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Benchmark R vs Julia dataframe on disk format
using CSV, Feather
#using JLD2
#using JLD#, JLSO
using JDF, FileIO, Blosc, StatsPlots, RCall
using DataFrames, WeakRefStrings # required for JLD2, JDF
Blosc.set_num_threads(6)
gen_benchmark(dirpath, largest_file, outpath, data_label; delim = ',', header=true) = begin
if !isdir(outpath)
mkpath(outpath)
end
csv_read1 = @elapsed df = CSV.read(joinpath(dirpath, largest_file), delim = delim, header = header, threaded=false);
csv_read2 = @elapsed CSV.read(joinpath(dirpath, largest_file), delim = delim, header = header, threaded=false);
csv_write1 = 0
csv_write2 = 0
try
csv_write1 = @elapsed CSV.write(joinpath(outpath, largest_file*".csv"), df);
csv_write2 = @elapsed CSV.write(joinpath(outpath, largest_file*".csv"), df);
catch err
end
R"""
library(data.table)
library(fst)
# memory.limit(Inf)
data_table_read1 = system.time(a <- data.table::fread($(joinpath(dirpath, largest_file))))[3]
data_table_read2 = system.time(data.table::fread($(joinpath(dirpath, largest_file))))[3]
data_table_write1 = system.time(data.table::fwrite(a, $(joinpath(outpath, largest_file*".data.table.csv"))))[3]
data_table_write2 = system.time(data.table::fwrite(a, $(joinpath(outpath, largest_file*".data.table.csv"))))[3]
fst_write1 = system.time(fst::write_fst(a, $(joinpath(outpath, largest_file*".fst"))))[3]
fst_write2 = system.time(fst::write_fst(a, $(joinpath(outpath, largest_file*".fst"))))[3]
fst_read1 = system.time(fst::read_fst($(joinpath(outpath, largest_file*".fst"))))[3]
fst_read2 = system.time(fst::read_fst($(joinpath(outpath, largest_file*".fst"))))[3]
parquet_r_write1 = system.time(arrow::write_parquet(a, $(joinpath(outpath, largest_file*".parquet"))))[3]
parquet_r_write2 = system.time(arrow::write_parquet(a, $(joinpath(outpath, largest_file*".parquet"))))[3]
parquet_r_read1 = system.time(arrow::read_parquet($(joinpath(outpath, largest_file*".parquet"))))[3]
parquet_r_read2 = system.time(arrow::read_parquet($(joinpath(outpath, largest_file*".parquet"))))[3]
rm(a)
gc()
"""
@rget data_table_read1
@rget data_table_read2
@rget data_table_write1
@rget data_table_write2
@rget fst_write1
@rget fst_write2
@rget fst_read1
@rget fst_read2
@rget parquet_r_read1
@rget parquet_r_read2
@rget parquet_r_write1
@rget parquet_r_write2
# jlso_write1 = 0
# jlso_write2 = 0
# try
# jlso_write1 = @elapsed JLSO.save(joinpath(outpath, largest_file*".jlso"), df);
# jlso_write2 = @elapsed JLSO.save(joinpath(outpath, largest_file*".jlso"), df);
# catch err
# end
# jld2_write1 = 0
# jld2_write2 = 0
# try
# jld2_write1 = @elapsed save(joinpath(outpath, largest_file*".jld2"), Dict("df" => df));
# jld2_write2 = @elapsed save(joinpath(outpath, largest_file*".jld2"), Dict("df" => df));
# catch err
# end
# jld_write1 = 0
# jld_write2 = 0
# try
# jld_write1 = @elapsed save(joinpath(outpath, largest_file*".jld"), Dict("df" => df));
# jld_write2 = @elapsed save(joinpath(outpath, largest_file*".jld"), Dict("df" => df));
# catch err
# end
jdf_write1 = 0
jdf_write2 = 0
try
jdf_write1 = @elapsed savejdf(joinpath(outpath, largest_file*".jdf"), df);
jdf_write2 = @elapsed savejdf(joinpath(outpath, largest_file*".jdf"), df);
catch err
end
# # feather can't handle all missing
for n in names(df)
if eltype(df[!,n]) == Missing
println("Removed $n for Feather.jl")
select!(df, Not(n))
df[!,n] = Vector{Union{Missing, Bool}}(missing, size(df, 1))
end
end
feather_write1 = 0
feather_write2 = 0
try
feather_write1 = @elapsed Feather.write(joinpath(outpath, largest_file*".feather"), df);
feather_write2 = @elapsed Feather.write(joinpath(outpath, largest_file*".feather"), df);
catch err
end
######################################### loading
feather_read1 = 0
feather_read2 = 0
try
feather_read1 = @elapsed Feather.read(joinpath(outpath, largest_file*".feather"));
feather_read2 = @elapsed Feather.read(joinpath(outpath, largest_file*".feather"));
catch err
end
# jld_read1 = 0
# jld_read2 = 0
# try
# jld_read1 = @elapsed load(joinpath(outpath, largest_file*".jld"))["df"];
# jld_read2 = @elapsed load(joinpath(outpath, largest_file*".jld"))["df"];
# catch err
# end
# jld2_read1 = 0
# jld2_read2 = 0
# try
# jld2_read1 = @elapsed load(joinpath(outpath, largest_file*".jld2"))["df"];
# jld2_read2 = @elapsed load(joinpath(outpath, largest_file*".jld2"))["df"];
# catch err
# end
#
# jlso_read1 = 0
# jlso_read2 = 0
# try
# jlso_read1 = @elapsed JLSO.load(joinpath(outpath, largest_file*".jlso"))["data"];
# jlso_read2 = @elapsed JLSO.load(joinpath(outpath, largest_file*".jlso"))["data"];
# catch err
# end
jdf_read1 = 0
jdf_read2 = 0
try
jdf_read1 = @elapsed loadjdf(joinpath(outpath, largest_file*".jdf"));
jdf_read2 = @elapsed loadjdf(joinpath(outpath, largest_file*".jdf"));
catch err
end
# write_perf = [jdf_write1, jdf_write2, csv_write1, csv_write2, feather_write1, feather_write2, jld2_write1, jld2_write2, jlso_write1, jlso_write2]
# read_perf = [jdf_read1, jdf_read2, csv_read1, csv_read2, feather_read1, feather_read2, jld2_read1, jld2_read2, jlso_read1, jlso_read2]
write_perf = [jdf_write1, jdf_write2, csv_write1, csv_write2, feather_write1, feather_write2, data_table_write1, data_table_write2, fst_write1, fst_write2, parquet_r_write1, parquet_r_write2]
read_perf = [jdf_read1, jdf_read2, csv_read1, csv_read2, feather_read1, feather_read2, data_table_read1, data_table_read2, fst_read1, fst_read2, parquet_r_read1, parquet_r_read2]
pkgs = repeat(["JDF.jl", "CSV.jl", "Feather.jl", "data.table", "fst", "parquet R"], inner = 2)
run_group = repeat(["1st", "2nd"], outer = 6)
plot_write = groupedbar(
pkgs,
write_perf,
group = run_group,
ylab = "Seconds",
title = "Disk-format Write performance comparison \n Data: $data_label data \n Size: $(size(df)) filesize:$(round(filesize(joinpath(dirpath, largest_file))/1024^3, digits=1))GB \n Julia $(VERSION)"
)
savefig(plot_write, joinpath(outpath, largest_file*"plot_write.png"))
# plot_write_wo_jlso = groupedbar(
# repeat(["JDF.jl", "CSV.jl", "Feather.jl", "JLD2.jl"], inner = 2),
# [jdf_write1, jdf_write2, csv_write1, csv_write2, feather_write1, feather_write2, jld2_write1, jld2_write2],
# group = repeat(["1st", "2nd"], outer = 4),
# ylab = "Seconds",
# title = "Disk-format Write performance comparison \n Data: $data_label data \n Size: $(size(df)) filesize:$(round(filesize(joinpath(dirpath, largest_file))/1024^3, digits=1))GB \n Julia $(VERSION)"
# )
# savefig(plot_write_wo_jlso, joinpath(outpath, largest_file*"plot_write_wo_jlso.png"))
plot_read = groupedbar(
pkgs,
read_perf,
group = run_group,
ylab = "Seconds",
title = "Disk-format Read performance comparison \n Data: $data_label data \n Size: $(size(df)) filesize:$(round(filesize(joinpath(dirpath, largest_file))/1024^3, digits=1))GB \n Julia $(VERSION)"
)
savefig(plot_read, joinpath(outpath, largest_file*"plot_read.png"))
# plot_read_wo_csv_jlso = groupedbar(
# repeat(["JDF.jl", "Feather.jl", "JLD2.jl"], inner = 2),
# [jdf_read1, jdf_read2, feather_read1, feather_read2, jld2_read1, jld2_read2],
# group = repeat(["1st", "2nd"], outer = 3),
# ylab = "Seconds",
# title = "Disk-format Read performance comparison \n Data: $data_label data \n Size: $(size(df)) filesize:$(round(filesize(joinpath(dirpath, largest_file))/1024^3, digits=1))GB \n Julia $(VERSION)"
# )
# savefig(plot_read_wo_csv_jlso, joinpath(outpath, largest_file*"plot_read_wo_csv_jlso.png"))
#
# plot_read_wo_jlso = groupedbar(
# repeat(["JDF.jl", "CSV.jl", "Feather.jl", "JLD2.jl"], inner = 2),
# [jdf_read1, jdf_read2, csv_read1, csv_read2, feather_read1, feather_read2, jld2_read1, jld2_read2],
# group = repeat(["1st", "2nd"], outer = 4),
# ylab = "Seconds",
# title = "Disk-format Read performance comparison \n Data: $data_label data \n Size: $(size(df)) filesize:$(round(filesize(joinpath(dirpath, largest_file))/1024^3, digits=1))GB \n Julia $(VERSION)"
# )
# savefig(plot_read_wo_jlso, joinpath(outpath, largest_file*"plot_read_wo_jlso.png"))
(write_perf, read_perf, dirpath, outpath, largest_file, df)
end
sum_file_size(dir) = begin
res = Int[]
for f in joinpath.(dir, readdir(dir))
if isfile(f)
push!(res, filesize(f))
elseif isdir(f)
println(f)
push!(res, sum(filesize.(joinpath.(f,readdir(f)))))
end
end
df = DataFrame(file = readdir(dir), fs = res)
tmpfn = (x->x[end-3:end])
df[!,:ext] = tmpfn.(df[!, :file])
filter!(r -> r.ext != ".png", df)
df = sort!(df, :ext)[[1:2;4], :]
df[:pkg] = ["CSV.jl", "JDF.jl", "Feather.jl"]
sort!(df, :pkg)
df
end
# Fannie Mae
# download("http://rapidsai-data.s3-website.us-east-2.amazonaws.com/notebook-mortgage-data/mortgage_2000-2007.tgz", "c:/data/mortgage_2000-2007.tgz")
# un-tar and uncompress the file
# ;tar zxvg mortgage_2000-2007.tgz
# uncomment for debugging
dirpath = "C:/data/perf/"
largest_file = "Performance_2004Q3.txt"
outpath = "c:/data/jdf-bench/Performance_2004Q3.txt"
data_label = "Fannie Mae Performance 2004Q3"
# delim = ','
# header = true
include("C:/Users/RTX2080/git/JDF/benchmarks/benchmarks.jl")
#@timegen_benchmark("c:/data/AirOnTimeCSV/", "airOT199302.csv", "c:/data/jdf-bench/airOT199302.csv", "Air On Time 199302")
@time res = gen_benchmark(dirpath, largest_file, outpath, data_label, delim = '|', header = false);
write_perf = res[1]
read_perf = res[2]
pkgs = repeat(["JDF.jl", "CSV.jl", "Feather.jl", "data.table", "fst", "parquet R"], inner = 2)
run_group = repeat(["1st", "2nd"], outer = 6)
write_perf = write_perf[pkgs .!= "Feather.jl"]
run_group = run_group[pkgs .!= "Feather.jl"]
pkgs1 = pkgs[pkgs .!= "Feather.jl"]
plot_write = groupedbar(
pkgs1,
write_perf,
group = run_group,
ylab = "Seconds",
title = "Disk-format Write performance comparison \n Julia $(VERSION)"
)
savefig(plot_write, joinpath(outpath, largest_file*"plot_write_less.png"))
pkgs = repeat(["JDF.jl", "CSV.jl", "Feather.jl", "data.table", "fst", "parquet R"], inner = 2)
run_group = repeat(["1st", "2nd"], outer = 6)
read_perf = read_perf[.!in.(pkgs, Ref(["CSV.jl", "parqeut R"]))]
run_group = run_group[.!in.(pkgs, Ref(["CSV.jl", "parqeut R"]))]
pkgs2 = pkgs[.!in.(pkgs, Ref(["CSV.jl", "parqeut R"]))]
plot_read = groupedbar(
pkgs2,
read_perf,
group = run_group,
ylab = "Seconds",
title = "Disk-format Read performance comparison \n Julia $(VERSION)"
)
savefig(plot_read, joinpath(outpath, largest_file*"plot_read_less.png"))
sizedf = sum_file_size(outpath)
using StatsPlots
p = plot(
sizedf.pkg,
sizedf.fs/1024^3,
linetype = :bar,
ylab = "Size (GB)",
legend = false,
title = "On-disk file Size for various formats\n $data_label data")
savefig(p, joinpath(outpath, largest_file*"_filesize.png"))
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