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#!/usr/bin/python3
# encoding: utf-8
from __future__ import (absolute_import, division,
print_function, unicode_literals)
import os, sys, re
import logging
import argparse
import collections
import datetime
import time
logging.basicConfig(stream=sys.stderr, level=logging.INFO)
logger = logging.getLogger(__name__)
PROGS_OF_INTEREST = set(['Trinity', 'Butterfly', 'samtools', 'inchworm', 'QuantifyGraph',
'BubbleUpClustering', 'jellyfish', 'GraphFromFasta', 'bowtie2'])
"""
Formatting from collectl -sZ
# PROCESS SUMMARY (counters are /sec)
# PID User PR PPID THRD S VSZ RSS CP SysT UsrT Pct AccuTime RKB WKB MajF MinF Command
1 root 20 0 0 S 32M 552K 2 0.00 0.00 0 00:04.20 0 0 0 0 /sbin/init
2 root 20 0 0 S 0 0 3 0.00 0.00 0 00:02.56 0 0 0 0 kthreadd
3 root RT 2 0 S 0 0 0 0.00 0.00 0 41:48.40 0 0 0 0 migration/0
4 root 20 2 0 S 0 0 0 0.00 0.00 0 00:36.52 0 0 0 0 ksoftirqd/0
"""
def main():
parser = argparse.ArgumentParser(description="generate time matrix from collectl dat file",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("--dat", dest="dat_file", type=str, default="", required=True,
help="collectl dat file")
parser.add_argument("--out_prefix", dest="out_prefix", type=str, default="collectl",
help="prefix for output files")
parser.add_argument("--debug", required=False, action="store_true", default=False, help="debug mode")
args = parser.parse_args()
if args.debug:
logger.setLevel(logging.DEBUG)
cpu_usage_matrix = collections.defaultdict(dict)
memory_usage_matrix = collections.defaultdict(dict)
IO_usage_matrix = collections.defaultdict(dict)
times = list()
prognames = list()
parse_collectl_dat(args.dat_file,
cpu_usage_matrix, memory_usage_matrix, IO_usage_matrix,
times, prognames)
output_prefix = args.out_prefix
cpu_usage_output_filename = output_prefix + ".cpu_usage.matrix"
mem_usage_output_filename = output_prefix + ".mem_usage.matrix"
IO_usage_output_filename = output_prefix + ".IO_usage.matrix"
cpu_usage_ofh = open(cpu_usage_output_filename, 'w')
mem_usage_ofh = open(mem_usage_output_filename, 'w')
IO_usage_ofh = open(IO_usage_output_filename, 'w')
# print headers
header = "time\t" + "\t".join(prognames)
cpu_usage_ofh.write(header + "\n")
mem_usage_ofh.write(header + "\n")
IO_usage_ofh.write(header + "\n")
for timeval in times:
memvals = list()
cpuvals = list()
IOvals = list()
timeval_in_hr = str(timeval / 60 / 60)
timeval = str(timeval)
memvals.append(timeval_in_hr)
cpuvals.append(timeval_in_hr)
IOvals.append(timeval_in_hr)
for progname in prognames:
memory_hash = memory_usage_matrix[timeval]
memory_val = "0"
if progname in memory_hash:
memory_val = str(memory_hash[progname])
memvals.append(memory_val)
cpu_val = "0"
cpu_hash = cpu_usage_matrix[timeval]
if progname in cpu_hash:
cpu_val = str(cpu_hash[progname])
cpuvals.append(cpu_val)
IO_val = "0"
IO_hash = IO_usage_matrix[timeval]
if progname in IO_hash:
IO_val = str(IO_hash[progname])
IOvals.append(IO_val)
mem_usage_ofh.write("\t".join(memvals) + "\n")
cpu_usage_ofh.write("\t".join(cpuvals) + "\n")
IO_usage_ofh.write("\t".join(IOvals) + "\n")
mem_usage_ofh.close()
cpu_usage_ofh.close()
IO_usage_ofh.close()
print("Done. See output files: " +
str([mem_usage_output_filename, cpu_usage_output_filename, IO_usage_output_filename]))
def parse_collectl_dat(collectl_dat_file, cpu_usage_matrix, memory_usage_matrix, IO_usage_matrix, times, prognames):
prev_time = 0
prognames_dict = dict()
"""
line formatting:
0 #Date
1 Time
2 PID
3 User
4 PR
5 PPID
6 THRD
7 S
8 VSZ
9 RSS
10 CP
11 SysT
12 UsrT
13 Pct
14 AccuTime
15 RKB
16 WKB
17 MajF
18 MinF
19 Command
"""
init_time = -1
with open(collectl_dat_file) as f:
for line in f:
vals = re.split("\s+", line)
if len(vals) < 20:
continue
day = vals[0]
timeval_str = vals[1]
timestruct = datetime.datetime.strptime("{} {}".format(day, timeval_str), "%Y%m%d %H:%M:%S")
timeval_numeric = time.mktime(timestruct.timetuple())
if init_time < 0:
init_time = timeval_numeric
timeval_numeric = 1
else:
timeval_numeric -= init_time
timeval_key_str = str(timeval_numeric)
if timeval_numeric > prev_time:
times.append(timeval_numeric)
prev_time = timeval_numeric
progname = os.path.basename(vals[19])
if progname == 'perl':
progname = os.path.basename(vals[20])
elif progname == 'java':
if re.search("Butterfly.jar", line):
progname = "Butterfly"
if progname not in PROGS_OF_INTEREST:
continue
cpu_usage_timehash = cpu_usage_matrix[timeval_key_str]
if progname not in cpu_usage_timehash:
cpu_usage_timehash[progname] = 1
else:
cpu_usage_timehash[progname] += 1
memory = compute_GB(vals[9])
progname_memory_hash = memory_usage_matrix[timeval_key_str]
if progname not in progname_memory_hash:
progname_memory_hash[progname] = memory
else:
progname_memory_hash[progname] += memory
#print("progname: {}, memoryG: {}".format(progname, memory))
RMB = compute_GB(vals[15]) * (1024**2)
WMB = compute_GB(vals[16]) * (1024**2)
sumMB = RMB + WMB
IO_usage_hash = IO_usage_matrix[timeval_key_str]
if progname not in IO_usage_hash:
IO_usage_hash[progname] = sumMB
else:
IO_usage_hash[progname] += sumMB
prognames_dict[progname] = 1
progname_list = prognames_dict.keys()
prognames += progname_list
def compute_GB(memory_val):
r = re.search("^(\d+)([MKG])$", memory_val)
if r:
numG = int(r.group(1))
metric = r.group(2)
if metric == 'M':
numG /= 1024
elif metric == 'K':
numG /= 1024**2
else:
memory_val = int(memory_val)
numG = memory_val / (1024**3)
return numG
####################
if __name__ == "__main__":
main()
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