performance measurements
Each table row shows performance measurements for this Cython program with a particular command-line input value N.
| N | CPU secs | Elapsed secs | Memory KB | Code B | ≈ CPU Load |
|---|---|---|---|---|---|
| 10,000 | 0.07 | 0.07 | ? | 618 | 0% 0% 0% 100% 12% 0% 0% 0% |
Read the ↓ make, command line, and program output logs to see how this program was run.
Read k-nucleotide benchmark to see what this program should do.
notes
k-nucleotide Cython program source code
# The Computer Language Benchmarks Game
# http://benchmarksgame.alioth.debian.org/
#
# submitted by Ian Osgood
# modified by Sokolov Yura
# modified by bearophile
# 2to3
from sys import stdin
def gen_freq(seq, int frame, frequences):
cdef int ns, ii
ns = len(seq) + 1 - frame
frequences.clear()
for ii in range(ns):
nucleo = seq[ii:ii + frame]
if nucleo in frequences:
frequences[nucleo] += 1
else:
frequences[nucleo] = 1
return ns, frequences
def sort_seq(seq, int length, frequences):
cdef int n
cdef float fr
n, frequences = gen_freq(seq, length, frequences)
l = sorted(list(frequences.items()), reverse=True, key=lambda seq_freq: (seq_freq[1], seq_freq[0]))
print('\n'.join("%s %.3f" % (st, 100.0*fr/n) for st, fr in l))
print()
def find_seq(seq, s, frequences):
n, t = gen_freq(seq, len(s), frequences)
print("%d\t%s" % (t.get(s, 0), s))
def main():
cdef int nl
frequences = {}
for line in stdin:
if line[0:3] == ">TH":
break
seq = []
for line in stdin:
if line[0] in ">;":
break
seq.append(line[:-1])
sequence = "".join(seq).upper()
for nl in 1, 2:
sort_seq(sequence, nl, frequences)
for se in "GGT GGTA GGTATT GGTATTTTAATT GGTATTTTAATTTATAGT".split():
find_seq(sequence, se, frequences)
main()
make, command-line, and program output logs
Thu, 23 Dec 2021 10:59:18 GMT MAKE: make[1]: Vstupuje se do adresáře „/home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp“ cp knucleotide.cython `echo knucleotide.cython | sed 's/cython-..//' | sed 's/.cython//'`.pyx cythonize -3 -bi `echo knucleotide.cython | sed 's/cython-..//' | sed 's/.cython//'`.pyx Compiling /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/knucleotide.pyx because it changed. [1/1] Cythonizing /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/knucleotide.pyx running build_ext building 'knucleotide' extension creating /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/tmp4e8gpgbh/home creating /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/tmp4e8gpgbh/home/dundee creating /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/tmp4e8gpgbh/home/dundee/work creating /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/tmp4e8gpgbh/home/dundee/work/pybenchmarks creating /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/tmp4e8gpgbh/home/dundee/work/pybenchmarks/bencher creating /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/tmp4e8gpgbh/home/dundee/work/pybenchmarks/bencher/tmp creating /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/tmp4e8gpgbh/home/dundee/work/pybenchmarks/bencher/tmp/knucleotide creating /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/tmp4e8gpgbh/home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fPIC -I/usr/include/python3.10 -c /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/knucleotide.c -o /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/tmp4e8gpgbh/home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/knucleotide.o gcc -pthread -shared -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/tmp4e8gpgbh/home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/knucleotide.o -L/usr/lib -o /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/knucleotide.cpython-310-x86_64-linux-gnu.so make[1]: Opouští se adresář „/home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp“ 2.34s to complete and log all make actions COMMAND LINE: /usr/bin/python3 -c "import knucleotide" 0 < knucleotide-input10000.txt PROGRAM OUTPUT: A 30.284 T 29.796 C 20.312 G 19.608 AA 9.212 AT 8.950 TT 8.948 TA 8.936 CA 6.166 CT 6.100 AC 6.086 TC 6.042 AG 6.036 GA 5.968 TG 5.868 GT 5.798 CC 4.140 GC 4.044 CG 3.906 GG 3.798 562 GGT 152 GGTA 15 GGTATT 0 GGTATTTTAATT 0 GGTATTTTAATTTATAGT