def runJavaIJapp(memory, appName, args, env=None):
env = env or {}
getEnviron = Config.getDomain().importFromPlugin('xmipp3', 'Plugin').getEnviron
env.update(getEnviron(xmippFirst=False))
# Add scipion variables
env[SCIPION_DOMAIN] = Config.SCIPION_DOMAIN
env[SCIPION_HOME_VAR]= Config.SCIPION_HOME
if Config.debugOn():
env[SCIPION_DEBUG] = "1"
# Add out python path to the PATH
env["PATH"] = ":".join([sys.executable, env.get("PATH", "")])
# Try chimera
try:
chimeraPlugin = Config.getDomain().importFromPlugin('chimera', 'Plugin', doRaise=True)
env["CHIMERA_LAUNCHER"] = chimeraPlugin.getProgram() + " %s"
except Exception as e:
pass
args = getJavaIJappArguments(memory, appName, args)
print('java %s' % args)
# return subprocess.Popen('java ' + args, shell=True, env=env)
cmd = ['java'] + shlex.split(args)
return subprocess.Popen(cmd, env=env)
def _drawNode(self, node):
""" Allocate node with x=0 and y=0. """
try:
parents = node.getParents()
if not parents:
print("EMPTY NODE ask JM")
return
maxParent = parents[0]
for p in parents[1:]:
if p.y > maxParent.y:
maxParent = p
siblings = maxParent.getChilds()
if len(siblings) == 1:
node.x = maxParent.x
node.y = maxParent.y + self.DY
else:
rightSibling = siblings[0]
for s in siblings:
if s.x > rightSibling.x:
rightSibling = s
node.x = rightSibling.x + rightSibling.width / 2 + self.DX + node.width / 2
node.y = rightSibling.y
except Exception as e:
from pyworkflow.utils import envVarOn
if Config.debugOn():
print("Can't draw node: %s" % node, e)
import traceback
traceback.print_stack()
else:
# Do nothing
return
def startDebugger(password='******'):
if Config.debugOn():
try:
# FIXME: rpdb2 does not support python 3
from rpdb2 import start_embedded_debugger
print("Starting debugger...")
start_embedded_debugger(password)
except Exception:
print(
"Error importing rpdb2 debugging module, consider installing winpdb."
)
def runCommand(command, env=None, cwd=None):
""" Execute command with given environment env and directory cwd """
# First let us create core dumps if in debug mode
if Config.debugOn(env):
import resource
resource.setrlimit(resource.RLIMIT_CORE,
(resource.RLIM_INFINITY, resource.RLIM_INFINITY))
# This is like "ulimit -u 99999999", so we can create core dumps
# TODO: maybe have to set PBS_NODEFILE in case it is used by "command"
# (useful for example with gnu parallel)
check_call(command,
shell=True,
stdout=sys.stdout,
stderr=sys.stderr,
env=env,
cwd=cwd)
def runJobMPISlave(mpiComm):
""" This slave will be receiving commands to execute
until 'None' is received.
"""
rank = mpiComm.Get_rank()
hostname = getLocalHostName()
print(" Running MPIWorker: ", rank)
exitResult = 0
# Listen for commands until we get 'None'
cwd = None # We run without changing directory by default
env = None # And we don't change the environment either!
while True:
# Receive command in a non-blocking way
req_recv = mpiComm.irecv(source=0, tag=TAG_RUN_JOB + rank)
while True:
done, command = req_recv.test()
if done:
break
sleep(1)
print(" Worker %s(rank %d) received command." % (hostname, rank))
# We need to convert to string because req_recv.test() returns bytes or None
if command == 'None':
print(" Stopping...")
return
else:
command = loads(command)
# Run the command and get the result (exit code or exception)
try:
if command.startswith("cwd="):
cwd = command.split("=", 1)[-1]
print(" Changing to dir %s ..." % cwd)
elif command.startswith("env="):
env = command.split("=", 1)[-1]
env = eval(env)
print(" Setting the environment...")
if Config.debugOn():
print(env)
else:
runCommand(command, cwd=cwd, env=env)
cwd = None # unset directory
env = None # unset environment
except Exception as e:
print(" Error in process %d (rank %d)" % (os.getpid(), rank))
import traceback
traceback.print_exc()
exitResult = str(e)
# Communicate to master, either error os success
req_send = mpiComm.isend(exitResult, dest=0, tag=TAG_RUN_JOB + rank)
t0 = time()
while not req_send.test()[0]:
sleep(1)
if time() - t0 > TIMEOUT:
msg = " Error in process %d, cannot send error message to master."
print(msg % os.getpid())
break