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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| library(amplicon) | ||
| beta_pcoa_stat() | ||
| beta_pcoa_stat | ||
| setwd("D:/BaiduNetdiskWorkspace/github/EasyMetagenome") | ||
| setwd("D:/BaiduNetdiskWorkspace/github/EasyMicrobiome/script") |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,138 @@ | ||
| #!/usr/bin/env python | ||
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| # https://github.com/drewkett/memusg | ||
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| import sys | ||
| import os | ||
| import signal | ||
| from time import sleep, time | ||
| from subprocess import * | ||
| from argparse import ArgumentParser, REMAINDER | ||
| import math | ||
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| parser = ArgumentParser() | ||
| parser.add_argument('-o', | ||
| '--output-to-file', | ||
| help="Output usage to file", | ||
| default="") | ||
| parser.add_argument('-t', | ||
| '--time', | ||
| help="Output run time of subprocess as well", | ||
| default=False, | ||
| action='store_true') | ||
| parser.add_argument( | ||
| '-p', | ||
| '--poll-interval', | ||
| help="Polling interval in seconds to check for current memory usage", | ||
| type=float, | ||
| default=0.1) | ||
| parser.add_argument( | ||
| '-w', | ||
| '--write-interval', | ||
| help="Interval in seconds to write current peak usage to stdout while process is running (Disable using 0)", | ||
| type=float, | ||
| default=0) | ||
| parser.add_argument( | ||
| '-H', | ||
| '--no-humanize', | ||
| help="No humanization of the value of time (second) and memory (KB) usage", | ||
| default=False, | ||
| action='store_true') | ||
| parser.add_argument('-s', | ||
| '--shell', | ||
| help="execute through shell, useful for multiple cmmands and commands with pipes", | ||
| default=False, | ||
| action='store_true') | ||
| parser.add_argument('args', nargs=REMAINDER) | ||
| args = parser.parse_args() | ||
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| def get_rssize(sid): | ||
| """Get total resident set memory of processes in session id""" | ||
| proc = Popen(['ps', '-o', 'rssize=', '--sid', str(sid)], stdout=PIPE) | ||
| stdout, _ = proc.communicate() | ||
| return sum(int(line.strip()) for line in stdout.split() if line.strip()) | ||
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| def human_time(t): | ||
| if t < 60: | ||
| return "{:.3f}s".format(t) | ||
| elif t < 60 * 60: | ||
| minutes = (t % 3600) // 60 | ||
| seconds = (t % 60) | ||
| return "{:.0f}m:{:02.0f}s".format(minutes, seconds) | ||
| elif t < 24 * 60 * 60: | ||
| hours = (t % (24 * 60 * 60)) // 3600 | ||
| minutes = (t % 3600) // 60 | ||
| seconds = (t % 60) | ||
| return "{:.0f}h:{:02.0f}m:{:02.0f}s".format(hours, minutes, seconds) | ||
| else: | ||
| days = t // (24 * 60 * 60) | ||
| hours = (t % (24 * 60 * 60)) // 3600 | ||
| minutes = (t % 3600) // 60 | ||
| seconds = (t % 60) | ||
| return "{}days {:.0f}h:{:02.0f}m:{:02.0f}s".format(days, hours, minutes, seconds) | ||
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| def human_size(size): | ||
| """Convert integer representing bytes to human readable string""" | ||
| size_name = ("KB", "MB", "GB", "TB", "PB", "EB", "ZB", "YB") | ||
| if size: | ||
| i = int(math.floor(math.log(size, 1024))) | ||
| p = math.pow(1024, i) | ||
| s = round(size / p, 2) | ||
| return '%s %s' % (s, size_name[i]) | ||
| else: | ||
| return '0B' | ||
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| if args.output_to_file: | ||
| stdout = open(args.output_to_file, "w") | ||
| else: | ||
| stdout = sys.stderr | ||
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| if args.time: | ||
| start_time = time() | ||
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| if sys.version_info >= (3, 0): | ||
| p = Popen(tuple(args.args), start_new_session=True, shell=args.shell) | ||
| else: | ||
| p = Popen(tuple(args.args), preexec_fn=os.setsid, shell=args.shell) | ||
|
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| # Catch interrupt signal and send to subprocesses | ||
| signal.signal(signal.SIGINT, lambda signum, frame: os.killpg(p.pid, signum)) | ||
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| if args.write_interval: | ||
| n_interval = int(args.write_interval / args.poll_interval) | ||
| last_peak = 0 | ||
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| peak = 0 | ||
| n = 0 | ||
| while p.poll() is None: | ||
| peak = max(peak, get_rssize(os.getsid(p.pid))) | ||
| n += 1 | ||
| # Check every {write_interval} seconds if current peak memory usage is | ||
| # greater than previously output peak memory usage | ||
| if args.write_interval and (n % n_interval) == 0: | ||
| if peak > last_peak: | ||
| sys.stdout.write("peak rss: {}\n".format( | ||
| human_size(peak) if not args.no_humanize else peak)) | ||
| last_peak = peak | ||
| sleep(args.poll_interval) | ||
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| stdout.write("\n") | ||
| if args.time: | ||
| elapsed_time = time() - start_time | ||
| stdout.write("elapsed time: {}\n".format(human_time( | ||
| elapsed_time) if not args.no_humanize else "{:.3f}".format(elapsed_time))) | ||
| stdout.write("peak rss: {}\n".format( | ||
| human_size(peak) if not args.no_humanize else peak)) | ||
| stdout.write("\n") | ||
|
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| # Return subprocess return code except when returncode is negative, which | ||
| # indicates the subprocess was killed by a signal. Don't know how to get | ||
| # returncode in that case | ||
| if p.returncode < 0: | ||
| sys.exit(255) | ||
| else: | ||
| sys.exit(p.returncode) |