add raxml-ng benchmark

2 files changed, 123 insertions, 3 deletions

diff --git a/src/benchmark.py b/src/benchmark.py
index df31068..d43c549 100644
--- a/src/benchmark.py
+++ b/src/benchmark.py
@@ -363,7 +363,7 @@ class Benchmark:
                     print_info0(i, "of", n, "\r", end='')
 
                     # Available substitutions in cmd
-                    substitutions = {"run": run}
+                    substitutions = {"run": run, "alloc": alloc_name}
                     substitutions.update(self.__dict__)
                     substitutions.update(alloc)
                     if perm:
@@ -404,13 +404,13 @@ class Benchmark:
 
                     result = {}
 
-                    if res.returncode != 0 or "ERROR: ld.so" in res.stderr:
+                    if res.returncode != 0 or "ERROR: ld.so" in res.stderr or "Segmentation fault" in res.stderr:
                         print()
                         print_debug("Stdout:\n" + res.stdout)
                         print_debug("Stderr:\n" + res.stderr)
                         if res.returncode != 0:
                             print_error("{} failed with exit code {} for {}".format(argv, res.returncode, alloc_name))
-                        else:
+                        elif "ERROR: ld.so" in res.stderr:
                             print_error("Preloading of {} failed for {}".format(alloc["LD_PRELOAD"], alloc_name))
 
                     # parse and store results
diff --git a/src/benchmarks/raxmlng.py b/src/benchmarks/raxmlng.py
new file mode 100644
index 0000000..119bab7
--- /dev/null
+++ b/src/benchmarks/raxmlng.py
@@ -0,0 +1,120 @@
+# 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.benchmark import Benchmark
+from src.util import print_info, download_reporthook
+
+
+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}/ng-tutorial/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
+
+        version = "0.9"
+        
+        url = "https://github.com/amkozlov/raxml-ng"
+        data_url = "https://github.com/amkozlov/ng-tutorial"
+        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)
+            
+            # 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)
+
+    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()