Benchmarking hdfqlr

Michael Koohafkan

2021-06-09

This document provides some benchmarks for comparing the performance of hdfqlr to the hdf5r package. This vignette previously included comparisons to the now-deprecated h5 package. Other packages that provide read (but not write) support for HDF files were not tested.

Writing HDF datasets 

write_hdfqlr = function() {
    test.file = tempfile(fileext = ".h5")
    hql_create_file(test.file)
    hql_use_file(test.file)
    for (i in paste0("vector", 1:6)) {
        write("DATASET", runif(10000), i)
    }
    hql_close_file(test.file)
}

write_hdf5r = function() {
    test.file = tempfile(fileext = ".h5")
    # create hdf5 file (6 vectors with 10k random numbers each)
    h5file = hdf5r::H5File$new(test.file, "w")
    for (i in paste0("vector", 1:6)) {
        h5file[[i]] = runif(10000)
    }
    h5file$close_all()
}

write.benchmark = microbenchmark(
        "hdf5r" = write_hdf5r(),
        "hdfqlr" = write_hdfqlr(),
    times = 1000L,
    unit = 'ms'
)
expr min lq mean median uq max neval
hdf5r 150.1851 185.27945 199.61208 198.1042 211.18990 399.0265 1000
hdfqlr 23.8104 29.05005 36.77295 37.1426 41.68425 88.0541 1000
plot of chunk write-benchmark
plot of chunk write-benchmark

Reading HDF datasets 

tf = tempfile(fileext = ".h5")
hql_create_file(tf)
hql_use_file(tf)
sets = paste0("vector", 1:6)
for (i in sets) {
    hql_write_dataset(runif(10000), i)
}
hql_close_file(tf)

read_hdfqlr = function(file, sets) {
    hql_use_file(file)
    result = lapply(sets, hql_read_dataset)
    hql_close_file(file)
    result
}

read_hdf5r = function(file, sets) {
    h5file = hdf5r::H5File$new(file, "r")
    result = lapply(sets, function(i) h5file[[i]][])
    h5file$close_all()
    result
}

read.benchmark = microbenchmark(
    "hdf5r" = read_hdf5r(tf, sets),
    "hdfqlr" = read_hdfqlr(tf, sets),
    times = 1000L,
    unit = 'ms'
)
expr min lq mean median uq max neval
hdf5r 116.4230 137.74210 143.90668 143.6394 148.6843 219.4179 1000
hdfqlr 12.5036 18.11385 21.01237 21.9278 23.0107 41.2884 1000
plot of chunk read-benchmark
plot of chunk read-benchmark