diff options
Diffstat (limited to 'src/benchmarks/raxmlng.py')
| -rw-r--r-- | src/benchmarks/raxmlng.py | 43 |
1 files changed, 23 insertions, 20 deletions
diff --git a/src/benchmarks/raxmlng.py b/src/benchmarks/raxmlng.py index 811721a..dd405f5 100644 --- a/src/benchmarks/raxmlng.py +++ b/src/benchmarks/raxmlng.py @@ -14,7 +14,6 @@ # # 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 @@ -27,21 +26,20 @@ 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") + + 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() @@ -49,36 +47,41 @@ class BenchmarkRaxmlng(Benchmark): if os.path.exists(self.build_dir): return - raxmlng_sources = GitArtifact("raxml-ng", "https://github.com/amkozlov/raxml-ng") + 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) + 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) + 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 = 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) + raxmlng_data.provide("f8f0b6a057a11397b4dad308440746e3436db8b4", + raxmlng_data_dir) def cleanup(self): for direntry in os.listdir(): |