def get_memory(suffix='M'):
"""
Queries a worker's /proc/meminfo for available memory and returns a float
of the specified suffix size
Args:
suffix (str): One of 'M', 'K' or 'G' to return memory in Mib, KiB or
GiB, respectively.
Returns:
float: total_memory read from meminfo in MiB, KiB or GiB
depending on specified suffix.
Raises:
dxpy.DXError is raised if suffix is not recognized or system memory
cannot be read.
"""
if suffix == 'K':
shift = 1
elif suffix == 'M':
shift = 1 << 10
elif suffix == 'G':
shift = 1 << 20
else:
raise dxpy.DXError(
'Unknown memory suffix {0}. Please choose from K, M, or G.'.
format(suffix))
# Calc amount of memory available for gatk and Picard.
total_mem = re.findall('^MemTotal:[\s]*([0-9]*) kB',
open('/proc/meminfo').read())
if (len(total_mem) != 1):
raise dxpy.DXError('Problem reading system memory from /proc/meminfo')
return float(total_mem[0]) / shift
def get_memory(suffix='M'):
if suffix == 'K':
shift = 1
elif suffix == 'M':
shift = 1 << 10
elif suffix == 'G':
shift = 1 << 20
else:
raise dxpy.DXError('Unknown memory suffix {0}. Please choose from K, M, or G.'.format(suffix))
# Calc amount of memory available for gatk and Picard.
total_mem = re.findall('^MemTotal:[\s]*([0-9]*) kB',
open('/proc/meminfo').read())
if(len(total_mem) != 1):
raise dxpy.DXError('Problem reading system memory from /proc/meminfo')
return float(total_mem[0]) / shift
def get_java_cmd():
# Calc amount of memory available for gatk and Picard.
total_mem = re.findall('^MemTotal:[\s]*([0-9]*) kB',
open('/proc/meminfo').read())
if (len(total_mem) != 1):
raise dxpy.DXError('Problem reading system memory from /proc/meminfo')
mem = int(0.9 * int(total_mem[0]) / 1024.0)
java_cmd = 'java -Xmx{mem}m '.format(mem=mem)
return java_cmd