[GR-15801] Size micro+meso benchmarks to run at least ~1s per iter + enable remaining meso benchmarks

PullRequest: graalpython/874

Author: timfel

graalpython/com.oracle.graal.python.benchmarks/python/meso/knucleotide-input.txt

@@ -45,13 +45,14 @@
 # modified by Justin Peel
 
 from collections import defaultdict
+import os
 
 
 def gen_freq(seq, frame, frequencies):
     if frame != 1:
         ns = len(seq) + 1 - frame
         frequencies.clear()
-        for ii in xrange(ns):
+        for ii in range(ns):
             frequencies[seq[ii:ii + frame]] += 1
         return ns, frequencies
     for nucleo in seq:
@@ -62,30 +63,30 @@ def gen_freq(seq, frame, frequencies):
 def sort_seq(seq, length, frequencies):
     n, frequencies = gen_freq(seq, length, frequencies)
 
-    l = sorted(frequencies.items(), reverse=True, key=lambda (seq,freq): (freq,seq))
+    l = sorted(list(frequencies.items()), reverse=True, key=lambda item: item)
 
-    print '\n'.join("%s %.3f" % (st, 100.0*fr/n) for st,fr in l)
-    print
+    print('\n'.join("%s %.3f" % (st, 100.0*fr/n) for st,fr in l))
 
 
 def find_seq(seq, s, frequencies):
     n,t = gen_freq(seq, len(s), frequencies)
-    print "%d\t%s" % (t.get(s, 0), s)
+    print("%d\t%s" % (t.get(s, 0), s))
 
 
-def main(stdin):
+def main():
     frequencies = defaultdict(int)
-    for line in stdin:
-        if line[0] == ">":
-            if line[1:3] == "TH":
+    with open(os.path.join(os.path.dirname(__file__), "knucleotide-input.txt")) as f:
+        for line in f:
+            if line[0] == ">":
+                if line[1:3] == "TH":
+                    break
+
+        seq = []
+        seq_append = seq.append
+        for line in f:
+            if line[0] in ">;":
                 break
-
-    seq = []
-    seq_append = seq.append
-    for line in stdin:
-        if line[0] in ">;":
-            break
-        seq_append(line)
+            seq_append(line)
     sequence = "".join(seq).replace('\n','').upper()
 
     for nl in 1,2:
@@ -96,5 +97,4 @@ def main(stdin):
 
 
 def __benchmark__(*args):
-    # main()  # provide proper input 
-    pass 
+    main()

graalpython/com.oracle.graal.python.benchmarks/python/meso/knucleotide.py

@@ -47,7 +47,7 @@
 def main(seq):
     ilen = len(seq)
 
-    seq = sub('>.*\n|\n', '', seq) 
+    seq = sub('>.*\n|\n', '', seq)
     clen = len(seq)
 
     variants = (
@@ -61,13 +61,13 @@ def main(seq):
           'agggta[cgt]a|t[acg]taccct',
           'agggtaa[cgt]|[acg]ttaccct')
     for f in variants:
-        print f, sum(1 for i in finditer(f, seq))
+        print(f, sum(1 for i in finditer(f, seq)))
 
     subst = {
           'B' : '(c|g|t)', 'D' : '(a|g|t)',   'H' : '(a|c|t)', 'K' : '(g|t)',
           'M' : '(a|c)',   'N' : '(a|c|g|t)', 'R' : '(a|g)',   'S' : '(c|g)',
           'V' : '(a|c|g)', 'W' : '(a|t)',     'Y' : '(c|t)'}
-    for f, r in subst.items():
+    for f, r in list(subst.items()):
         seq = sub(f, r, seq)
 
     print(ilen)
@@ -76,5 +76,7 @@ def main(seq):
 
 
 def __benchmark__(*args):
-  # main(seq) #  TODO provide proper input 
-  pass
+    import os
+    with open(os.path.join(os.path.dirname(__file__), "knucleotide-input.txt")) as f:
+        seq = f.read()
+    main(seq)

graalpython/com.oracle.graal.python.benchmarks/python/meso/pads-bipartite.py renamed to graalpython/com.oracle.graal.python.benchmarks/python/meso/pads-bipartite-sized.py

@@ -48,20 +48,18 @@
 
 
 def main(n, n_threads=503, cycle=itertools.cycle):
-
     def worker(worker_id):
         n = 1
         while True:
-            print(n)
             if n > 0:
                 n = (yield (n - 1))
             else:
                 print(worker_id)
-                raise StopIteration
+                return
 
 
     threadRing = [worker(w) for w in range(1, n_threads + 1)]
-    for t in threadRing: foo = t.next()           # start exec. gen. funcs
+    for t in threadRing: foo = next(t)            # start exec. gen. funcs
     sendFuncRing = [t.send for t in threadRing]   # speed...
     for send in cycle(sendFuncRing):
         try:
@@ -70,5 +68,5 @@ def worker(worker_id):
             break
 
 
-def __bnenchmark__(num=100):
+def __benchmark__(num=100):
     main(num)

graalpython/com.oracle.graal.python.benchmarks/python/meso/regexdna.py

@@ -48,4 +48,4 @@ def measure(num):
 
 
 def __benchmark__(num=50):
-    measure(50)
+    measure(num)

graalpython/com.oracle.graal.python.benchmarks/python/meso/sieve.py renamed to graalpython/com.oracle.graal.python.benchmarks/python/meso/sieve-sized.py

@@ -84,7 +84,7 @@ def no_object_do_stuff():
 
 
 def measure(num):
-    for i in range(num):  # 50000
+    for i in range(num):
         result = do_stuff()
 
     print(result)

graalpython/com.oracle.graal.python.benchmarks/python/meso/threadring.py

@@ -31,12 +31,12 @@ def call_len(num, ll):
     return length
 
 
-def measure():
+def measure(num):
     ll = tuple(range(1000))
-    length = call_len(1000000000, ll)  # 1000000
+    length = call_len(num, ll)
 
     print("Final length ", length)
 
 
-def __benchmark__(*args):
-    measure()
+def __benchmark__(num):
+    measure(num)