def getOptions(self):
"""
Returns the list of options used by the JVM.
:rtype: list
"""
return jnius_config.get_options()
def run(self, *args: str):
try:
jnius_config.add_options(*args)
log.info("Configured jvm options:%s" % jnius_config.get_options())
from jnius import autoclass
DebeziumServer = autoclass('io.debezium.server.Main')
_dbz = DebeziumServer()
return _dbz.main()
finally:
from jnius import detach
detach()
def __init__(self, name, index, k, num_threads, Xms=None, Xmx=None):
super().__init__(name)
if Xms and Xmx:
# to solve Insufficient memory for the Java Runtime Environment
jnius_config.add_options("-Xms{}".format(Xms),
"-Xmx{}".format(Xmx),
"-XX:-UseGCOverheadLimit")
print("Configured options:", jnius_config.get_options())
self.num_threads = min(num_threads, int(multiprocessing.cpu_count()))
# initialize a ranker per thread
self.arguments = []
for id in tqdm(range(self.num_threads)):
self.arguments.append({
"id": id,
"index": index,
"k": k,
})
"""Handles all imports from jnius to prevent conflicts resulting from attempts
to set JVM options while the VM is already running."""
import jnius_config
if '-Xmx4g' not in jnius_config.get_options():
if not jnius_config.vm_running:
jnius_config.add_options('-Xmx4g')
else:
warnings.warn("Couldn't set memory limit for Java VM because the VM "
"is already running.")
from jnius import autoclass, JavaException, cast
def get_options():
return jnius_config.get_options()
logger = logging.getLogger(__name__)
def _has_xmx(options):
for option in options:
if option.startswith('-Xmx'):
return True
return False
default_mem_limit = get_config("INDRA_DEFAULT_JAVA_MEM_LIMIT")
if default_mem_limit is None:
# Set to 8g if not specified in the configuration
default_mem_limit = '8g'
if not _has_xmx(jnius_config.get_options()):
if not jnius_config.vm_running:
jnius_config.add_options('-Xmx%s' % default_mem_limit)
else:
logger.warning("Couldn't set memory limit for Java VM because the VM "
"is already running.")
path_here = os.path.dirname(os.path.realpath(__file__))
cp = os.path.join(path_here, 'sources/biopax/jars/paxtools.jar')
cp_existing = os.environ.get('CLASSPATH')
if cp_existing is not None:
os.environ['CLASSPATH'] = cp + ':' + cp_existing
else:
os.environ['CLASSPATH'] = cp
"""Handles all imports from jnius to prevent conflicts resulting from attempts
to set JVM options while the VM is already running."""
import os
import warnings
import jnius_config
if "-Xmx4g" not in jnius_config.get_options():
if not jnius_config.vm_running:
jnius_config.add_options("-Xmx4g")
else:
warnings.warn("Couldn't set memory limit for Java VM because the VM " "is already running.")
path_here = os.path.dirname(os.path.realpath(__file__))
cp = path_here + "/biopax/jars/paxtools.jar"
os.environ["CLASSPATH"] = cp
from jnius import autoclass, JavaException, cast
logger = logging.getLogger(__name__)
def _has_xmx(options):
for option in options:
if option.startswith('-Xmx'):
return True
return False
default_mem_limit = get_config("INDRA_DEFAULT_JAVA_MEM_LIMIT")
if default_mem_limit is None:
# Set to 8g if not specified in the configuration
default_mem_limit = '8g'
if not _has_xmx(jnius_config.get_options()):
if not jnius_config.vm_running:
jnius_config.add_options('-Xmx%s' % default_mem_limit)
else:
logger.warning("Couldn't set memory limit for Java VM because the VM "
"is already running.")
path_here = os.path.dirname(os.path.realpath(__file__))
cp = os.path.join(path_here, 'sources/biopax/jars/paxtools.jar')
cp_existing = os.environ.get('CLASSPATH')
if cp_existing is not None:
os.environ['CLASSPATH'] = cp + ':' + cp_existing
else:
os.environ['CLASSPATH'] = cp