Benchpress/minebench

benchpress/benchmarks.yml

@@ -26,3 +26,25 @@ silo:
     - latency:
         - avg_latency
 
+minebench_kmeans:
+  parser: minebench_kmeans
+  path: ./benchmarks/minebench/time_wrap.sh
+  metrics:
+    - execution_time:
+      - real
+      - user
+      - sys
+
+minebench_plsa:
+  parser: minebench_plsa
+  path: ./benchmarks/minebench/plsa
+  metrics:
+    - execution_time:
+      - total_time
+
+minebench_rsearch:
+  parser: minebench_rsearch
+  path: ./benchmarks/minebench/rsearch/bin/rsearch
+  metrics:
+    - execution_time:
+      - total_time

benchpress/benchpress/lib/job.py

@@ -91,7 +91,12 @@ def run(self):
 
         try:
             logger.info('Starting "{}"'.format(self.name))
-            cmd = [self.binary] + self.args
+            safe_args = []
+            for arg in self.args:
+                for sub_arg in arg.split(' '):
+                    safe_args.append(sub_arg)
+
+            cmd = [self.binary] + safe_args
             process = subprocess.Popen(cmd,
                                        stdout=subprocess.PIPE,
                                        stderr=subprocess.PIPE)

benchpress/benchpress/plugins/parsers/__init__.py

@@ -9,6 +9,9 @@
 from .fio import FioParser
 from .generic import JSONParser
 from .ltp import LtpParser
+from .minebench import KMeansParser
+from .minebench import PLSAParser
+from .minebench import RSearchParser
 from .returncode import ReturncodeParser
 from .schbench import SchbenchParser
 from .silo import SiloParser
@@ -18,6 +21,9 @@ def register_parsers(factory):
     factory.register('fio', FioParser)
     factory.register('json', JSONParser)
     factory.register('ltp', LtpParser)
+    factory.register('minebench_kmeans', KMeansParser)
+    factory.register('minebench_plsa', PLSAParser)
+    factory.register('minebench_rsearch', RSearchParser)
     factory.register('returncode', ReturncodeParser)
     factory.register('schbench', SchbenchParser)
     factory.register('silo', SiloParser)

benchpress/benchpress/plugins/parsers/minebench.py

@@ -0,0 +1,73 @@
+# Copyright (c) 2018-present, Facebook, Inc.
+# All rights reserved.
+#
+# This source code is licensed under the BSD-style license found in the
+# LICENSE file in the root directory of this source tree. An additional grant
+# of patent rights can be found in the PATENTS file in the same directory.
+
+import re
+
+from benchpress.lib.parser import Parser
+
+
+def _minebench_regex_parser(regex, output):
+    m = re.search(regex, output)
+    return m.groupdict() if m else {}
+
+
+def _field_map(d, keys, f):
+    return {k: f(d[k]) for k in keys if k in d}
+
+
+class KMeansParser(Parser):
+    """Example output:
+    real 2.00
+    user 1.50
+    sys 0.02
+    """
+
+    TIME_REGEX = (
+        r'^real\s(?P<real>\d+\.\d+)'
+        r'user\s(?P<user>\d+\.\d+)'
+        r'sys\s(?P<sys>\d+\.\d+)'
+    )
+
+    def parse(self, stdout, stderr, returncode):
+        output = ''.join(stderr)
+        times = _minebench_regex_parser(KMeansParser.TIME_REGEX, output)
+        times = _field_map(times, ['real', 'user', 'sys'], float)
+        return {'execution_time': times}
+
+
+class PLSAParser(Parser):
+    """Example output:
+    Forward time: 26.47s
+    BackwardFindPathsForHugeBlock Time: 7.60
+    Second phase in backward period Time: 6.19
+
+    Success!
+    Total time: 40.26s
+    """
+
+    PLSA_REGEX = r'Total\stime:\s(?P<total_time>\d+\.\d+)s'
+
+    def parse(self, stdout, stderr, returncode):
+        output = ''.join(stdout)
+        times = _minebench_regex_parser(PLSAParser.PLSA_REGEX, output)
+        times = _field_map(times, ['total_time'], float)
+        return {'execution_time': times}
+
+
+class RSearchParser(Parser):
+    """Example output:
+    we cost 199.2 seconds totally, 22.0 for making histogram
+    Fin
+    """
+
+    RSEARCH_REGEX = r'we\scost\s(?P<total_time>\d+\.\d+)\sseconds'
+
+    def parse(self, stdout, stderr, returncode):
+        output = ''.join(stdout)
+        times = _minebench_regex_parser(RSearchParser.RSEARCH_REGEX, output)
+        times = _field_map(times, ['total_time'], float)
+        return {'execution_time': times}

benchpress/install_minebench.sh

@@ -0,0 +1,68 @@
+#!/bin/bash
+set -e
+set -x
+
+NU_MINEBENCH_VERSION='NU-MineBench-3.0.1'
+NU_MINEBENCH_TAR_FILE="${NU_MINEBENCH_VERSION}.tar.gz"
+NU_MINEBENCH_DOWNLOAD_URL="http://cucis.ece.northwestern.edu/projects/DMS"
+
+KMEANS_DATASET_TAR_FILE="kmeans.tar.gz"
+PLSA_DATASET_TAR_FILE="PLSA.tar.gz"
+RSEARCH_DATASET_TAR_FILE="rsearch.tar.gz"
+NU_MINEBENCH_DATASETS="${KMEANS_DATASET_TAR_FILE} ${PLSA_DATASET_TAR_FILE} ${RSEARCH_DATASET_TAR_FILE}"
+
+BENCHMARKS_DIR="$(pwd)/benchmarks"
+mkdir -p "${BENCHMARKS_DIR}"
+mkdir -p "${BENCHMARKS_DIR}/minebench"
+mkdir -p "${BENCHMARKS_DIR}/minebench/datasets"
+
+
+
+echo 'Downloading NU-MineBench and its datasets'
+cd "${BENCHMARKS_DIR}/minebench/datasets/"
+for dataset in $NU_MINEBENCH_DATASETS; do
+  wget "${NU_MINEBENCH_DOWNLOAD_URL}/DATASETS/$dataset"
+  tar -zxvf $dataset
+done
+cd "${BENCHMARKS_DIR}/.."
+
+cp templates/time_wrap.sh "${BENCHMARKS_DIR}/minebench/"
+chmod u+x "${BENCHMARKS_DIR}/minebench/time_wrap.sh"
+
+rm -rf build
+mkdir -p build
+cd build
+
+wget "${NU_MINEBENCH_DOWNLOAD_URL}/${NU_MINEBENCH_TAR_FILE}"
+tar -xzvf "${NU_MINEBENCH_TAR_FILE}"
+cd "$NU_MINEBENCH_VERSION"
+
+
+
+echo 'Compiling and Installing KMeans'
+cd 'KMeans/'
+make OPTFLAGS="-O3" example
+cp 'example' "${BENCHMARKS_DIR}/minebench/kmeans"
+cd ../
+echo 'Done installing KMeans'
+
+echo 'Compiling and Installing PLSA'
+cd 'PLSA/'
+make COMPILEOPTION='-g -Wno-write-strings -fopenmp -O3' -f Makefile.omp
+cp 'parasw.mt' "${BENCHMARKS_DIR}/minebench/plsa"
+cd ../
+echo 'Done installing PLSA'
+
+echo 'Compiling and Installing RSearch'
+cd 'RSEARCH/'
+./configure --prefix="${BENCHMARKS_DIR}/minebench/rsearch"
+make CFLAGS="-O3 -fopenmp"
+make install
+cd ../
+echo 'Done installing RSearch'
+
+cd ../../
+
+rm -rf build/
+
+echo "NU-MineBench installed into ${BENCHMARKS_DIR}/minebench"

benchpress/jobs/jobs.yml

@@ -1,5 +1,5 @@
 - benchmark: schbench
-  name: schbench default 
+  name: schbench default
   description: defaults for schbench
   args:
     message-threads: 2
@@ -72,3 +72,40 @@
     scale-factor: 1
     runtime: 1
 
+- benchmark: minebench_kmeans
+  name: minebench_kmeans default
+  description: defaults for minebench_kmeans
+  args:
+    - 'benchmarks/minebench/kmeans'
+    - '-b'  # binary input
+    - '-o'  # output time
+    - '-p 32'  # threads to use
+    - '-m 50'  # max number of clusters
+    - '-n 4'   # min number of clusters
+    - '-f'     # fuzzy kmeans
+    - '-i benchmarks/minebench/datasets/kmeans/edge'  # dataset to cluster
+
+- benchmark: minebench_plsa
+  name: minebench_plsa default
+  description: defaults for minebench_plsa
+  args:
+    - 'benchmarks/minebench/datasets/PLSA/30k_1.txt'
+    - 'benchmarks/minebench/datasets/PLSA/30k_2.txt'
+    - 'benchmarks/minebench/datasets/PLSA/pam120.bla'
+    - '600'
+    - '400'
+    - '3'
+    - '3'
+    - '1'
+    - '32'
+
+- benchmark: minebench_rsearch
+  name: minebench_rsearch default
+  description: defaults for minebench_rsearch
+  args:
+    - '-n 100000'
+    - '-c'
+    - '-E 100'
+    - '-m benchmarks/minebench/datasets/rsearch/matrices/RIBOSUM85-60.mat'
+    - 'benchmarks/minebench/datasets/rsearch/Queries/mir-40.stk'
+    - 'benchmarks/minebench/datasets/rsearch/Databasefile/100Kdb.fa'

benchpress/templates/time_wrap.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+set -e
+
+/usr/bin/time -p "$@"

benchpress/tests/data/plsa_output.txt

@@ -0,0 +1,14 @@
+Parellel Smith Waterman Algorithm implementation for OpenMP
+Threads Number=2
+The file 'benchmarks/minebench/datasets/PLSA/pam120.bla' was opened
+The file 'benchmarks/minebench/datasets/PLSA/30k_1.txt' was opened
+The file 'benchmarks/minebench/datasets/PLSA/30k_2.txt' was opened
+Seqence(1) Length=30144, Sequence Length(2)=29696
+ Adjust block height=17, block width=17
+score=101948  x=29567 y=29696 globalstart.i=3 globalstart.j=130
+Forward time: 29.22s
+BackwardFindPathsForHugeBlock Time: 8.35
+Second phase in backward period Time: 6.12
+
+Success!
+Total time: 43.69s

benchpress/tests/data/rsearch_output.txt

@@ -0,0 +1,121 @@
+Random seed: 1524699649
+D scale of 2.0
+Matrix: RIBOSUM85-60
+Alpha: 10.00
+Beta: 5.00
+Alpha': 0.00
+Beta': 15.00
+Query file: benchmarks/minebench/datasets/rsearch/Queries/mir-40.stk
+Database file: benchmarks/minebench/datasets/rsearch/Databasefile/100Kdb.fa
+
+
+beginsc = 0.000000
+endsc = -15.000000
+Making histogram cost 24.8 seconds
+Statistics calculated with simulation of 100 samples of length 388
+No partition points
+GC = 0	lambda = 0.0000	mu = inf
+GC = 1	lambda = 0.0000	mu = inf
+GC = 2	lambda = 0.0000	mu = inf
+GC = 3	lambda = 0.0000	mu = inf
+GC = 4	lambda = 0.0000	mu = inf
+GC = 5	lambda = 0.0000	mu = inf
+GC = 6	lambda = 0.0000	mu = inf
+GC = 7	lambda = 0.0000	mu = inf
+GC = 8	lambda = 0.0000	mu = inf
+GC = 9	lambda = 0.0000	mu = inf
+GC = 10	lambda = 0.0000	mu = inf
+GC = 11	lambda = 0.0000	mu = inf
+GC = 12	lambda = 0.0000	mu = inf
+GC = 13	lambda = 0.0000	mu = inf
+GC = 14	lambda = 0.0000	mu = inf
+GC = 15	lambda = 0.0000	mu = inf
+GC = 16	lambda = 0.0000	mu = inf
+GC = 17	lambda = 0.0000	mu = inf
+GC = 18	lambda = 0.0000	mu = inf
+GC = 19	lambda = 0.0000	mu = inf
+GC = 20	lambda = 0.0000	mu = inf
+GC = 21	lambda = 0.0000	mu = inf
+GC = 22	lambda = 0.0000	mu = inf
+GC = 23	lambda = 0.0000	mu = inf
+GC = 24	lambda = 0.0000	mu = inf
+GC = 25	lambda = 0.0000	mu = inf
+GC = 26	lambda = 0.0000	mu = inf
+GC = 27	lambda = 0.0000	mu = inf
+GC = 28	lambda = 0.0000	mu = inf
+GC = 29	lambda = 0.0000	mu = inf
+GC = 30	lambda = 0.0000	mu = inf
+GC = 31	lambda = 0.0000	mu = inf
+GC = 32	lambda = 0.0000	mu = inf
+GC = 33	lambda = 0.0000	mu = inf
+GC = 34	lambda = 0.0000	mu = inf
+GC = 35	lambda = 0.0000	mu = inf
+GC = 36	lambda = 0.0000	mu = inf
+GC = 37	lambda = 0.0000	mu = inf
+GC = 38	lambda = 0.0000	mu = inf
+GC = 39	lambda = 0.0000	mu = inf
+GC = 40	lambda = 0.0000	mu = inf
+GC = 41	lambda = 0.0000	mu = inf
+GC = 42	lambda = 0.0000	mu = inf
+GC = 43	lambda = 0.0000	mu = inf
+GC = 44	lambda = 0.0000	mu = inf
+GC = 45	lambda = 0.0000	mu = inf
+GC = 46	lambda = 0.0000	mu = inf
+GC = 47	lambda = 0.0000	mu = inf
+GC = 48	lambda = 0.0000	mu = inf
+GC = 49	lambda = 0.0000	mu = inf
+GC = 50	lambda = 0.0000	mu = inf
+GC = 51	lambda = 0.0000	mu = inf
+GC = 52	lambda = 0.0000	mu = inf
+GC = 53	lambda = 0.0000	mu = inf
+GC = 54	lambda = 0.0000	mu = inf
+GC = 55	lambda = 0.0000	mu = inf
+GC = 56	lambda = 0.0000	mu = inf
+GC = 57	lambda = 0.0000	mu = inf
+GC = 58	lambda = 0.0000	mu = inf
+GC = 59	lambda = 0.0000	mu = inf
+GC = 60	lambda = 0.0000	mu = inf
+GC = 61	lambda = 0.0000	mu = inf
+GC = 62	lambda = 0.0000	mu = inf
+GC = 63	lambda = 0.0000	mu = inf
+GC = 64	lambda = 0.0000	mu = inf
+GC = 65	lambda = 0.0000	mu = inf
+GC = 66	lambda = 0.0000	mu = inf
+GC = 67	lambda = 0.0000	mu = inf
+GC = 68	lambda = 0.0000	mu = inf
+GC = 69	lambda = 0.0000	mu = inf
+GC = 70	lambda = 0.0000	mu = inf
+GC = 71	lambda = 0.0000	mu = inf
+GC = 72	lambda = 0.0000	mu = inf
+GC = 73	lambda = 0.0000	mu = inf
+GC = 74	lambda = 0.0000	mu = inf
+GC = 75	lambda = 0.0000	mu = inf
+GC = 76	lambda = 0.0000	mu = inf
+GC = 77	lambda = 0.0000	mu = inf
+GC = 78	lambda = 0.0000	mu = inf
+GC = 79	lambda = 0.0000	mu = inf
+GC = 80	lambda = 0.0000	mu = inf
+GC = 81	lambda = 0.0000	mu = inf
+GC = 82	lambda = 0.0000	mu = inf
+GC = 83	lambda = 0.0000	mu = inf
+GC = 84	lambda = 0.0000	mu = inf
+GC = 85	lambda = 0.0000	mu = inf
+GC = 86	lambda = 0.0000	mu = inf
+GC = 87	lambda = 0.0000	mu = inf
+GC = 88	lambda = 0.0000	mu = inf
+GC = 89	lambda = 0.0000	mu = inf
+GC = 90	lambda = 0.0000	mu = inf
+GC = 91	lambda = 0.0000	mu = inf
+GC = 92	lambda = 0.0000	mu = inf
+GC = 93	lambda = 0.0000	mu = inf
+GC = 94	lambda = 0.0000	mu = inf
+GC = 95	lambda = 0.0000	mu = inf
+GC = 96	lambda = 0.0000	mu = inf
+GC = 97	lambda = 0.0000	mu = inf
+GC = 98	lambda = 0.0000	mu = inf
+GC = 99	lambda = 0.0000	mu = inf
+GC = 100	lambda = 0.0000	mu = inf
+N = 235320
+Using E cutoff of 10.00
+we cost 225.7 seconds totally, 24.8 for making histogram
+Fin