Hi, Sergey!
thanks for the patch! LGTM
Sergey
This patch adjusts the aforementioned test to use the benchmark
framework introduced before. The default arguments are adjusted
according to the <PARAM_x86.txt> file. The arguments to the script still
can be provided in the command line run.
The benchmark input is given by redirecting the corresponding
<FASTA_5000000> file generated by the `libs/fasta.lua 5e6`. The output
from the benchmark is redirected to /dev/null. Checks are skipped since
the output is very huge, and it is overkill to store it in the
repository.
---
perf/LuaJIT-benches/revcomp.lua | 84 +++++++++++++++++++++++----------
1 file changed, 59 insertions(+), 25 deletions(-)
diff --git a/perf/LuaJIT-benches/revcomp.lua b/perf/LuaJIT-benches/revcomp.lua
index 34fe347b..6e8a7049 100644
--- a/perf/LuaJIT-benches/revcomp.lua
+++ b/perf/LuaJIT-benches/revcomp.lua
@@ -1,3 +1,14 @@
+-- The benchmark to check the performance of hash table lookups by
+-- constant keys, string manipulations, and read/write
+-- operations.
+-- This benchmark reads the line-by-line a redirected FASTA format
+-- file from stdin, which is generated by the <fasta.lua>
+-- benchmark, and writes the id, description, and the
+-- reverse-complement sequence in FASTA format to stdout.
+-- For the details see:
+-- https://benchmarksgame-team.pages.debian.net/benchmarksgame/description/revcomp.html
+
+local bench = require("bench").new(arg)
local sub = string.sub
iubc = setmetatable({
@@ -9,29 +20,52 @@ iubc = setmetatable({
}, { __index = function(t, s)
local r = t[sub(s, 2)]..t[sub(s, 1, 1)]; t[s] = r; return r end })
-local wcode = [=[
-return function(t, n)
- if n == 1 then return end
- local iubc, sub, write = iubc, string.sub, io.write
- local s = table.concat(t, "", 1, n-1)
- for i=#s-59,1,-60 do
- write(]=]
-for i=59,3,-4 do wcode = wcode.."iubc[sub(s, i+"..(i-3)..", i+"..i..")], " end
-wcode = wcode..[=["\n")
- end
- local r = #s % 60
- if r ~= 0 then
- for i=r,1,-4 do write(iubc[sub(s, i-3 < 1 and 1 or i-3, i)]) end
- write("\n")
- end
-end
-]=]
-local writerev = loadstring(wcode)()
+local stdout = io.output()
+
+bench:add({
+ name = "revcomp",
+ -- The compare with the result output file is inconvenient.
+ skip_check = true,
+ setup = function()
+ io.output("/dev/null")
+ end,
+ payload = function()
+ local wcode = [=[
+ return function(t, n)
+ if n == 1 then return end
+ local iubc, sub, write = iubc, string.sub, io.write
+ local s = table.concat(t, "", 1, n - 1)
+ for i = #s - 59, 1, -60 do
+ write(]=]
+ for i = 59, 3, -4 do
+ wcode = wcode.."iubc[sub(s, i + "..(i - 3)..", i + "..i..")], "
+ end
+ wcode = wcode..[=["\n")
+ end
+ local r = #s % 60
+ if r ~= 0 then
+ for i = r, 1, -4 do write(iubc[sub(s, i - 3 < 1 and 1 or i - 3, i)]) end
+ write("\n")
+ end
+ end
+ ]=]
could you also apply the patch below with formatting?
diff --git a/perf/LuaJIT-benches/revcomp.lua
b/perf/LuaJIT-benches/revcomp.lua
index 6e8a7049..9050110e 100644
--- a/perf/LuaJIT-benches/revcomp.lua
+++ b/perf/LuaJIT-benches/revcomp.lua
@@ -38,9 +38,9 @@ bench:add({
for i = #s - 59, 1, -60 do
write(]=]
for i = 59, 3, -4 do
- wcode = wcode.."iubc[sub(s, i + "..(i - 3)..", i +
"..i..")], "
+ wcode = wcode .. "iubc[sub(s, i + " .. (i - 3) .. ", i + "
.. i .. ")], "
end
- wcode = wcode..[=["\n")
+ wcode = wcode .. [=["\n")
end
local r = #s % 60
if r ~= 0 then
@@ -54,7 +54,10 @@ bench:add({
local t, n = {}, 1
for line in io.lines() do
local c = sub(line, 1, 1)
- if c == ">" then writerev(t, n); io.write(line, "\n"); n
= 1
+ if c == ">" then
+ writerev(t, n);
+ io.write(line, "\n");
+ n = 1
elseif c ~= ";" then t[n] = line; n = n + 1 end
end
writerev(t, n)
+ local writerev = loadstring(wcode)()
+
+ local t, n = {}, 1
+ for line in io.lines() do
+ local c = sub(line, 1, 1)
+ if c == ">" then writerev(t, n); io.write(line, "\n"); n = 1
+ elseif c ~= ";" then t[n] = line; n = n + 1 end
+ end
+ writerev(t, n)
+ -- Repeat operation several times.
+ io.stdin:seek("set", 0)
+ end,
+ teardown = function()
+ io.output(stdout)
+ end,
+ -- Amount of symbols in the input file.
+ items = 5e6,
+})
-local t, n = {}, 1
-for line in io.lines() do
- local c = sub(line, 1, 1)
- if c == ">" then writerev(t, n); io.write(line, "\n"); n = 1
- elseif c ~= ";" then t[n] = line; n = n + 1 end
-end
-writerev(t, n)
+bench:run_and_report()