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# Copyright 2018-2019 Florian Fischer <florian.fl.fischer@fau.de>
#
# This file is part of allocbench.
#
# allocbench is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# allocbench is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with allocbench. If not, see <http://www.gnu.org/licenses/>.
"""Definition of the RAxML-ng benchmark"""
import os
import re
import subprocess
import sys
from urllib.request import urlretrieve
from src.artifact import GitArtifact
from src.benchmark import Benchmark
from src.util import print_info
RUNTIME_RE = re.compile("Elapsed time: (?P<runtime>(\\d*.\\d*)) seconds")
class BenchmarkRaxmlng(Benchmark):
"""RAxML-ng benchmark
"""
def __init__(self):
name = "raxmlng"
super().__init__(name)
self.cmd = (f"raxml-ng --msa {self.build_dir}/data/prim.phy --model GTR+G"
" --redo --threads 2 --seed 2")
def prepare(self):
super().prepare()
if os.path.exists(self.build_dir):
return
raxmlng_sources = GitArtifact("raxml-ng", "https://github.com/amkozlov/raxml-ng")
raxmlng_version = "0.9.0"
raxmlng_dir = os.path.join(self.build_dir, "raxml-ng-git")
raxmlng_builddir = os.path.join(raxmlng_dir, "build")
self.results["facts"]["versions"]["raxml-ng"] = raxmlng_version
raxmlng_sources.provide(raxmlng_version, raxmlng_dir)
# Create builddir
os.makedirs(raxmlng_builddir, exist_ok=True)
# building raxml-ng
proc = subprocess.run(["cmake", ".."],
cwd=raxmlng_builddir,
# stdout=subprocess.PIPE, stderr=subprocess.PIPE,
universal_newlines=True)
proc = subprocess.run(["make"],
cwd=raxmlng_builddir,
# stdout=subprocess.PIPE, stderr=subprocess.PIPE,
universal_newlines=True)
# create symlinks
for exe in ["raxml-ng"]:
src = os.path.join(raxmlng_dir, "bin", exe)
dest = os.path.join(self.build_dir,exe)
os.link(src, dest)
raxmlng_data = GitArtifact("raxml-ng-data", "https://github.com/amkozlov/ng-tutorial")
raxmlng_data_dir = os.path.join(self.build_dir, "data")
raxmlng_data.provide("f8f0b6a057a11397b4dad308440746e3436db8b4", raxmlng_data_dir)
def cleanup(self):
for direntry in os.listdir():
if direntry.startswith("prim.raxml"):
os.remove(direntry)
@staticmethod
def process_output(result, stdout, stderr, allocator, perm):
result["runtime"] = RUNTIME_RE.search(stdout).group("runtime")
def summary(self):
self.barplot_single_arg("{runtime}",
ylabel='"runtime in s"',
title='"raxml-ng tree inference benchmark"',
filepostfix="runtime")
self.export_stats_to_dataref("runtime")
self.barplot_single_arg("{VmHWM}",
ylabel='"VmHWM in KB"',
title='"raxml-ng memusage"',
filepostfix="memusage")
self.export_stats_to_dataref("VmHWM")
raxmlng = BenchmarkRaxmlng()
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