diff options
Diffstat (limited to 'src/benchmarks/raxmlng.py')
| -rw-r--r-- | src/benchmarks/raxmlng.py | 76 |
1 files changed, 32 insertions, 44 deletions
diff --git a/src/benchmarks/raxmlng.py b/src/benchmarks/raxmlng.py index 119bab7..811721a 100644 --- a/src/benchmarks/raxmlng.py +++ b/src/benchmarks/raxmlng.py @@ -23,8 +23,9 @@ 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, download_reporthook +from src.util import print_info RUNTIME_RE = re.compile("Elapsed time: (?P<runtime>(\\d*.\\d*)) seconds") @@ -39,64 +40,51 @@ class BenchmarkRaxmlng(Benchmark): super().__init__(name) - self.cmd = (f"raxml-ng --msa {self.build_dir}/ng-tutorial/prim.phy --model GTR+G" + 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() - # git clone --recursive - # cd raxml-ng - # mkdir build && cd build - # cmake .. - # make + if os.path.exists(self.build_dir): + return - version = "0.9" - - url = "https://github.com/amkozlov/raxml-ng" - data_url = "https://github.com/amkozlov/ng-tutorial" + 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"] = version - - if not os.path.isdir(raxmlng_dir): - proc = subprocess.run(["git", "clone", "--recursive", url, raxmlng_dir], - # stdout=subprocess.PIPE, stderr=subprocess.PIPE, - universal_newlines=True) + 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) - - # clone test data - proc = subprocess.run(["git", "clone", data_url], - cwd=self.build_dir, - # stdout=subprocess.PIPE, stderr=subprocess.PIPE, - universal_newlines=True) + # 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") |