def jobs(self):
"""
Find the amount of cpu cores to set the default amount of tasks executed in parallel. At
runtime the options can be obtained from :py:const:`waflib.Options.options` ::
from waflib.Options import options
njobs = options.jobs
:return: the amount of cpu cores
:rtype: int
"""
count = int(os.environ.get('JOBS', 0))
if count < 1:
if 'NUMBER_OF_PROCESSORS' in os.environ:
# on Windows, use the NUMBER_OF_PROCESSORS environment variable
count = int(os.environ.get('NUMBER_OF_PROCESSORS', 1))
else:
# on everything else, first try the POSIX sysconf values
if hasattr(os, 'sysconf_names'):
if 'SC_NPROCESSORS_ONLN' in os.sysconf_names:
count = int(os.sysconf('SC_NPROCESSORS_ONLN'))
elif 'SC_NPROCESSORS_CONF' in os.sysconf_names:
count = int(os.sysconf('SC_NPROCESSORS_CONF'))
if not count and os.name not in ('nt', 'java'):
try:
tmp = self.cmd_and_log(['sysctl', '-n', 'hw.ncpu'], quiet=0)
except Exception:
pass
else:
if re.match('^[0-9]+$', tmp):
count = int(tmp)
if count < 1:
count = 1
elif count > 1024:
count = 1024
return count
python类sysconf()的实例源码
def jobs(self):
"""
Find the amount of cpu cores to set the default amount of tasks executed in parallel. At
runtime the options can be obtained from :py:const:`waflib.Options.options` ::
from waflib.Options import options
njobs = options.jobs
:return: the amount of cpu cores
:rtype: int
"""
count = int(os.environ.get('JOBS', 0))
if count < 1:
if 'NUMBER_OF_PROCESSORS' in os.environ:
# on Windows, use the NUMBER_OF_PROCESSORS environment variable
count = int(os.environ.get('NUMBER_OF_PROCESSORS', 1))
else:
# on everything else, first try the POSIX sysconf values
if hasattr(os, 'sysconf_names'):
if 'SC_NPROCESSORS_ONLN' in os.sysconf_names:
count = int(os.sysconf('SC_NPROCESSORS_ONLN'))
elif 'SC_NPROCESSORS_CONF' in os.sysconf_names:
count = int(os.sysconf('SC_NPROCESSORS_CONF'))
if not count and os.name not in ('nt', 'java'):
try:
tmp = self.cmd_and_log(['sysctl', '-n', 'hw.ncpu'], quiet=0)
except Exception:
pass
else:
if re.match('^[0-9]+$', tmp):
count = int(tmp)
if count < 1:
count = 1
elif count > 1024:
count = 1024
return count
def jobs(self):
"""
Find the amount of cpu cores to set the default amount of tasks executed in parallel. At
runtime the options can be obtained from :py:const:`waflib.Options.options` ::
from waflib.Options import options
njobs = options.jobs
:return: the amount of cpu cores
:rtype: int
"""
count = int(os.environ.get('JOBS', 0))
if count < 1:
if 'NUMBER_OF_PROCESSORS' in os.environ:
# on Windows, use the NUMBER_OF_PROCESSORS environment variable
count = int(os.environ.get('NUMBER_OF_PROCESSORS', 1))
else:
# on everything else, first try the POSIX sysconf values
if hasattr(os, 'sysconf_names'):
if 'SC_NPROCESSORS_ONLN' in os.sysconf_names:
count = int(os.sysconf('SC_NPROCESSORS_ONLN'))
elif 'SC_NPROCESSORS_CONF' in os.sysconf_names:
count = int(os.sysconf('SC_NPROCESSORS_CONF'))
if not count and os.name not in ('nt', 'java'):
try:
tmp = self.cmd_and_log(['sysctl', '-n', 'hw.ncpu'], quiet=0)
except Exception:
pass
else:
if re.match('^[0-9]+$', tmp):
count = int(tmp)
if count < 1:
count = 1
elif count > 1024:
count = 1024
return count
def cpu_count():
"""Returns the number of processors on this machine."""
if multiprocessing is None:
return 1
try:
return multiprocessing.cpu_count()
except NotImplementedError:
pass
try:
return os.sysconf("SC_NPROCESSORS_CONF")
except ValueError:
pass
gen_log.error("Could not detect number of processors; assuming 1")
return 1
def cpu_count():
"""Returns the number of processors on this machine."""
if multiprocessing is None:
return 1
try:
return multiprocessing.cpu_count()
except NotImplementedError:
pass
try:
return os.sysconf("SC_NPROCESSORS_CONF")
except ValueError:
pass
gen_log.error("Could not detect number of processors; assuming 1")
return 1
def cpu_count():
"""Returns the number of processors on this machine."""
if multiprocessing is None:
return 1
try:
return multiprocessing.cpu_count()
except NotImplementedError:
pass
try:
return os.sysconf("SC_NPROCESSORS_CONF")
except ValueError:
pass
gen_log.error("Could not detect number of processors; assuming 1")
return 1
def _close_fds():
try:
max_fd = os.sysconf("SC_OPEN_MAX")
except ValueError:
max_fd = 65536
for i in range(max_fd):
try:
os.close(i)
except OSError:
pass
def initgroups(uid, primaryGid):
"""Initializes the group access list.
This is done by reading the group database /etc/group and using all
groups of which C{uid} is a member. The additional group
C{primaryGid} is also added to the list.
If the given user is a member of more than C{NGROUPS}, arbitrary
groups will be silently discarded to bring the number below that
limit.
"""
try:
# Try to get the maximum number of groups
max_groups = os.sysconf("SC_NGROUPS_MAX")
except:
# No predefined limit
max_groups = 0
username = pwd.getpwuid(uid)[0]
l = []
if primaryGid is not None:
l.append(primaryGid)
for groupname, password, gid, userlist in grp.getgrall():
if username in userlist:
l.append(gid)
if len(l) == max_groups:
break # No more groups, ignore any more
try:
_setgroups_until_success(l)
except OSError, e:
# We might be able to remove this code now that we
# don't try to setgid/setuid even when not asked to.
if e.errno == errno.EPERM:
for g in getgroups():
if g not in l:
raise
else:
raise
def cpu_count():
'''
Returns the number of CPUs in the system
'''
if sys.platform == 'win32':
try:
num = int(os.environ['NUMBER_OF_PROCESSORS'])
except (ValueError, KeyError):
num = 0
elif 'bsd' in sys.platform or sys.platform == 'darwin':
comm = '/sbin/sysctl -n hw.ncpu'
if sys.platform == 'darwin':
comm = '/usr' + comm
try:
with os.popen(comm) as p:
num = int(p.read())
except ValueError:
num = 0
else:
try:
num = os.sysconf('SC_NPROCESSORS_ONLN')
except (ValueError, OSError, AttributeError):
num = 0
if num >= 1:
return num
else:
raise NotImplementedError('cannot determine number of cpus')
def cpu_count_logical():
"""Return the number of logical CPUs in the system."""
try:
return os.sysconf("SC_NPROCESSORS_ONLN")
except ValueError:
# as a second fallback we try to parse /proc/cpuinfo
num = 0
with open_binary('%s/cpuinfo' % get_procfs_path()) as f:
for line in f:
if line.lower().startswith(b'processor'):
num += 1
# unknown format (e.g. amrel/sparc architectures), see:
# https://github.com/giampaolo/psutil/issues/200
# try to parse /proc/stat as a last resort
if num == 0:
search = re.compile('cpu\d')
with open_text('%s/stat' % get_procfs_path()) as f:
for line in f:
line = line.split(' ')[0]
if search.match(line):
num += 1
if num == 0:
# mimic os.cpu_count()
return None
return num
def virtual_memory():
# we could have done this with kstat, but imho this is good enough
total = os.sysconf('SC_PHYS_PAGES') * PAGE_SIZE
# note: there's no difference on Solaris
free = avail = os.sysconf('SC_AVPHYS_PAGES') * PAGE_SIZE
used = total - free
percent = usage_percent(used, total, _round=1)
return svmem(total, avail, percent, used, free)
def cpu_count_logical():
"""Return the number of logical CPUs in the system."""
try:
return os.sysconf("SC_NPROCESSORS_ONLN")
except ValueError:
# mimic os.cpu_count() behavior
return None
def cpu_count_logical():
"""Return the number of logical CPUs in the system."""
try:
return os.sysconf("SC_NPROCESSORS_ONLN")
except ValueError:
# as a second fallback we try to parse /proc/cpuinfo
num = 0
with open_binary('%s/cpuinfo' % get_procfs_path()) as f:
for line in f:
if line.lower().startswith(b'processor'):
num += 1
# unknown format (e.g. amrel/sparc architectures), see:
# https://github.com/giampaolo/psutil/issues/200
# try to parse /proc/stat as a last resort
if num == 0:
search = re.compile('cpu\d')
with open_text('%s/stat' % get_procfs_path()) as f:
for line in f:
line = line.split(' ')[0]
if search.match(line):
num += 1
if num == 0:
# mimic os.cpu_count()
return None
return num
def virtual_memory():
# we could have done this with kstat, but imho this is good enough
total = os.sysconf('SC_PHYS_PAGES') * PAGE_SIZE
# note: there's no difference on Solaris
free = avail = os.sysconf('SC_AVPHYS_PAGES') * PAGE_SIZE
used = total - free
percent = usage_percent(used, total, _round=1)
return svmem(total, avail, percent, used, free)
def cpu_count_logical():
"""Return the number of logical CPUs in the system."""
try:
return os.sysconf("SC_NPROCESSORS_ONLN")
except ValueError:
# as a second fallback we try to parse /proc/cpuinfo
num = 0
with open_binary('%s/cpuinfo' % get_procfs_path()) as f:
for line in f:
if line.lower().startswith(b'processor'):
num += 1
# unknown format (e.g. amrel/sparc architectures), see:
# https://github.com/giampaolo/psutil/issues/200
# try to parse /proc/stat as a last resort
if num == 0:
search = re.compile('cpu\d')
with open_text('%s/stat' % get_procfs_path()) as f:
for line in f:
line = line.split(' ')[0]
if search.match(line):
num += 1
if num == 0:
# mimic os.cpu_count()
return None
return num
def virtual_memory():
# we could have done this with kstat, but imho this is good enough
total = os.sysconf('SC_PHYS_PAGES') * PAGE_SIZE
# note: there's no difference on Solaris
free = avail = os.sysconf('SC_AVPHYS_PAGES') * PAGE_SIZE
used = total - free
percent = usage_percent(used, total, _round=1)
return svmem(total, avail, percent, used, free)
def cpu_count_logical():
"""Return the number of logical CPUs in the system."""
try:
return os.sysconf("SC_NPROCESSORS_ONLN")
except ValueError:
# mimic os.cpu_count() behavior
return None
def cpu_count_logical():
"""Return the number of logical CPUs in the system."""
try:
return os.sysconf("SC_NPROCESSORS_ONLN")
except ValueError:
# as a second fallback we try to parse /proc/cpuinfo
num = 0
with open_binary('%s/cpuinfo' % get_procfs_path()) as f:
for line in f:
if line.lower().startswith(b'processor'):
num += 1
# unknown format (e.g. amrel/sparc architectures), see:
# https://github.com/giampaolo/psutil/issues/200
# try to parse /proc/stat as a last resort
if num == 0:
search = re.compile('cpu\d')
with open_text('%s/stat' % get_procfs_path()) as f:
for line in f:
line = line.split(' ')[0]
if search.match(line):
num += 1
if num == 0:
# mimic os.cpu_count()
return None
return num
def virtual_memory():
# we could have done this with kstat, but imho this is good enough
total = os.sysconf('SC_PHYS_PAGES') * PAGE_SIZE
# note: there's no difference on Solaris
free = avail = os.sysconf('SC_AVPHYS_PAGES') * PAGE_SIZE
used = total - free
percent = usage_percent(used, total, _round=1)
return svmem(total, avail, percent, used, free)
def calculate_memory_for_sort():
"""Calculate available memory for ``samtools sort`` function.
If there is enough memory, no temp files are created. **Enough**
is defined as at least 1G per CPU.
Returns
-------
sort_memory: str or None
String to use directly with *-m* option in sort, or None.
"""
avail_memory = None
if HAVE_PSUTIL == True:
mem = virtual_memory()
avail_memory = mem.total
else:
try:
avail_memory = os.sysconf('SC_PAGE_SIZE') * os.sysconf('SC_PHYS_PAGES') # e.g. 4015976448
except ValueError:
logging.error("If you're in Mac OS you need to have the psutil Python library.")
raise SystemExit
avail_cpu = multiprocessing.cpu_count()
sort_memory = avail_memory / avail_cpu / 1024 ** 2
# samtools default from documentation is 768M, to be conservative
# only use -m option when there is more than 1G per CPU.
if sort_memory < 1024:
sort_memory = None
else:
sort_memory = "%sG" % (int(floor(sort_memory / 1024)))
return sort_memory
# --------------------------------------------------------------------------------------------------
