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benchmark: introduce benchmark_driver.gem

Browse source 
Makefile.in: Clone benchmark-driver repository in benchmark/benchmark-driver
  `make update-benchmark-driver`, like simplecov.
win32/Makefile.sub: Roughly do the same thing.
.gitignore: Ignore the cloned repository.
common.mk: Trigger `make update-benchmark-driver` to run `make benchmark`
  and adjust arguments for benchmark_driver.gem.

benchmark/require.yml: renamed from benchmark/bm_require.rb, benchmark/prepare_require.rb
benchmark/require_thread.yml: renamed from benchmark/bm_require_thread.rb, benchmark/prepare_require_thread.rb
benchmark/so_count_words.yml: renamed from benchmark/bm_so_count_words.rb, benchmark/prepare_so_count_words.rb,
  benchmark/wc.input.base
benchmark/so_k_nucleotide.yml: renamed from benchmark/bm_so_k_nucleotide.rb, benchmark/prepare_so_k_nucleotide.rb,
  benchmark/make_fasta_output.rb
benchmark/so_reverse_complement.yml: renamed from benchmark/bm_so_reverse_complement.rb, benchmark/prepare_so_reverse_complement.rb,
  benchmark/make_fasta_output.rb

I'm sorry but I made some duplications between benchmark/require.yml and benchmark/require_thread.yml,
and between benchmark/so_k_nucleotide.yml and benchmark/so_reverse_complement.yml.

If you're not comfortable with it, please combine these YAMLs to share
the same prelude. One YAML file can have multiple benchmark definitions
sharing prelude.

benchmark/driver.rb: Replace its core feature with benchmark_driver.gem.
  Some old features are gone for now, but I'll add them again later.

[Misc #14902]

git-svn-id: svn+ssh://ci.ruby-lang.org/ruby/trunk@63888 b2dd03c8-39d4-4d8f-98ff-823fe69b080e
This commit is contained in:
k0kubun 2018-07-08 14:38:05 +00:00
parent 1f4541cb98
commit 3293322a39
21 changed files with 504 additions and 562 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

1
.gitignore vendored
View file

@ -60,6 +60,7 @@ lcov*.info
/archive
/autom4te*.cache
/automake
/benchmark/benchmark-driver
/beos
/bmlog-*
/breakpoints.gdb

5
Makefile.in
View file

@ -515,6 +515,11 @@ gcov:
lcov:
$(Q) $(BASERUBY) $(srcdir)/tool/run-lcov.rb
update-benchmark-driver:
$(Q) $(srcdir)/tool/git-refresh -C $(srcdir)/benchmark $(Q1:0=-q) \
--branch $(BENCHMARK_DRIVER_GIT_REF) \
$(BENCHMARK_DRIVER_GIT_URL) benchmark-driver $(GIT_OPTS)
update-doclie:
$(Q) $(srcdir)/tool/git-refresh -C $(srcdir)/coverage $(Q1:0=-q) \
--branch $(DOCLIE_GIT_REF) \

7
benchmark/bm_require.rb
View file

@ -1,7 +0,0 @@
$:.push File.join(File.dirname(__FILE__), "bm_require.data")
1.upto(10000) do |i|
require "c#{i}"
end
$:.pop

15
benchmark/bm_require_thread.rb
View file

@ -1,15 +0,0 @@
$:.push File.join(File.dirname(__FILE__), "bm_require.data")
i=0
t = Thread.new do
while true
i = i+1 # dummy loop
end
end
1.upto(100) do |i|
require "c#{i}"
end
$:.pop
t.kill

19
benchmark/bm_so_count_words.rb
View file

@ -1,19 +0,0 @@
#!/usr/bin/ruby
# -*- mode: ruby -*-
# $Id: wc-ruby.code,v 1.4 2004/11/13 07:43:32 bfulgham Exp $
# http://www.bagley.org/~doug/shootout/
# with help from Paul Brannan
input = open(File.join(File.dirname($0), 'wc.input'), 'rb')
nl = nw = nc = 0
while true
tmp = input.read(4096) or break
data = tmp << (input.gets || "")
nc += data.length
nl += data.count("\n")
((data.strip! || data).tr!("\n", " ") || data).squeeze!
nw += data.count(" ") + 1
end
# STDERR.puts "#{nl} #{nw} #{nc}"

48
benchmark/bm_so_k_nucleotide.rb
View file

@ -1,48 +0,0 @@
# The Computer Language Shootout
# http://shootout.alioth.debian.org
#
# contributed by jose fco. gonzalez
# modified by Sokolov Yura
seq = String.new
def frecuency( seq,length )
n, table = seq.length - length + 1, Hash.new(0)
f, i = nil, nil
(0 ... length).each do |f|
(f ... n).step(length) do |i|
table[seq[i,length]] += 1
end
end
[n,table]
end
def sort_by_freq( seq,length )
n,table = frecuency( seq,length )
a, b, v = nil, nil, nil
table.sort{|a,b| b[1] <=> a[1]}.each do |v|
puts "%s %.3f" % [v[0].upcase,((v[1]*100).to_f/n)]
end
puts
end
def find_seq( seq,s )
n,table = frecuency( seq,s.length )
puts "#{table[s].to_s}\t#{s.upcase}"
end
input = open(File.join(File.dirname($0), 'fasta.output.100000'), 'rb')
line = input.gets while line !~ /^>THREE/
line = input.gets
while (line !~ /^>/) & line do
seq << line.chomp
line = input.gets
end
[1,2].each {|i| sort_by_freq( seq,i ) }
%w(ggt ggta ggtatt ggtattttaatt ggtattttaatttatagt).each{|s| find_seq( seq,s) }

30
benchmark/bm_so_reverse_complement.rb
View file

@ -1,30 +0,0 @@
#!/usr/bin/ruby
# The Great Computer Language Shootout
# http://shootout.alioth.debian.org/
#
# Contributed by Peter Bjarke Olsen
# Modified by Doug King
seq=Array.new
def revcomp(seq)
seq.reverse!.tr!('wsatugcyrkmbdhvnATUGCYRKMBDHVN','WSTAACGRYMKVHDBNTAACGRYMKVHDBN')
stringlen=seq.length
0.step(stringlen-1,60) {|x| print seq.slice(x,60) , "\n"}
end
input = open(File.join(File.dirname($0), 'fasta.output.2500000'), 'rb')
while input.gets
if $_ =~ />/
if seq.length != 0
revcomp(seq.join)
seq=Array.new
end
puts $_
else
$_.sub(/\n/,'')
seq.push $_
end
end
revcomp(seq.join)

399
benchmark/driver.rb
View file

@ -10,256 +10,66 @@ rescue LoadError
require 'optparse'
end
require 'benchmark'
require 'pp'
require 'shellwords'
require 'tempfile'
class BenchmarkDriver
def self.benchmark(opt)
driver = self.new(opt[:execs], opt[:dir], opt)
begin
driver.run
ensure
driver.show_results
# Run benchmark-driver prepared by `make update-benchmark-driver`
def self.run(*args)
benchmark_driver = File.expand_path('./benchmark-driver/exe/benchmark-driver', __dir__)
command = [benchmark_driver, *args]
unless system(command.shelljoin)
abort "Failed to execute: #{command.shelljoin}"
end
end
def self.load(input, type, opt)
case type
when 'yaml'
require 'yaml'
h = YAML.load(input)
when 'json'
require 'json'
h = JSON.load(input)
else
h = eval(input.read)
end
results = h[:results] || h["results"]
obj = allocate
obj.instance_variable_set("@execs", h[:executables] || h["executables"])
obj.instance_variable_set("@results", results)
obj.instance_variable_set("@opt", opt)
[1, 2].each do |i|
loop = results.assoc((n = "loop_whileloop#{i}").intern) || results.assoc(n)
obj.instance_variable_set("@loop_wl#{i}", loop ? loop[1].map {|t,*|t} : nil)
end
obj.instance_variable_set("@measure_target", opt[:measure_target] || opt["measure_target"])
obj
end
def output *args
puts(*args)
@output and @output.puts(*args)
end
def message *args
output(*args) if @verbose
end
def message_print *args
if @verbose
print(*args)
STDOUT.flush
@output and @output.print(*args)
end
end
def progress_message *args
unless STDOUT.tty?
STDERR.print(*args)
STDERR.flush
end
end
def initialize execs, dir, opt = {}
@execs = execs.map{|e|
e.strip!
next if e.empty?
if /(.+)::(.+)/ =~ e
# ex) ruby-a::/path/to/ruby-a
label = $1.strip
path = $2
version = `#{path} --version`.chomp
else
path = e
version = label = `#{path} --version`.chomp
end
[path, label, version]
}.compact
def initialize(dir, opt = {})
@dir = dir
@repeat = opt[:repeat] || 1
@repeat = 1 if @repeat < 1
@pattern = opt[:pattern] || nil
@exclude = opt[:exclude] || nil
@verbose = opt[:quiet] ? false : (opt[:verbose] || false)
@output = opt[:output] ? open(opt[:output], 'w') : nil
@loop_wl1 = @loop_wl2 = nil
@ruby_arg = opt[:ruby_arg] || nil
@measure_target = opt[:measure_target]
@opt = opt
# [[name, [[r-1-1, r-1-2, ...], [r-2-1, r-2-2, ...]]], ...]
@results = []
if @verbose
@start_time = Time.now
message @start_time
@execs.each_with_index{|(path, label, version), i|
message "target #{i}: " + (label == version ? "#{label}" : "#{label} (#{version})") + " at \"#{path}\""
}
message "measure target: #{@measure_target}"
end
end
def adjusted_results name, results
s = nil
results.each_with_index{|e, i|
r = e.min
case name
when /^vm1_/
if @loop_wl1
r -= @loop_wl1[i]
r = 0 if r < 0
s = '*'
end
when /^vm2_/
if @loop_wl2
r -= @loop_wl2[i]
r = 0 if r < 0
s = '*'
def with_yamls(&block)
ios = files.map do |file|
Tempfile.open.tap do |io|
if file.end_with?('.yml')
io.write(File.read(file))
else
io.write(build_yaml(file))
end
io.close
end
yield r
}
s
end
block.call(ios.map(&:path))
ensure
ios.each(&:close)
end
def show_results
case @opt[:format]
when :tsv
strformat = "\t%1$s"
numformat = "\t%1$*2$.3f"
minwidth = 0
name_width = 0
when :markdown
markdown = true
strformat = "|%1$-*2$s"
numformat = "|%1$*2$.3f"
when :plain
strformat = " %1$-*2$s"
numformat = " %1$*2$.3f"
private
def build_yaml(file)
magic_comment = '# prelude' # bm_so_nsieve_bits hangs without magic comment
name = File.basename(file).sub(/\Abm_/, '').sub(/\.rb\z/, '')
script = File.read(file).sub(/^__END__\n(.+\n)*/m, '').sub(/\A(^#.+\n)+/m) do |comment|
magic_comment = comment
''
end
name_width ||= @results.map {|v, result|
v.size + (case v; when /^vm1_/; @loop_wl1; when /^vm2_/; @loop_wl2; end ? 1 : 0)
}.max
minwidth ||= 7
width = @execs.map{|(_, v)| [v.size, minwidth].max}
output
if @verbose
message '-----------------------------------------------------------'
message 'raw data:'
message
message PP.pp(@results, "", 79)
message
message "Elapsed time: #{Time.now - @start_time} (sec)"
end
if rawdata_output = @opt[:rawdata_output]
h = {}
h[:cpuinfo] = File.read('/proc/cpuinfo') if File.exist?('/proc/cpuinfo')
h[:executables] = @execs
h[:results] = @results
if (type = File.extname(rawdata_output)).empty?
type = rawdata_output
rawdata_output = @output.path.sub(/\.[^.\/]+\z/, '') << '.' << rawdata_output
end
case type
when 'yaml'
require 'yaml'
h = YAML.dump(h)
when 'json'
require 'json'
h = JSON.pretty_generate(h)
else
require 'pp'
h = h.pretty_inspect
end
open(rawdata_output, 'w') {|f| f.puts h}
end
output '-----------------------------------------------------------'
output 'benchmark results:'
if @verbose and @repeat > 1
output "minimum results in each #{@repeat} measurements."
end
output({
real: "Execution time (sec)",
utime: "user CPU time",
stime: "system CPU time",
cutime: "user CPU time of children",
cstime: "system CPU time of children",
total: "all CPU time",
peak: "Memory usage (peak) (B)",
size: "Memory usage (last size) (B)",
}[@measure_target])
output if markdown
output ["name".ljust(name_width), @execs.map.with_index{|(_, v), i| sprintf(strformat, v, width[i])}].join("").rstrip
output ["-"*name_width, width.map{|n|":".rjust(n, "-")}].join("|") if markdown
@results.each{|v, result|
rets = []
s = adjusted_results(v, result){|r|
rets << sprintf(numformat, r, width[rets.size])
}
v += s if s
output [v.ljust(name_width), rets].join("")
}
if @execs.size > 1
output
output({
real: "Speedup ratio: compare with the result of `#{@execs[0][1]}' (greater is better)",
peak: "Memory consuming ratio (peak) with the result of `#{@execs[0][1]}' (greater is better)",
size: "Memory consuming ratio (size) with the result of `#{@execs[0][1]}' (greater is better)",
}[@measure_target])
output if markdown
output ["name".ljust(name_width), @execs[1..-1].map.with_index{|(_, v), i| sprintf(strformat, v, width[i])}].join("").rstrip
output ["-"*name_width, width[1..-1].map{|n|":".rjust(n, "-")}].join("|") if markdown
@results.each{|v, result|
rets = []
first_value = nil
s = adjusted_results(v, result){|r|
if first_value
if r == 0
rets << "Error"
else
rets << sprintf(numformat, first_value/Float(r), width[rets.size+1])
end
else
first_value = r
end
}
v += s if s
output [v.ljust(name_width), rets].join("")
}
end
if @opt[:output]
output
output "Log file: #{@opt[:output]}"
end
<<-YAML
prelude: |
#{magic_comment.gsub(/^/, ' ')}
benchmark:
#{name}: |
#{script.gsub(/^/, ' ')}
loop_count: 1
YAML
end
def files
flag = {}
@files = Dir.glob(File.join(@dir, 'bm*.rb')).map{|file|
legacy_files = Dir.glob(File.join(@dir, 'bm*.rb'))
yaml_files = Dir.glob(File.join(@dir, '*.yml'))
files = (legacy_files + yaml_files).map{|file|
next if @pattern && /#{@pattern}/ !~ File.basename(file)
next if @exclude && /#{@exclude}/ =~ File.basename(file)
case file
@ -270,90 +80,13 @@ class BenchmarkDriver
}.compact
if flag['vm1'] && !flag['whileloop']
@files << File.join(@dir, 'bm_loop_whileloop.rb')
files << File.join(@dir, 'bm_loop_whileloop.rb')
elsif flag['vm2'] && !flag['whileloop2']
@files << File.join(@dir, 'bm_loop_whileloop2.rb')
files << File.join(@dir, 'bm_loop_whileloop2.rb')
end
@files.sort!
progress_message "total: #{@files.size * @repeat} trial(s) (#{@repeat} trial(s) for #{@files.size} benchmark(s))\n"
@files
end
def run
files.each_with_index{|file, i|
@i = i
r = measure_file(file)
if /bm_loop_whileloop.rb/ =~ file
@loop_wl1 = r[1].map{|e| e.min}
elsif /bm_loop_whileloop2.rb/ =~ file
@loop_wl2 = r[1].map{|e| e.min}
end
}
end
def measure_file file
name = File.basename(file, '.rb').sub(/^bm_/, '')
prepare_file = File.join(File.dirname(file), "prepare_#{name}.rb")
load prepare_file if FileTest.exist?(prepare_file)
if @verbose
output
output '-----------------------------------------------------------'
output name
output
output File.read(file)
output
end
result = [name]
result << @execs.map{|(e, v)|
(0...@repeat).map{
message_print "#{v}\t"
progress_message '.'
m = measure(e, file)
message "#{m}"
m
}
}
@results << result
result
end
unless defined?(File::NULL)
if File.exist?('/dev/null')
File::NULL = '/dev/null'
end
end
def measure executable, file
case @measure_target
when :real, :utime, :stime, :cutime, :cstime, :total
cmd = "#{executable} #{@ruby_arg} #{file}"
m = Benchmark.measure{
system(cmd, out: File::NULL)
}
result = m.__send__(@measure_target)
when :peak, :size
tmp = Tempfile.new("benchmark-memory-wrapper-data")
wrapper = "#{File.join(__dir__, 'memory_wrapper.rb')} #{tmp.path} #{@measure_target}"
cmd = "#{executable} #{@ruby_arg} #{wrapper} #{file}"
system(cmd, out: File::NULL)
result = tmp.read.to_i
tmp.close
else
raise "unknown measure target"
end
if $? != 0
raise $?.inspect if $? && $?.signaled?
output "\`#{cmd}\' exited with abnormal status (#{$?})"
0
else
result
end
files.sort!
files
end
end
@ -362,15 +95,7 @@ if __FILE__ == $0
:execs => [],
:dir => File.dirname(__FILE__),
:repeat => 1,
:measure_target => :real,
:output => nil,
:raw_output => nil,
:format => :tsv,
}
formats = {
:tsv => ".tsv",
:markdown => ".md",
:plain => ".txt",
:verbose => 1,
}
parser = OptionParser.new{|o|
@ -397,44 +122,18 @@ if __FILE__ == $0
o.on('-r', '--repeat-count [NUM]', "Repeat count"){|n|
opt[:repeat] = n.to_i
}
o.on('-o', '--output-file [FILE]', "Output file"){|f|
opt[:output] = f
}
o.on('--ruby-arg [ARG]', "Optional argument for ruby"){|a|
opt[:ruby_arg] = a
}
o.on('--measure-target [TARGET]',
'real (execution time), peak, size (memory), total'){|mt|
opt[:measure_target] = mt.to_sym
}
o.on('--rawdata-output [FILE]', 'output rawdata'){|r|
opt[:rawdata_output] = r
}
o.on('--load-rawdata=FILE', 'input rawdata'){|r|
opt[:rawdata_input] = r
}
o.on('-f', "--format=FORMAT", "output format (#{formats.keys.join(",")})", formats.keys){|r|
opt[:format] = r
}
o.on('-v', '--verbose'){|v|
opt[:verbose] = v
opt[:verbose] = 2
}
o.on('-q', '--quiet', "Run without notify information except result table."){|q|
opt[:quiet] = q
opt[:verbose] = false
opt[:verbose] = 0
}
}
parser.parse!(ARGV)
if input = opt[:rawdata_input]
b = open(input) {|f|
BenchmarkDriver.load(f, File.extname(input)[1..-1], opt)
}
b.show_results
else
opt[:output] ||= "bmlog-#{Time.now.strftime('%Y%m%d-%H%M%S')}.#{$$}#{formats[opt[:format]]}"
BenchmarkDriver.benchmark(opt)
execs = opt[:execs].map { |exec| ['--executables', exec.shellsplit.join(',')] }.flatten
BenchmarkDriver.new(opt[:dir], opt).with_yamls do |yamls|
BenchmarkDriver.run(*yamls, *execs, "--verbose=#{opt[:verbose]}", "--repeat-count=#{opt[:repeat]}")
end
end

19
benchmark/make_fasta_output.rb
View file

@ -1,19 +0,0 @@
# prepare 'fasta.output'
def prepare_fasta_output n
filebase = File.join(File.dirname($0), 'fasta.output')
script = File.join(File.dirname($0), 'bm_so_fasta.rb')
file = "#{filebase}.#{n}"
unless FileTest.exist?(file)
STDERR.puts "preparing #{file}"
open(file, 'w'){|f|
ARGV[0] = n
$stdout = f
load script
$stdout = STDOUT
}
end
end

25
benchmark/prepare_require.rb
View file

@ -1,25 +0,0 @@
require "fileutils"
def prepare
num_files = 10000
basename = File.dirname($0)
data_dir = File.join(basename, "bm_require.data")
# skip if all of files exists
if File.exist?(File.join(data_dir, "c#{num_files}.rb"))
return
end
FileUtils.mkdir_p(data_dir)
1.upto(num_files) do |i|
f = File.open("#{data_dir}/c#{i}.rb", "w")
f.puts <<-END
class C#{i}
end
END
end
end
prepare

2
benchmark/prepare_require_thread.rb
View file

@ -1,2 +0,0 @@
load File.join(File.dirname(__FILE__), "prepare_require.rb")

15
benchmark/prepare_so_count_words.rb
View file

@ -1,15 +0,0 @@
# prepare 'wc.input'
def prepare_wc_input
wcinput = File.join(File.dirname($0), 'wc.input')
wcbase = File.join(File.dirname($0), 'wc.input.base')
unless FileTest.exist?(wcinput)
data = File.read(wcbase)
13.times{
data << data
}
open(wcinput, 'w'){|f| f.write data}
end
end
prepare_wc_input

2
benchmark/prepare_so_k_nucleotide.rb
View file

@ -1,2 +0,0 @@
require_relative 'make_fasta_output'
prepare_fasta_output(100_000)

2
benchmark/prepare_so_reverse_complement.rb
View file

@ -1,2 +0,0 @@
require_relative 'make_fasta_output'
prepare_fasta_output(2_500_000)

36
benchmark/require.yml Normal file
View file

@ -0,0 +1,36 @@
prelude: |
require "fileutils"
def prepare
num_files = 10000
basename = File.dirname($0)
data_dir = File.join(basename, "bm_require.data")
# skip if all of files exists
if File.exist?(File.join(data_dir, "c#{num_files}.rb"))
return
end
FileUtils.mkdir_p(data_dir)
1.upto(num_files) do |i|
f = File.open("#{data_dir}/c#{i}.rb", "w")
f.puts <<-END
class C#{i}
end
END
end
end
prepare
benchmark:
require: |
$:.push File.join(File.dirname(__FILE__), "bm_require.data")
1.upto(10000) do |i|
require "c#{i}"
end
$:.pop
loop_count: 1

44
benchmark/require_thread.yml Normal file
View file

@ -0,0 +1,44 @@
prelude: |
require "fileutils"
def prepare
num_files = 10000
basename = File.dirname($0)
data_dir = File.join(basename, "bm_require.data")
# skip if all of files exists
if File.exist?(File.join(data_dir, "c#{num_files}.rb"))
return
end
FileUtils.mkdir_p(data_dir)
1.upto(num_files) do |i|
f = File.open("#{data_dir}/c#{i}.rb", "w")
f.puts <<-END
class C#{i}
end
END
end
end
prepare
benchmark:
require_thread: |
$:.push File.join(File.dirname(__FILE__), "bm_require.data")
i=0
t = Thread.new do
while true
i = i+1 # dummy loop
end
end
1.upto(100) do |i|
require "c#{i}"
end
$:.pop
t.kill
loop_count: 1

85
benchmark/wc.input.base → benchmark/so_count_words.yml
View file

File diff suppressed because one or more lines are too long

155
benchmark/so_k_nucleotide.yml Normal file
View file

@ -0,0 +1,155 @@
prelude: |
bm_so_fasta = <<'EOS'
# The Computer Language Shootout
# http://shootout.alioth.debian.org/
# Contributed by Sokolov Yura
$last = 42.0
def gen_random(max, im=139968, ia=3877, ic=29573)
(max * ($last = ($last * ia + ic) % im)) / im
end
alu =
"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG"+
"GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA"+
"CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT"+
"ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA"+
"GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG"+
"AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC"+
"AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA"
iub = [
["a", 0.27],
["c", 0.12],
["g", 0.12],
["t", 0.27],
["B", 0.02],
["D", 0.02],
["H", 0.02],
["K", 0.02],
["M", 0.02],
["N", 0.02],
["R", 0.02],
["S", 0.02],
["V", 0.02],
["W", 0.02],
["Y", 0.02],
]
homosapiens = [
["a", 0.3029549426680],
["c", 0.1979883004921],
["g", 0.1975473066391],
["t", 0.3015094502008],
]
def make_repeat_fasta(id, desc, src, n)
puts ">#{id} #{desc}"
v = nil
width = 60
l = src.length
s = src * ((n / l) + 1)
s.slice!(n, l)
puts(s.scan(/.{1,#{width}}/).join("\n"))
end
def make_random_fasta(id, desc, table, n)
puts ">#{id} #{desc}"
rand, v = nil,nil
width = 60
chunk = 1 * width
prob = 0.0
table.each{|v| v[1]= (prob += v[1])}
for i in 1..(n/width)
puts((1..width).collect{
rand = gen_random(1.0)
table.find{|v| v[1]>rand}[0]
}.join)
end
if n%width != 0
puts((1..(n%width)).collect{
rand = gen_random(1.0)
table.find{|v| v[1]>rand}[0]
}.join)
end
end
n = (ARGV[0] or 250_000).to_i
make_repeat_fasta('ONE', 'Homo sapiens alu', alu, n*2)
make_random_fasta('TWO', 'IUB ambiguity codes', iub, n*3)
make_random_fasta('THREE', 'Homo sapiens frequency', homosapiens, n*5)
EOS
benchmark:
- name: so_k_nucleotide
prelude: |
script = File.join(File.dirname($0), 'bm_so_fasta.rb')
File.write(script, bm_so_fasta)
def prepare_fasta_output n
filebase = File.join(File.dirname($0), 'fasta.output')
script = File.join(File.dirname($0), 'bm_so_fasta.rb')
file = "#{filebase}.#{n}"
unless FileTest.exist?(file)
STDERR.puts "preparing #{file}"
open(file, 'w'){|f|
ARGV[0] = n
$stdout = f
load script
$stdout = STDOUT
}
end
end
prepare_fasta_output(100_000)
script: |
# The Computer Language Shootout
# http://shootout.alioth.debian.org
#
# contributed by jose fco. gonzalez
# modified by Sokolov Yura
seq = String.new
def frecuency( seq,length )
n, table = seq.length - length + 1, Hash.new(0)
f, i = nil, nil
(0 ... length).each do |f|
(f ... n).step(length) do |i|
table[seq[i,length]] += 1
end
end
[n,table]
end
def sort_by_freq( seq,length )
n,table = frecuency( seq,length )
a, b, v = nil, nil, nil
table.sort{|a,b| b[1] <=> a[1]}.each do |v|
puts "%s %.3f" % [v[0].upcase,((v[1]*100).to_f/n)]
end
puts
end
def find_seq( seq,s )
n,table = frecuency( seq,s.length )
puts "#{table[s].to_s}\t#{s.upcase}"
end
input = open(File.join(File.dirname($0), 'fasta.output.100000'), 'rb')
line = input.gets while line !~ /^>THREE/
line = input.gets
while (line !~ /^>/) & line do
seq << line.chomp
line = input.gets
end
[1,2].each {|i| sort_by_freq( seq,i ) }
%w(ggt ggta ggtatt ggtattttaatt ggtattttaatttatagt).each{|s| find_seq( seq,s) }
loop_count: 1

137
benchmark/so_reverse_complement.yml Normal file
View file

@ -0,0 +1,137 @@
prelude: |
bm_so_fasta = <<'EOS'
# The Computer Language Shootout
# http://shootout.alioth.debian.org/
# Contributed by Sokolov Yura
$last = 42.0
def gen_random(max, im=139968, ia=3877, ic=29573)
(max * ($last = ($last * ia + ic) % im)) / im
end
alu =
"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG"+
"GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA"+
"CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT"+
"ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA"+
"GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG"+
"AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC"+
"AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA"
iub = [
["a", 0.27],
["c", 0.12],
["g", 0.12],
["t", 0.27],
["B", 0.02],
["D", 0.02],
["H", 0.02],
["K", 0.02],
["M", 0.02],
["N", 0.02],
["R", 0.02],
["S", 0.02],
["V", 0.02],
["W", 0.02],
["Y", 0.02],
]
homosapiens = [
["a", 0.3029549426680],
["c", 0.1979883004921],
["g", 0.1975473066391],
["t", 0.3015094502008],
]
def make_repeat_fasta(id, desc, src, n)
puts ">#{id} #{desc}"
v = nil
width = 60
l = src.length
s = src * ((n / l) + 1)
s.slice!(n, l)
puts(s.scan(/.{1,#{width}}/).join("\n"))
end
def make_random_fasta(id, desc, table, n)
puts ">#{id} #{desc}"
rand, v = nil,nil
width = 60
chunk = 1 * width
prob = 0.0
table.each{|v| v[1]= (prob += v[1])}
for i in 1..(n/width)
puts((1..width).collect{
rand = gen_random(1.0)
table.find{|v| v[1]>rand}[0]
}.join)
end
if n%width != 0
puts((1..(n%width)).collect{
rand = gen_random(1.0)
table.find{|v| v[1]>rand}[0]
}.join)
end
end
n = (ARGV[0] or 250_000).to_i
make_repeat_fasta('ONE', 'Homo sapiens alu', alu, n*2)
make_random_fasta('TWO', 'IUB ambiguity codes', iub, n*3)
make_random_fasta('THREE', 'Homo sapiens frequency', homosapiens, n*5)
EOS
benchmark:
- name: so_reverse_complement
prelude: |
script = File.join(File.dirname($0), 'bm_so_fasta.rb')
File.write(script, bm_so_fasta)
def prepare_fasta_output n
filebase = File.join(File.dirname($0), 'fasta.output')
script = File.join(File.dirname($0), 'bm_so_fasta.rb')
file = "#{filebase}.#{n}"
unless FileTest.exist?(file)
STDERR.puts "preparing #{file}"
open(file, 'w'){|f|
ARGV[0] = n
$stdout = f
load script
$stdout = STDOUT
}
end
end
prepare_fasta_output(2_500_000)
script: |
# The Great Computer Language Shootout
# http://shootout.alioth.debian.org/
#
# Contributed by Peter Bjarke Olsen
# Modified by Doug King
seq=Array.new
def revcomp(seq)
seq.reverse!.tr!('wsatugcyrkmbdhvnATUGCYRKMBDHVN','WSTAACGRYMKVHDBNTAACGRYMKVHDBN')
stringlen=seq.length
0.step(stringlen-1,60) {|x| print seq.slice(x,60) , "\n"}
end
input = open(File.join(File.dirname($0), 'fasta.output.2500000'), 'rb')
while input.gets
if $_ =~ />/
if seq.length != 0
revcomp(seq.join)
seq=Array.new
end
puts $_
else
$_.sub(/\n/,'')
seq.push $_
end
end
revcomp(seq.join)
loop_count: 1

16
common.mk
View file

@ -41,6 +41,8 @@ GEM_HOME =
GEM_PATH =
GEM_VENDOR =
BENCHMARK_DRIVER_GIT_URL = https://github.com/benchmark-driver/benchmark-driver
BENCHMARK_DRIVER_GIT_REF = v0.13.2
SIMPLECOV_GIT_URL = git://github.com/colszowka/simplecov.git
SIMPLECOV_GIT_REF = v0.15.0
SIMPLECOV_HTML_GIT_URL = git://github.com/colszowka/simplecov-html.git
@ -1117,14 +1119,16 @@ OPTS =
# for example,
# $ make benchmark COMPARE_RUBY="ruby-trunk" OPTS="-e ruby-2.2.2"
# This command compares trunk and built-ruby and 2.2.2
benchmark: miniruby$(EXEEXT) PHONY
$(BASERUBY) $(srcdir)/benchmark/driver.rb -v \
--executables="$(COMPARE_RUBY) -I$(srcdir)/lib -I. -I$(EXTOUT)/common --disable-gem; built-ruby::$(MINIRUBY) -r$(srcdir)/prelude --disable-gem" \
benchmark: miniruby$(EXEEXT) update-benchmark-driver PHONY
$(BASERUBY) $(srcdir)/benchmark/driver.rb \
--executables="compare-ruby::$(COMPARE_RUBY) -I$(EXTOUT)/common --disable-gem" \
--executables="built-ruby::$(MINIRUBY) -r$(srcdir)/prelude --disable-gem" \
--pattern='bm_' --directory=$(srcdir)/benchmark $(OPTS)
benchmark-each: miniruby$(EXEEXT) PHONY
$(BASERUBY) $(srcdir)/benchmark/driver.rb -v \
--executables="$(COMPARE_RUBY) -I$(srcdir)/lib -I. -I$(EXTOUT)/common --disable-gem; built-ruby::$(MINIRUBY) -r$(srcdir)/prelude --disable-gem" \
benchmark-each: miniruby$(EXEEXT) update-benchmark-driver PHONY
$(BASERUBY) $(srcdir)/benchmark/driver.rb \
--executables="compare-ruby::$(COMPARE_RUBY) -I$(EXTOUT)/common --disable-gem" \
--executables="built-ruby::$(MINIRUBY) -r$(srcdir)/prelude --disable-gem" \
--pattern=$(ITEM) --directory=$(srcdir)/benchmark $(OPTS)
run.gdb:

4
win32/Makefile.sub
View file

@ -1182,6 +1182,10 @@ test-bundled-gems-run:
exit /b %STATUS% \
)
update-benchmark-driver:
$(GIT) clone https://github.com/benchmark-driver/benchmark-driver $(srcdir)/benchmark/benchmark-driver || \
$(GIT) -C $(srcdir)/benchmark/benchmark-driver pull origin master
$(ruby_pc): $(RBCONFIG)
@$(BOOTSTRAPRUBY) $(srcdir)/tool/expand-config.rb \
-output=$@ -mode=$(INSTALL_DATA_MODE) -config=rbconfig.rb \