R: Benchmarks for High-Performance Computing Environments

# Benchmarks for High-Performance Computing Environments

## Documentation for package ‘RHPCBenchmark’ version 0.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

RHPCBenchmark-package | RHPCBenchmark: A package for performance testing intrinsic R functionality and established packages relevant to high-performance computing
CholeskyAllocator | Allocates and initializes input to the Cholesky factorization dense matrix kernel microbenchmarks
CholeskyMicrobenchmark | Conducts a single performance trial with the Cholesky factorization dense matrix kernel
ClaraClusteringMicrobenchmark | Conducts a single performance trial with the cluster::clara function
ClusteringAllocator | Allocates and initializes input to the clustering for machine learning microbenchmarks
ClusteringMicrobenchmark | This class specifies a clustering for machine learning microbenchmark.
ComputeAverageTime | Computes the average of a vector of performance trial times
ComputeStandardDeviation | Computes the standard deviation of a vector of performance trial times
CrossprodAllocator | Allocates and populates input to the matrix cross product dense matrix kernel microbenchmarks
CrossprodMicrobenchmark | Conducts a single performance trial with the matrix cross product dense matrix kernel
DeformtransAllocator | Allocates and populates input to the matrix deformation and transpose dense matrix kernel microbenchmarks
DeformtransMicrobenchmark | Conducts a single performance trial with the matrix deformation and transpose dense matrix kernel
DenseMatrixMicrobenchmark | This class specifies a dense matrix microbenchmark.
DeterminantAllocator | Allocates and populates input to the matrix determinant dense matrix kernel microbenchmarks
DeterminantMicrobenchmark | Conducts a single performance trial with the matrix determinant dense matrix kernel
EigenAllocator | Allocates and populates input to the matrix eigendecomposition kernel microbenchmarks
EigenMicrobenchmark | Conducts a single performance trial with the matrix eigendecomposition dense matrix kernel
GenerateClusterData | Generates clusters from multivariate normal distributions
GetClusteringDefaultMicrobenchmarks | Initializes the list of default clustering microbenchmarks
GetClusteringExampleMicrobenchmarks | Initializes the list of example clustering microbenchmarks
GetConfigurableEnvParameter | Retrieves the value of an environment variable referenced by another environment variable
GetDenseMatrixDefaultMicrobenchmarks | Initializes the list of default dense matrix microbenchmarks
GetDenseMatrixExampleMicrobenchmarks | Initializes the list of example dense matrix microbenchmarks
GetNumberOfThreads | Retrieves the number of threads from the environment
GetSparseCholeskyDefaultMicrobenchmarks | Initializes the list of default sparse Cholesky factorization microbenchmarks
GetSparseCholeskyExampleMicrobenchmarks | Initializes the list of example sparse Cholesky factorization microbenchmarks
GetSparseLuDefaultMicrobenchmarks | Initializes the list of default sparse LU factorization microbenchmarks
GetSparseMatrixVectorDefaultMicrobenchmarks | Initializes the list of default sparse matrix-vector microbenchmarks
GetSparseMatrixVectorExampleMicrobenchmarks | Initializes the list of example sparse matrix-vector microbenchmarks
GetSparseQrDefaultMicrobenchmarks | Initializes the list of default sparse QR factorization microbenchmarks
LsfitAllocator | Allocates and populates input to the matrix least squares fit dense matrix kernel microbenchmarks
LsfitMicrobenchmark | Conducts a single performance trial with the matrix least squares fit dense matrix kernel
MatmatAllocator | Allocates and populates input to the matrix-matrix multiplication dense matrix kernel microbenchmarks
MatmatMicrobenchmark | Conducts a single performance trial with the matrix-matrix multiplication dense matrix kernel
MatvecAllocator | Allocates and populates input to the matrix-vector multiplication dense matrix kernel microbenchmarks
MatvecMicrobenchmark | Conducts a single performance trial with the matrix-vector multiplication dense matrix kernel
MicrobenchmarkClusteringKernel | Performs microbenchmarking of a clustering for machine learning kernel
MicrobenchmarkDenseMatrixKernel | Performs microbenchmarking of a dense matrix linear algebra kernel
MicrobenchmarkSparseMatrixKernel | Performs microbenchmarking of a sparse matrix linear algebra kernel
PamClusteringMicrobenchmark | Conducts a single performance trial with the cluster::pam function
PerformClusteringMicrobenchmarking | Performs microbenchmarking of machine learning functions specified by an input list
PerformSparseMatrixKernelMicrobenchmarking | Performs microbenchmarking of sparse matrix kernels specified by an input list
PrintClusteringMicrobenchmarkResults | Prints results of a clustering for machine learning microbenchmark
PrintDenseMatrixMicrobenchmarkResults | Prints results of a dense matrix microbenchmark
PrintSparseMatrixMicrobenchmarkResults | Prints results of a sparse matrix microbenchmark
QrAllocator | Allocates and populates input to the QR factorization dense matrix kernel microbenchmarks
QrMicrobenchmark | Conducts a single performance trial with the QR factorization dense matrix kernel
RHPCBenchmark | RHPCBenchmark: A package for performance testing intrinsic R functionality and established packages relevant to high-performance computing
RunDenseMatrixBenchmark | Runs all of the dense matrix microbenchmarks
RunMachineLearningBenchmark | Runs all of the machine learning microbenchmarks
RunSparseMatrixBenchmark | Runs all of the sparse matrix microbenchmarks
SolveAllocator | Allocates and populates input to the dense matrix kernel microbenchmark for computing the solution to a system of linear equations with multiple right-hand sides
SolveMicrobenchmark | Conducts a single performance trial with the dense matrix kernel for computing the solution to a system of linear equations with multiple right-hand sides
SparseCholeskyAllocator | Allocates and initializes input to the Cholesky factorization sparse matrix kernel microbenchmarks
SparseCholeskyMicrobenchmark | Conducts a single performance trial with the Cholesky factorization sparse matrix kernel
SparseLuAllocator | Allocates and initializes input to the LU factorization sparse matrix kernel microbenchmarks
SparseLuMicrobenchmark | Conducts a single performance trial with the LU factorization sparse matrix kernel
SparseMatrixMicrobenchmark | This class specifies a sparse matrix microbenchmark.
SparseMatrixVectorAllocator | Allocates and initializes input to the matrix-vector multiplication sparse matrix kernel microbenchmarks
SparseMatrixVectorMicrobenchmark | Conducts a single performance trial with the matrix-vector multiplication sparse matrix kernel
SparseQrAllocator | Allocates and initializes input to the QR factorization sparse matrix kernel microbenchmarks
SparseQrMicrobenchmark | Conducts a single performance trial with the QR factorization sparse matrix kernel
SvdAllocator | Allocates and populates input to the singular value decomposition (SVD) dense matrix kernel microbenchmarks
SvdMicrobenchmark | Conducts a single performance trial with the singular value decomposition (SVD) dense matrix kernel
TransposeAllocator | Allocates and populates input to the matrix transpose dense matrix kernel microbenchmarks
TransposeMicrobenchmark | Conducts a single performance trial with the matrix transpose dense matrix kernel
WriteClusteringPerformanceResultsCsv | Appends performance test results of a clustering microbenchmark to a file in CSV format
WriteDenseMatrixPerformanceResultsCsv | Appends dense matrix performance test results to a file in CSV format
WriteSparseMatrixPerformanceResultsCsv | Appends sparse matrix performance test results to a file in CSV format