within BEAGLE’s memory space
to minimize data transfers. A single function call will then request one or more
integration operations to calculate partial likelihoods over some or all nodes. The
operations are performed in the order they are provided, typically dictated by a postorder
traversal of the tree topology. The client needs only specify nodes for which the partial
likelihoods need updating, but it is up to the calling software to keep track of these
dependencies. The final step in evaluating the phylogenetic model is done using an API
call that yields a single log likelihood for the model given the data.
Aspects of the BEAGLE API design support both maximum likelihood (ML) and Bayesian
phylogenetic tree inference. For ML inference, API calls can calculate first and second
derivatives of the likelihood with respect to the lengths of edges (branches). In both
cases, BEAGLE provides the ability to cache and reuse previously computed partial
likelihood results, which can yield a tremendous speedup over recomputing the entire
likelihood every time a new phylogenetic model is evaluated.
Author
Likelihood API Working Group
Daniel Ayres
Peter Beerli
Michael Cummings
Aaron Darling
Mark Holder
John Huelsenbeck
Paul Lewis
Michael Ott
Andrew Rambaut
Fredrik Ronquist
Marc Suchard
David Swofford
Derrick Zwickl
Enumeration Type Documentation
enum BeagleBenchmarkFlags
Benchmarking mode flags for resource performance evaluation with
beagleGetOrderedResourceList.
This enumerates all possible benchmarking mode flags. Each mode is a bit in a 'long'
Enumerator
BEAGLE_BENCHFLAG_SCALING_NONE
No scaling
BEAGLE_BENCHFLAG_SCALING_ALWAYS
Scale at every iteration
BEAGLE_BENCHFLAG_SCALING_DYNAMIC
Scale every fixed number of iterations or when a numerical error occurs, and re-use
scale factors for subsequent iterations
enum BeagleFlags
Hardware and implementation capability flags.
This enumerates all possible hardware and implementation capability flags. Each capability
is a bit in a 'long'
Enumerator
BEAGLE_FLAG_PRECISION_SINGLE
Single precision computation
BEAGLE_FLAG_PRECISION_DOUBLE
Double precision computation
BEAGLE_FLAG_COMPUTATION_SYNCH
Synchronous computation (blocking)
BEAGLE_FLAG_COMPUTATION_ASYNCH
Asynchronous computation (non-blocking)
BEAGLE_FLAG_EIGEN_REAL
Real eigenvalue computation
BEAGLE_FLAG_EIGEN_COMPLEX
Complex eigenvalue computation
BEAGLE_FLAG_SCALING_MANUAL
Manual scaling
BEAGLE_FLAG_SCALING_AUTO
Auto-scaling on (deprecated, may not work correctly)
BEAGLE_FLAG_SCALING_ALWAYS
Scale at every updatePartials (deprecated, may not work correctly)
BEAGLE_FLAG_SCALING_DYNAMIC
Manual scaling with dynamic checking (deprecated, may not work correctly)
BEAGLE_FLAG_SCALERS_RAW
Save raw scalers
BEAGLE_FLAG_SCALERS_LOG
Save log scalers
BEAGLE_FLAG_INVEVEC_STANDARD
Inverse eigen vectors passed to BEAGLE have not been transposed
BEAGLE_FLAG_INVEVEC_TRANSPOSED
Inverse eigen vectors passed to BEAGLE have been transposed
BEAGLE_FLAG_VECTOR_SSE
SSE computation
BEAGLE_FLAG_VECTOR_AVX
AVX computation
BEAGLE_FLAG_VECTOR_NONE
No vector computation
BEAGLE_FLAG_THREADING_CPP
C++11 threading
BEAGLE_FLAG_THREADING_OPENMP
OpenMP threading
BEAGLE_FLAG_THREADING_NONE
No threading (default)
BEAGLE_FLAG_PROCESSOR_CPU
Use CPU as main processor
BEAGLE_FLAG_PROCESSOR_GPU
Use GPU as main processor
BEAGLE_FLAG_PROCESSOR_FPGA
Use FPGA as main processor
BEAGLE_FLAG_PROCESSOR_CELL
Use Cell as main processor
BEAGLE_FLAG_PROCESSOR_PHI
Use Intel Phi as main processor
BEAGLE_FLAG_PROCESSOR_OTHER
Use other type of processor
BEAGLE_FLAG_FRAMEWORK_CUDA
Use CUDA implementation with GPU resources
BEAGLE_FLAG_FRAMEWORK_OPENCL
Use OpenCL implementation with GPU resources
BEAGLE_FLAG_FRAMEWORK_CPU
Use CPU implementation
BEAGLE_FLAG_PARALLELOPS_STREAMS
Operations in updatePartials may be assigned to separate device streams
BEAGLE_FLAG_PARALLELOPS_GRID
Operations in updatePartials may be folded into single kernel launch (necessary for
partitions; typically performs better for problems with fewer pattern sites)
enum BeagleOpCodes
Operation codes.
This enumerates all possible BEAGLE operation codes.
Enumerator
BEAGLE_OP_COUNT
Total number of integers per beagleUpdatePartials operation
BEAGLE_PARTITION_OP_COUNT
Total number of integers per beagleUpdatePartialsByPartition operation
BEAGLE_OP_NONE
Specify no use for indexed buffer
enum BeagleReturnCodes
Error return codes.
This enumerates all possible BEAGLE return codes. Error codes are always negative.
Enumerator
BEAGLE_SUCCESS
Success
BEAGLE_ERROR_GENERAL
Unspecified error
BEAGLE_ERROR_OUT_OF_MEMORY
Not enough memory could be allocated
BEAGLE_ERROR_UNIDENTIFIED_EXCEPTION
Unspecified exception
BEAGLE_ERROR_UNINITIALIZED_INSTANCE
The instance index is out of range, or the instance has not been created
BEAGLE_ERROR_OUT_OF_RANGE
One of the indices specified exceeded the range of the array
BEAGLE_ERROR_NO_RESOURCE
No resource matches requirements
BEAGLE_ERROR_NO_IMPLEMENTATION
No implementation matches requirements
BEAGLE_ERROR_FLOATING_POINT
Floating-point error (e.g., NaN)
Function Documentation
BEAGLE_DLLEXPORT int beagleAccumulateScaleFactors (int instance, const int * scaleIndices, int
count, int cumulativeScaleIndex)
Accumulate scale factors. This function adds (log) scale factors from a list of
scaleBuffers to a cumulative scale buffer. It is used to calculate the marginal scaling at
a specific node for each site.
Parameters
instance Instance number (input)
scaleIndices List of scaleBuffers to add (input)
count Number of scaleBuffers in list (input)
cumulativeScaleIndex Index number of scaleBuffer to accumulate factors into (input)
BEAGLE_DLLEXPORT int beagleAccumulateScaleFactorsByPartition (int instance, const int *
scaleIndices, int count, int cumulativeScaleIndex, int partitionIndex)
Accumulate scale factors by partition. This function adds (log) scale factors from a list
of scaleBuffers to a cumulative scale buffer. It is used to calculate the marginal scaling
at a specific node for each site.
Parameters
instance Instance number (input)
scaleIndices List of scaleBuffers to add (input)
count Number of scaleBuffers in list (input)
cumulativeScaleIndex Index number of scaleBuffer to accumulate factors into (input)
partitionIndex Index of partition to accumulate into (input)
BEAGLE_DLLEXPORT int beagleCalculateEdgeLogLikelihoods (int instance, const int *
parentBufferIndices, const int * childBufferIndices, const int * probabilityIndices, const
int * firstDerivativeIndices, const int * secondDerivativeIndices, const int *
categoryWeightsIndices, const int * stateFrequenciesIndices, const int *
cumulativeScaleIndices, int count, double * outSumLogLikelihood, double *
outSumFirstDerivative, double * outSumSecondDerivative)
Calculate site log likelihoods and derivatives along an edge. This function integrates a
list of partials at a parent and child node with respect to a set of partials-weights and
state frequencies to return the log likelihood and first and second derivative sums
Parameters
instance Instance number (input)
parentBufferIndices List of indices of parent partialsBuffers (input)
childBufferIndices List of indices of child partialsBuffers (input)
probabilityIndices List indices of transition probability matrices for this edge
(input)
firstDerivativeIndices List indices of first derivative matrices (input)
secondDerivativeIndices List indices of second derivative matrices (input)
categoryWeightsIndices List of weights to apply to each partialsBuffer (input)
stateFrequenciesIndices List of state frequencies for each partialsBuffer (input).
There should be one set for each of parentBufferIndices
cumulativeScaleIndices List of scaleBuffers containing accumulated factors to apply to
each partialsBuffer (input). There should be one index for each of parentBufferIndices
count Number of partialsBuffers (input)
outSumLogLikelihood Pointer to destination for resulting log likelihood (output)
outSumFirstDerivative Pointer to destination for resulting first derivative (output)
outSumSecondDerivative Pointer to destination for resulting second derivative (output)
Returns
error code
BEAGLE_DLLEXPORT int beagleCalculateEdgeLogLikelihoodsByPartition (int instance, const int *
parentBufferIndices, const int * childBufferIndices, const int * probabilityIndices, const
int * firstDerivativeIndices, const int * secondDerivativeIndices, const int *
categoryWeightsIndices, const int * stateFrequenciesIndices, const int *
cumulativeScaleIndices, const int * partitionIndices, int partitionCount, int count,
double * outSumLogLikelihoodByPartition, double * outSumLogLikelihood, double *
outSumFirstDerivativeByPartition, double * outSumFirstDerivative, double *
outSumSecondDerivativeByPartition, double * outSumSecondDerivative)
Calculate multiple site log likelihoods and derivatives along an edge with per partition
buffers. This function integrates lists of partials at a parent and child node with
respect to a set of partials-weights and state frequencies to return the log likelihood
and first and second derivative sums
Parameters
instance Instance number (input)
parentBufferIndices List of indices of parent partialsBuffers (input)
childBufferIndices List of indices of child partialsBuffers (input)
probabilityIndices List indices of transition probability matrices for this edge
(input)
firstDerivativeIndices List indices of first derivative matrices (input)
secondDerivativeIndices List indices of second derivative matrices (input)
categoryWeightsIndices List of weights to apply to each partialsBuffer (input)
stateFrequenciesIndices List of state frequencies for each partialsBuffer (input).
There should be one set for each of parentBufferIndices
cumulativeScaleIndices List of scaleBuffers containing accumulated factors to apply to
each partialsBuffer (input). There should be one index for each of parentBufferIndices
partitionIndices List of partition indices indicating which sites in each
partialsBuffer should be used (input). There should be one index for each of
parentBufferIndices
partitionCount Number of distinct partitionIndices (input)
count Number of sets of partitions to integrate across (input)
outSumLogLikelihoodByPartition Pointer to destination for resulting log likelihoods
for each partition (output)
outSumLogLikelihood Pointer to destination for resulting log likelihood (output)
outSumFirstDerivativeByPartition Pointer to destination for resulting first derivative
for each partition (output)
outSumFirstDerivative Pointer to destination for resulting first derivative (output)
outSumSecondDerivativeByPartition Pointer to destination for resulting second
derivative for each partition (output)
outSumSecondDerivative Pointer to destination for resulting second derivative (output)
Returns
error code
BEAGLE_DLLEXPORT int beagleCalculateRootLogLikelihoods (int instance, const int *
bufferIndices, const int * categoryWeightsIndices, const int * stateFrequenciesIndices,
const int * cumulativeScaleIndices, int count, double * outSumLogLikelihood)
Calculate site log likelihoods at a root node. This function integrates a list of partials
at a node with respect to a set of partials-weights and state frequencies to return the
log likelihood sum
Parameters
instance Instance number (input)
bufferIndices List of partialsBuffer indices to integrate (input)
categoryWeightsIndices List of weights to apply to each partialsBuffer (input). There
should be one categoryCount sized set for each of parentBufferIndices
stateFrequenciesIndices List of state frequencies for each partialsBuffer (input).
There should be one set for each of parentBufferIndices
cumulativeScaleIndices List of scaleBuffers containing accumulated factors to apply to
each partialsBuffer (input). There should be one index for each of parentBufferIndices
count Number of partialsBuffer to integrate (input)
outSumLogLikelihood Pointer to destination for resulting log likelihood (output)
Returns
error code
BEAGLE_DLLEXPORT int beagleCalculateRootLogLikelihoodsByPartition (int instance, const int *
bufferIndices, const int * categoryWeightsIndices, const int * stateFrequenciesIndices,
const int * cumulativeScaleIndices, const int * partitionIndices, int partitionCount, int
count, double * outSumLogLikelihoodByPartition, double * outSumLogLikelihood)
Calculate site log likelihoods at a root node with per partition buffers. This function
integrates lists of partials at a node with respect to a set of partials-weights and state
frequencies to return the log likelihood sums
Parameters
instance Instance number (input)
bufferIndices List of partialsBuffer indices to integrate (input)
categoryWeightsIndices List of weights to apply to each partialsBuffer (input). There
should be one categoryCount sized set for each of bufferIndices
stateFrequenciesIndices List of state frequencies for each partialsBuffer (input).
There should be one set for each of bufferIndices
cumulativeScaleIndices List of scaleBuffers containing accumulated factors to apply to
each partialsBuffer (input). There should be one index for each of bufferIndices
partitionIndices List of partition indices indicating which sites in each
partialsBuffer should be used (input). There should be one index for each of
bufferIndices
partitionCount Number of distinct partitionIndices (input)
count Number of sets of partitions to integrate across (input)
outSumLogLikelihoodByPartition Pointer to destination for resulting log likelihoods
for each partition (output)
outSumLogLikelihood Pointer to destination for resulting log likelihood (output)
Returns
error code
BEAGLE_DLLEXPORT int beagleConvolveTransitionMatrices (int instance, const int * firstIndices,
const int * secondIndices, const int * resultIndices, int matrixCount)
Set partitions by pattern weight. This function defines partitions by setting their
vectors of pattern-weights for an instance. It should be called after beagleSetTipPartials
or beagleSetTipStates.
Parameters
instance Instance number (input)
inPartitionPatternWeights partitionCount arrays, each containing patternCount pattern
weights (input)
partitionCount Number of partitions (input)
Returns
error code
Convolve lists of transition probability matrices
This function convolves two lists of transition probability matrices.
Parameters
instance Instance number (input)
firstIndices List of indices of the first transition probability matrices to convolve
(input)
secondIndices List of indices of the second transition probability matrices to
convolve (input)
resultIndices List of indices of resulting transition probability matrices (input)
matrixCount Length of lists
BEAGLE_DLLEXPORT int beagleCopyScaleFactors (int instance, int destScalingIndex, int
srcScalingIndex)
Copy scale factors. This function copies scale factors from one buffer to another.
Parameters
instance Instance number (input)
destScalingIndex Destination scaleBuffer (input)
srcScalingIndex Source scaleBuffer (input)
BEAGLE_DLLEXPORT int beagleCreateInstance (int tipCount, int partialsBufferCount, int
compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int
matrixBufferCount, int categoryCount, int scaleBufferCount, int * resourceList, int
resourceCount, long preferenceFlags, long requirementFlags, BeagleInstanceDetails *
returnInfo)
Create a single instance. This function creates a single instance of the BEAGLE library
and can be called multiple times to create multiple data partition instances each
returning a unique identifier.
Parameters
tipCount Number of tip data elements (input)
partialsBufferCount Number of partials buffers to create (input)
compactBufferCount Number of compact state representation buffers to create (input)
stateCount Number of states in the continuous-time Markov chain (input)
patternCount Number of site patterns to be handled by the instance (input)
eigenBufferCount Number of rate matrix eigen-decomposition, category weight, category
rates, and state frequency buffers to allocate (input)
matrixBufferCount Number of transition probability matrix buffers (input)
categoryCount Number of rate categories (input)
scaleBufferCount Number of scale buffers to create, ignored for auto scale or always
scale (input)
resourceList List of potential resources on which this instance is allowed (input,
NULL implies no restriction)
resourceCount Length of resourceList list (input)
preferenceFlags Bit-flags indicating preferred implementation characteristics, see
BeagleFlags (input)
requirementFlags Bit-flags indicating required implementation characteristics, see
BeagleFlags (input)
returnInfo Pointer to return implementation and resource details
Returns
the unique instance identifier (<0 if failed, see BeagleReturnCodes)
BEAGLE_DLLEXPORT int beagleFinalize (void)
Finalize the library. This function finalizes the library and releases all allocated
memory. This function is automatically called under GNU C via attribute ((destructor)).
Returns
error code
BEAGLE_DLLEXPORT int beagleFinalizeInstance (int instance)
Finalize this instance. This function finalizes the instance by releasing allocated memory
Parameters
instance Instance number
Returns
error code
BEAGLE_DLLEXPORT BeagleBenchmarkedResourceList * beagleGetBenchmarkedResourceList (int
tipCount, int compactBufferCount, int stateCount, int patternCount, int categoryCount, int
* resourceList, int resourceCount, long preferenceFlags, long requirementFlags, int
eigenModelCount, int partitionCount, int calculateDerivatives, long benchmarkFlags)
Get a benchmarked list of hardware resources for the given analysis parameters. This
function returns a pointer to a BeagleBenchmarkedResourceList struct, which includes a
BeagleBenchmarkedResource array describing the available hardware resources with benchmark
times and CPU performance ratios for each resource. Resources are benchmarked with the
given analysis parameters and the array is ordered from fastest to slowest. If there is an
error the function returns NULL.
Parameters
tipCount Number of tip data elements (input)
compactBufferCount Number of compact state representation tips (input)
stateCount Number of states in the continuous-time Markov chain (input)
patternCount Number of site patterns (input)
categoryCount Number of rate categories (input)
resourceList List of resources to be benchmarked, NULL implies no restriction (input)
resourceCount Length of resourceList list (input)
preferenceFlags Bit-flags indicating preferred implementation characteristics, see
BeagleFlags (input)
requirementFlags Bit-flags indicating required implementation characteristics, see
BeagleFlags (input)
eigenModelCount Number of full-alignment rate matrix eigen-decomposition models
(input)
partitionCount Number of partitions (input)
calculateDerivatives Indicates if calculation of derivatives are required (input)
benchmarkFlags Bit-flags indicating benchmarking preferences (input)
Returns
An ordered (fastest to slowest) list of hardware resources available to the library as
a BeagleBenchmarkedResourceList for the specified analysis parameters
BEAGLE_DLLEXPORT const char * beagleGetCitation (void)
Get citation. This function returns a pointer to a string describing the version of the
library and how to cite it.
Returns
A string describing the version of the library and how to cite it
BEAGLE_DLLEXPORT int beagleGetDerivatives (int instance, double * outSumFirstDerivative,
double * outSumSecondDerivative)
Returns derivative sums subsequent to an asynchronous integration call. This function is
optional and only has to be called by clients that use the non-blocking asynchronous
computation mode (BEAGLE_FLAG_COMPUTATION_ASYNCH).
If used, this function must be called after a beagleCalculateEdgeLogLikelihoods call. The
library will block until the derivatiives have been calculated.
Parameters
instance Instance number (input)
outSumFirstDerivative Pointer to destination for resulting first derivative (output)
outSumSecondDerivative Pointer to destination for resulting second derivative (output)
Returns
error code
BEAGLE_DLLEXPORT int beagleGetLogLikelihood (int instance, double * outSumLogLikelihood)
Returns log likelihood sum and subsequent to an asynchronous integration call. This
function is optional and only has to be called by clients that use the non-blocking
asynchronous computation mode (BEAGLE_FLAG_COMPUTATION_ASYNCH).
If used, this function must be called after a beagleCalculateRootLogLikelihoods or
beagleCalculateEdgeLogLikelihoods call. The library will block until the likelihood has
been calculated.
Parameters
instance Instance number (input)
outSumLogLikelihood Pointer to destination for resulting log likelihood (output)
Returns
error code
BEAGLE_DLLEXPORT int beagleGetPartials (int instance, int bufferIndex, int scaleIndex, double
* outPartials)
Get partials from an instance buffer. This function copies an instance buffer into the
array outPartials. The outPartials array should be stateCount * patternCount *
categoryCount in length.
Parameters
instance Instance number from which to get partialsBuffer (input)
bufferIndex Index of source partialsBuffer (input)
scaleIndex Index of scaleBuffer to apply to partialsBuffer (input)
outPartials Pointer to which to receive partialsBuffer (output)
Returns
error code
BEAGLE_DLLEXPORT BeagleResourceList * beagleGetResourceList (void)
Get list of hardware resources. This function returns a pointer to a BeagleResourceList
struct, which includes a BeagleResource array describing the available hardware resources.
Returns
A list of hardware resources available to the library as a BeagleResourceList
BEAGLE_DLLEXPORT int beagleGetScaleFactors (int instance, int srcScalingIndex, double *
outScaleFactors)
Get scale factors. This function retrieves a buffer of scale factors.
Parameters
instance Instance number (input)
srcScalingIndex Source scaleBuffer (input)
outScaleFactors Pointer to which to receive scaleFactors (output)
BEAGLE_DLLEXPORT int beagleGetSiteDerivatives (int instance, double * outFirstDerivatives,
double * outSecondDerivatives)
Get site derivatives for last beagleCalculateEdgeLogLikelihoods call. This function
returns the derivatives for each site
Parameters
instance Instance number (input)
outFirstDerivatives Pointer to destination for resulting first derivatives (output)
outSecondDerivatives Pointer to destination for resulting second derivatives (output)
Returns
error code
BEAGLE_DLLEXPORT int beagleGetSiteLogLikelihoods (int instance, double * outLogLikelihoods)
Get site log likelihoods for last beagleCalculateRootLogLikelihoods or
beagleCalculateEdgeLogLikelihoods call. This function returns the log likelihoods for each
site
Parameters
instance Instance number (input)
outLogLikelihoods Pointer to destination for resulting log likelihoods (output)
Returns
error code
BEAGLE_DLLEXPORT int beagleGetTransitionMatrix (int instance, int matrixIndex, double *
outMatrix)
Get a finite-time transition probability matrix. This function copies a finite-time
transition matrix buffer into the array outMatrix. The outMatrix array should be of size
stateCount * stateCount * categoryCount and will be filled with one matrix for each rate
category.
Parameters
instance Instance number (input)
matrixIndex Index of matrix buffer (input)
outMatrix Pointer to destination transition probability matrix (output)
Returns
error code
BEAGLE_DLLEXPORT const char * beagleGetVersion (void)
Get version. This function returns a pointer to a string with the library version number.
Returns
A string with the version number
BEAGLE_DLLEXPORT int beagleRemoveScaleFactors (int instance, const int * scaleIndices, int
count, int cumulativeScaleIndex)
Remove scale factors. This function removes (log) scale factors from a cumulative scale
buffer. The scale factors to be removed are indicated in a list of scaleBuffers.
Parameters
instance Instance number (input)
scaleIndices List of scaleBuffers to remove (input)
count Number of scaleBuffers in list (input)
cumulativeScaleIndex Index number of scaleBuffer containing accumulated factors
(input)
BEAGLE_DLLEXPORT int beagleRemoveScaleFactorsByPartition (int instance, const int *
scaleIndices, int count, int cumulativeScaleIndex, int partitionIndex)
Remove scale factors by partition. This function removes (log) scale factors from a
cumulative scale buffer. The scale factors to be removed are indicated in a list of
scaleBuffers.
Parameters
instance Instance number (input)
scaleIndices List of scaleBuffers to remove (input)
count Number of scaleBuffers in list (input)
cumulativeScaleIndex Index number of scaleBuffer containing accumulated factors
(input)
partitionIndex Index of partition to remove from (input)
BEAGLE_DLLEXPORT int beagleResetScaleFactors (int instance, int cumulativeScaleIndex)
Reset scalefactors. This function resets a cumulative scale buffer.
Parameters
instance Instance number (input)
cumulativeScaleIndex Index number of cumulative scaleBuffer (input)
BEAGLE_DLLEXPORT int beagleResetScaleFactorsByPartition (int instance, int
cumulativeScaleIndex, int partitionIndex)
Reset scalefactors by partition. This function resets a cumulative scale buffer.
Parameters
instance Instance number (input)
cumulativeScaleIndex Index number of cumulative scaleBuffer (input)
partitionIndex Index of partition to reset (input)
BEAGLE_DLLEXPORT int beagleSetCategoryRates (int instance, const double * inCategoryRates)
Set the default category rates buffer. This function sets the default vector of category
rates for an instance.
Parameters
instance Instance number (input)
inCategoryRates Array containing categoryCount rate scalers (input)
Returns
error code
BEAGLE_DLLEXPORT int beagleSetCategoryRatesWithIndex (int instance, int categoryRatesIndex,
const double * inCategoryRates)
Set a category rates buffer. This function sets the vector of category rates for a given
buffer in an instance.
Parameters
instance Instance number (input)
categoryRatesIndex Index of category rates buffer (input)
inCategoryRates Array containing categoryCount rate scalers (input)
Returns
error code
BEAGLE_DLLEXPORT int beagleSetCategoryWeights (int instance, int categoryWeightsIndex, const
double * inCategoryWeights)
Set a category weights buffer. This function copies a category weights array into an
instance buffer.
Parameters
instance Instance number (input)
categoryWeightsIndex Index of category weights buffer (input)
inCategoryWeights Category weights array (categoryCount) (input)
Returns
error code
BEAGLE_DLLEXPORT int beagleSetCPUThreadCount (int instance, int threadCount)
Set number of threads for native CPU implementation. This function sets the max number of
worker threads to be used with a native CPU implementation. It should only be called after
beagleCreateInstance and requires the BEAGLE_FLAG_THREADING_CPP flag to be set. It has no
effect on GPU-based implementations. It has no effect with the default
BEAGLE_FLAG_THREADING_NONE setting. If BEAGLE_FLAG_THREADING_CPP is set and this function
is not called BEAGLE will use a heuristic to set an appropriate number of threads.
Parameters
instance Instance number (input)
threadCount Number of threads (input)
Returns
error code
BEAGLE_DLLEXPORT int beagleSetEigenDecomposition (int instance, int eigenIndex, const double *
inEigenVectors, const double * inInverseEigenVectors, const double * inEigenValues)
Set an eigen-decomposition buffer. This function copies an eigen-decomposition into an
instance buffer.
Parameters
instance Instance number (input)
eigenIndex Index of eigen-decomposition buffer (input)
inEigenVectors Flattened matrix (stateCount x stateCount) of eigen-vectors (input)
inInverseEigenVectors Flattened matrix (stateCount x stateCount) of inverse-eigen-
vectors (input)
inEigenValues Vector of eigenvalues
Returns
error code
BEAGLE_DLLEXPORT int beagleSetPartials (int instance, int bufferIndex, const double *
inPartials)
Set an instance partials buffer. This function copies an array of partials into an
instance buffer. The inPartials array should be stateCount * patternCount * categoryCount
in length.
Parameters
instance Instance number in which to set a partialsBuffer (input)
bufferIndex Index of destination partialsBuffer (input)
inPartials Pointer to partials values to set (input)
Returns
error code
BEAGLE_DLLEXPORT int beagleSetPatternPartitions (int instance, int partitionCount, const int *
inPatternPartitions)
Set pattern partition assignments. This function sets the vector of pattern partition
indices for an instance. It should only be called after beagleSetTipPartials and
beagleSetPatternWeights.
Parameters
instance Instance number (input)
partitionCount Number of partitions (input)
inPatternPartitions Array containing partitionCount partition indices (input)
Returns
error code
BEAGLE_DLLEXPORT int beagleSetPatternWeights (int instance, const double * inPatternWeights)
Set pattern weights. This function sets the vector of pattern weights for an instance.
Parameters
instance Instance number (input)
inPatternWeights Array containing patternCount weights (input)
Returns
error code
BEAGLE_DLLEXPORT int beagleSetStateFrequencies (int instance, int stateFrequenciesIndex, const
double * inStateFrequencies)
Set a state frequency buffer. This function copies a state frequency array into an
instance buffer.
Parameters
instance Instance number (input)
stateFrequenciesIndex Index of state frequencies buffer (input)
inStateFrequencies State frequencies array (stateCount) (input)
Returns
error code
BEAGLE_DLLEXPORT int beagleSetTipPartials (int instance, int tipIndex, const double *
inPartials)
Set an instance partials buffer for tip node. This function copies an array of partials
into an instance buffer. The inPartials array should be stateCount * patternCount in
length. For most applications this will be used to set the partial likelihoods for the
observed states. Internally, the partials will be copied categoryCount times.
Parameters
instance Instance number in which to set a partialsBuffer (input)
tipIndex Index of destination partialsBuffer (input)
inPartials Pointer to partials values to set (input)
Returns
error code
BEAGLE_DLLEXPORT int beagleSetTipStates (int instance, int tipIndex, const int * inStates)
Set the compact state representation for tip node. This function copies a compact state
representation into an instance buffer. Compact state representation is an array of
states: 0 to stateCount - 1 (missing = stateCount). The inStates array should be
patternCount in length (replication across categoryCount is not required).
Parameters
instance Instance number (input)
tipIndex Index of destination compactBuffer (input)
inStates Pointer to compact states (input)
Returns
error code
BEAGLE_DLLEXPORT int beagleSetTransitionMatrices (int instance, const int * matrixIndices,
const double * inMatrices, const double * paddedValues, int count)
Set multiple transition matrices. This function copies multiple transition matrices into
matrix buffers. This function is used when the application wishes to explicitly set the
transition matrices rather than using the beagleSetEigenDecomposition and
beagleUpdateTransitionMatrices functions. The inMatrices array should be of size
stateCount * stateCount * categoryCount * count.
Parameters
instance Instance number (input)
matrixIndices Indices of matrix buffers (input)
inMatrices Pointer to source transition matrices (input)
paddedValues Values to be used for padding for ambiguous states (e.g. 1 for
probability matrices, 0 for derivative matrices) (input)
count Number of transition matrices (input)
Returns
error code
BEAGLE_DLLEXPORT int beagleSetTransitionMatrix (int instance, int matrixIndex, const double *
inMatrix, double paddedValue)
Set a finite-time transition probability matrix. This function copies a finite-time
transition probability matrix into a matrix buffer. This function is used when the
application wishes to explicitly set the transition probability matrix rather than using
the beagleSetEigenDecomposition and beagleUpdateTransitionMatrices functions. The inMatrix
array should be of size stateCount * stateCount * categoryCount and will contain one
matrix for each rate category.
Parameters
instance Instance number (input)
matrixIndex Index of matrix buffer (input)
inMatrix Pointer to source transition probability matrix (input)
paddedValue Value to be used for padding for ambiguous states (e.g. 1 for probability
matrices, 0 for derivative matrices) (input)
Returns
error code
BEAGLE_DLLEXPORT int beagleUpdatePartials (const int instance, const BeagleOperation *
operations, int operationCount, int cumulativeScaleIndex)
Calculate or queue for calculation partials using a list of operations. This function
either calculates or queues for calculation a list partials. Implementations supporting
ASYNCH may queue these calculations while other implementations perform these operations
immediately and in order.
Parameters
instance Instance number (input)
operations BeagleOperation list specifying operations (input)
operationCount Number of operations (input)
cumulativeScaleIndex Index number of scaleBuffer to store accumulated factors (input)
Returns
error code
BEAGLE_DLLEXPORT int beagleUpdatePartialsByPartition (const int instance, const
BeagleOperationByPartition * operations, int operationCount)
Calculate or queue for calculation partials using a list of partition operations. This
function either calculates or queues for calculation a list partitioned partials.
Implementations supporting ASYNCH may queue these calculations while other implementations
perform these operations immediately and in order.
Parameters
instance Instance number (input)
operations BeagleOperation list specifying operations (input)
operationCount Number of operations (input)
Returns
error code
BEAGLE_DLLEXPORT int beagleUpdateTransitionMatrices (int instance, int eigenIndex, const int *
probabilityIndices, const int * firstDerivativeIndices, const int *
secondDerivativeIndices, const double * edgeLengths, int count)
Calculate a list of transition probability matrices. This function calculates a list of
transition probabilities matrices and their first and second derivatives (if requested).
Parameters
instance Instance number (input)
eigenIndex Index of eigen-decomposition buffer (input)
probabilityIndices List of indices of transition probability matrices to update
(input)
firstDerivativeIndices List of indices of first derivative matrices to update (input,
NULL implies no calculation)
secondDerivativeIndices List of indices of second derivative matrices to update
(input, NULL implies no calculation)
edgeLengths List of edge lengths with which to perform calculations (input)
count Length of lists
Returns
error code
BEAGLE_DLLEXPORT int beagleUpdateTransitionMatricesWithMultipleModels (int instance, const int
* eigenIndices, const int * categoryRateIndices, const int * probabilityIndices, const int
* firstDerivativeIndices, const int * secondDerivativeIndices, const double * edgeLengths,
int count)
Calculate a list of transition probability matrices with multiple models. This function
calculates a list of transition probabilities matrices and their first and second
derivatives (if requested).
Parameters
instance Instance number (input)
eigenIndices List of indices of eigen-decomposition buffers to use for updates (input)
categoryRateIndices List of indices of category-rate buffers to use for updates
(input)
probabilityIndices List of indices of transition probability matrices to update
(input)
firstDerivativeIndices List of indices of first derivative matrices to update (input,
NULL implies no calculation)
secondDerivativeIndices List of indices of second derivative matrices to update
(input, NULL implies no calculation)
edgeLengths List of edge lengths with which to perform calculations (input)
count Length of lists
Returns
error code
BEAGLE_DLLEXPORT int beagleWaitForPartials (const int instance, const int *
destinationPartials, int destinationPartialsCount)
Block until all calculations that write to the specified partials have completed. This
function is optional and only has to be called by clients that 'recycle' partials.
If used, this function must be called after a beagleUpdatePartials call and must refer to
indices of 'destinationPartials' that were used in a previous beagleUpdatePartials call.
The library will block until those partials have been calculated.
Parameters
instance Instance number (input)
destinationPartials List of the indices of destinationPartials that must be calculated
before the function returns
destinationPartialsCount Number of destinationPartials (input)
Returns
error code
Author
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