def setUp(self):
dbname = "/tmp/test.db"
if os.path.exists(dbname):
os.remove(dbname)
self.db = DbStore(dbname)
self.db.put(FileItem("/tmp"))
self.db.put(FileItem("/tmp/1"))
self.db.put(FileItem("/tmp/2"))
def workq_init(self, dbname=None, resume=False):
# NOTE: the db filename and its rank is seprated with "-"
# we rely on this to separate, so the filename itself (within our control)
# should not use dash ... the default is to use "." for sepration
# Yes, this is very fragile, hopefully we will fix this later
if G.resume == True:
self.dbname = os.path.join(self.workdir, ".pcp_workq.%s.%s.db" % (G.rid, self.rank))
if os.path.exists(self.dbname):
self.workq_db = DbStore(self.dbname, G.resume)
else:
if dbname is None:
self.dbname = os.path.join(G.tempdir, "workq-%s" % self.rank)
else:
self.dbname = os.path.join(G.tempdir, "%s.workq-%s" % (dbname, self.rank))
self.workq_db = DbStore(self.dbname, resume=G.resume)
def workq_init(self, dbname=None, resume=False):
# NOTE: the db filename and its rank is seprated with "-"
# we rely on this to separate, so the filename itself (within our control)
# should not use dash ... the default is to use "." for sepration
# Yes, this is very fragile, hopefully we will fix this later
if G.resume == True:
self.dbname = os.path.join(self.workdir, ".pcp_workq.%s.%s.db" % (G.rid, self.rank))
if os.path.exists(self.dbname):
self.workq_db = DbStore(self.dbname, G.resume)
else:
if dbname is None:
self.dbname = os.path.join(G.tempdir, "workq-%s" % self.rank)
else:
self.dbname = os.path.join(G.tempdir, "%s.workq-%s" % (dbname, self.rank))
self.workq_db = DbStore(self.dbname, resume=G.resume)
def setUp(self):
dbname = "/tmp/test.db"
if os.path.exists(dbname):
os.remove(dbname)
self.db = DbStore(dbname)
self.db.put(FileItem("/tmp"))
self.db.put(FileItem("/tmp/1"))
self.db.put(FileItem("/tmp/2"))
class Circle:
def __init__(self, name="Circle", split="equal", k=2, dbname=None, resume=False):
random.seed() # use system time to seed
self.comm = MPI.COMM_WORLD
self.comm.Set_name(name)
self.size = self.comm.Get_size()
self.rank = self.comm.Get_rank()
self.d = {"rank": "rank %s" % self.rank}
self.logger = getLogger(__name__)
self.useStore = G.use_store
self.split = split
self.dbname = dbname
self.resume = resume
self.reduce_time_interval = G.reduce_interval
self.task = None
self.abort = False
self.requestors = []
# workq buffer
if self.useStore:
self.workq_buf = deque()
# counters
self.work_requested = 0
self.work_processed = 0
self.work_request_received = 0
self.workreq_outstanding = False
self.workreq_rank = None
# reduction
self.reduce_enabled = True
self.reduce_time_last = MPI.Wtime()
self.reduce_outstanding = False
self.reduce_replies = 0
self.reduce_buf = {}
self.reduce_status = None
# barriers
self.barrier_started = False
self.barrier_up = False # flag to indicate barrier sent to parent
self.barrier_replies = 0
self.workdir = os.getcwd()
self.tempdir = os.path.join(self.workdir, ".pcircle")
if not os.path.exists(self.tempdir):
try:
os.mkdir(self.tempdir)
except OSError:
pass
# token
self.token = Token(self)
# tree init
self.k = k
self.parent_rank = MPI.PROC_NULL
self.child_ranks = [] # [MPI.PROC_NULL] * k is too much C
self.children = 0
# compute rank of parent if we have one
if self.rank > 0:
self.parent_rank = (self.rank - 1) / k
# identify ranks of what would be leftmost and rightmost children
left = self.rank * k + 1
right = self.rank * k + k
# if we have at least one child
# compute number of children and list of child ranks
if left < self.size:
# adjust right child in case we don't have a full set of k
if right >= self.size:
right = self.size - 1
# compute number of children and the list
self.children = right - left + 1
for i in range(self.children):
self.child_ranks.append(left + i)
self.logger.debug("parent: %s, children: %s" % (self.parent_rank, self.child_ranks),
extra=self.d)
# workq init
# TODO: compare list vs. deque
if G.use_store:
self.workq_init(dbname, resume)
else:
self.workq = []
self.logger.debug("Circle initialized", extra=self.d)
def finalize(self, cleanup=True):
if cleanup and G.use_store:
self.workq.cleanup()
def workq_init(self, dbname=None, resume=False):
# NOTE: the db filename and its rank is seprated with "-"
# we rely on this to separate, so the filename itself (within our control)
# should not use dash ... the default is to use "." for sepration
# Yes, this is very fragile, hopefully we will fix this later
if dbname is None:
self.dbname = os.path.join(self.tempdir, "workq-%s" % self.rank)
else:
self.dbname = os.path.join(self.tempdir, "%s-%s" % (dbname, self.rank))
self.workq = DbStore(self.dbname, resume=resume)
def next_proc(self):
""" Note next proc could return rank of itself """
if self.size == 1:
return MPI.PROC_NULL
else:
return random.randint(0, self.size - 1)
def workq_info(self):
s = "has %s items in work queue\n" % len(self.workq)
return s
def qsize(self):
return len(self.workq)
def begin(self, task):
""" entry point to work """
self.task = task
self.task.create()
self.comm.barrier()
self.loop()
if self.rank == 0:
self.logger.debug("Loop finished, cleaning up ... ", extra=self.d)
self.cleanup()
self.comm.barrier()
if len(self.workq) != 0:
pprint("Rank %s workq.len = %s" % (self.rank, self.qsize()))
pprint(self.__dict__)
sys.stdout.flush()
self.comm.Abort(1)
def loop(self):
""" central loop to finish the work """
while True:
# check for and service requests
self.workreq_check()
if self.reduce_enabled:
self.reduce_check()
if len(self.workq) == 0:
self.request_work()
# if I have work, and no abort signal, process one
if len(self.workq) > 0 and not self.abort:
self.task.process()
self.work_processed += 1
else:
status = self.token.check_for_term()
if status == G.TERMINATE:
break
def enq(self, work):
if work is None:
self.logger.warn("enq work item is None", extra=self.d)
return
self.workq.append(work)
def preq(self, work):
self.workq.insert(0, work)
def setq(self, q):
self.workq = q
def deq(self):
if len(self.workq) > 0:
return self.workq.pop()
else:
return None
def barrier_start(self):
self.barrier_started = True
def barrier_test(self):
if not self.barrier_started:
return False
# check if we have received message from all children
if self.barrier_replies < self.children:
# still waiting for barries from children
st = MPI.Status()
flag = self.comm.Iprobe(MPI.ANY_SOURCE, T.BARRIER, st)
if flag:
child = st.Get_source()
self.comm.recv(source=child, tag=T.BARRIER)
self.barrier_replies += 1
# if we have not sent a message to our parent, and we
# have received a message from all of our children (or we have no children)
# send a message to our parent
if not self.barrier_up and self.barrier_replies == self.children:
if self.parent_rank != MPI.PROC_NULL:
self.comm.send(None, self.parent_rank, T.BARRIER)
# transition to state where we're waiting for parent
# to notify us that the barrier is complete
self.barrier_up = True
# wait for message to come back down from parent to mark end of barrier
complete = False
if self.barrier_up:
if self.parent_rank != MPI.PROC_NULL:
# check for message from parent
flag = self.comm.Iprobe(self.parent_rank, T.BARRIER)
if flag:
self.comm.recv(source=self.parent_rank, tag=T.BARRIER)
# mark barrier as complete
complete = True
else:
# we have no parent, we must be root
# so mark the barrier complete
complete = True
# barrier is complete, send messages to children if any and return true
if complete:
for child in self.child_ranks:
self.comm.send(None, dest=child, tag=T.BARRIER)
# reset state for another barrier
self.barrier_started = False
self.barrier_up = False
self.barrier_replies = 0
return True
# barrier still not complete
return False
def bcast_abort(self):
self.abort = True
buf = G.ABORT
for i in range(self.size):
if (i != self.rank):
self.comm.send(buf, dest=i, tag=T.WORK_REQUEST)
self.logger.warn("abort message sent to %s" % i, extra=self.d)
def cleanup(self):
while True:
# start non-block barrier if we have no outstanding items
if not self.reduce_outstanding and \
not self.workreq_outstanding and \
self.token.send_req == MPI.REQUEST_NULL:
self.barrier_start()
# break the loop when non-blocking barrier completes
if self.barrier_test():
break
# send no work message for any work request that comes in
self.workreq_check(cleanup=True)
# clean up any outstanding reduction
if self.reduce_enabled:
self.reduce_check(cleanup=True)
# recv any incoming work reply messages
self.request_work(cleanup=True)
# check and recv any incoming token
self.token.check_and_recv()
# if we have an outstanding token, check if it has been recv'ed
# I don't think this is needed as there seem no side effect
if self.token.send_req != MPI.REQUEST_NULL:
if self.token.send_req.Test():
self.token.send_req = MPI.REQUEST_NULL
def workreq_check(self, cleanup=False):
""" for any process that sends work request message:
add the process to the requester list
if my work queue is not empty:
distribute the work evenly
else:
send "no work" message to each requester
reset the requester list to empty
"""
while True:
st = MPI.Status()
ret = self.comm.Iprobe(source=MPI.ANY_SOURCE, tag=T.WORK_REQUEST, status=st)
if not ret: # no work request, break out the loop
break
# we have work request message
rank = st.Get_source()
buf = self.comm.recv(source=rank, tag=T.WORK_REQUEST, status=st)
if buf == G.ABORT:
self.logger.warn("Abort request from rank %s" % rank, extra=self.d)
self.abort = True
self.send_no_work(rank)
return
else:
self.logger.debug("receive work request from requestor [%s]" % rank, extra=self.d)
# add rank to requesters
self.requestors.append(rank)
# out of while loop
if not self.requestors:
return
else:
self.logger.debug("have %s requesters, with %s work items in queue" %
(len(self.requestors), len(self.workq)), extra=self.d)
# have work requesters
if len(self.workq) == 0 or cleanup:
for rank in self.requestors:
self.send_no_work(rank)
else:
# we do have work
self.send_work_to_many()
self.requestors = []
def spread_counts(self, rcount, wcount):
"""
@rcount: # of requestors
@wcount: # of work items
@return: spread it evenly among all requesters
case 1: wcount == rcount:
base = 0
extra = wcount
each requestor get 1
case 2: wcount < rcount:
base = 0
extra = wcount
first "wcount" requester get 1
case 3: wcount > rcount:
is it possible?
"""
if self.split != "equal":
raise NotImplementedError
base = wcount / (rcount + 1) # leave self a base number of works
extra = wcount - base * (rcount + 1)
assert extra <= rcount
sizes = [base] * rcount
for i in xrange(extra):
sizes[i] += 1
return sizes
def send_no_work(self, rank):
""" send no work reply to someone requesting work"""
buf = {G.KEY: G.ABORT} if self.abort else {G.KEY: G.ZERO}
r = self.comm.isend(buf, dest=rank, tag=T.WORK_REPLY)
r.wait()
self.logger.debug("Send no work reply to %s" % rank, extra=self.d)
def send_work_to_many(self):
rcount = len(self.requestors)
wcount = len(self.workq)
sizes = self.spread_counts(rcount, wcount)
self.logger.debug("requester count: %s, work count: %s, spread: %s" %
(rcount, wcount, sizes), extra=self.d)
for idx, dest in enumerate(self.requestors):
self.send_work(dest, sizes[idx])
def send_work(self, rank, witems):
"""
@dest - the rank of requester
@count - the number of work to send
"""
if witems <= 0:
self.send_no_work(rank)
return
# for termination detection
if (rank < self.rank) or (rank == self.token.src):
self.token.proc = G.BLACK
buf = None
# based on if it is memory or store-based
# we have different ways of constructing buf
if self.useStore:
objs, size = self.workq.mget(witems)
buf = {G.KEY: witems, G.VAL: objs}
else:
buf = {G.KEY: witems, G.VAL: self.workq[0:witems]}
self.comm.send(buf, dest=rank, tag=T.WORK_REPLY)
self.logger.debug("%s work items sent to rank %s" % (witems, rank), extra=self.d)
# remove (witems) of work items
# for DbStotre, all we need is a number, not the actual objects
# for KVStore, we do need the object list for its key value
# the "size" is a bit awkward use - we know the size after we do mget()
# however, it is not readily available when we do mdel(), so we keep
# previous data and pass it back in to save us some time.
#
if self.useStore:
self.workq.mdel(witems, size)
else:
del self.workq[0:witems]
def request_work(self, cleanup=False):
if self.workreq_outstanding:
st = MPI.Status()
reply = self.comm.Iprobe(source=self.work_requested_rank,
tag=T.WORK_REPLY, status=st)
if reply:
self.work_receive(self.work_requested_rank)
# flip flag to indicate we no longer waiting for reply
self.workreq_outstanding = False
# else:
# self.logger.debug("has req outstanding, dest = %s, no reply" %
# self.work_requested_rank, extra = self.d)
elif not cleanup:
# send request
dest = self.next_proc()
if dest == self.rank or dest == MPI.PROC_NULL:
# have no one to ask, we are done
return
buf = G.ABORT if self.abort else G.MSG
# blocking send
self.logger.debug("send work request to rank %s : %s" % (dest, G.str[buf]),
extra=self.d)
self.comm.send(buf, dest, T.WORK_REQUEST)
self.workreq_outstanding = True
self.work_requested_rank = dest
def work_receive(self, rank):
""" when incoming work reply detected """
buf = self.comm.recv(source=rank, tag=T.WORK_REPLY)
if buf[G.KEY] == G.ABORT:
self.logger.debug("receive abort signal", extra=self.d)
self.abort = True
return
elif buf[G.KEY] == G.ZERO:
self.logger.debug("receive no work signal", extra=self.d)
return
else:
assert type(buf[G.VAL]) == list
self.workq.extend(buf[G.VAL])
def reduce(self, buf):
# copy data from user buffer
self.reduce_buf = copy(buf)
def reduce_check(self, cleanup=False):
"""
initiate and progress a reduce operation at specified interval,
ensure progress of reduction in background, stop reduction if cleanup flag is True
"""
if self.reduce_outstanding:
# if we have outstanding reduce, check message from children
# otherwise, check whether we should start new reduce
for child in self.child_ranks:
if self.comm.Iprobe(source=child, tag=T.REDUCE):
# receive message from child
# 'status' element is G.MSG_VALID or not
# the rest is opaque
inbuf = self.comm.recv(source=child, tag=T.REDUCE)
self.reduce_replies += 1
self.logger.debug("client data from %s: %s" %
(child, inbuf), extra=self.d)
if inbuf['status'] == G.MSG_INVALID:
self.reduce_status = False
else:
self.reduce_status = True
# invoke user's callback to reduce user data
if hasattr(self.task, "reduce"):
self.task.reduce(self.reduce_buf, inbuf)
# check if we have gotten replies from all children
if self.reduce_replies == self.children:
# all children replied
# add our own contents to reduce buffer
# send message to parent if we have one
if self.parent_rank != MPI.PROC_NULL:
self.comm.send(self.reduce_buf, self.parent_rank, T.REDUCE)
else:
# we are the root, print results if we have valid data
if self.reduce_status and hasattr(self.task, "reduce_report"):
self.task.reduce_report(self.reduce_buf)
# invoke callback on root to deliver final results
if hasattr(self.task, "reduce_finish"):
self.task.reduce_finish(self.reduce_buf)
# disable flag to indicate we got what we want
self.reduce_outstanding = False
else:
# we don't have an outstanding reduction
# determine if a new reduce should be started
# only bother checking if we think it is about time or
# we are in cleanup mode
start_reduce = False
time_now = MPI.Wtime()
time_next = self.reduce_time_last + self.reduce_time_interval
if time_now >= time_next or cleanup:
if self.parent_rank == MPI.PROC_NULL:
# we are root, kick it off
start_reduce = True
elif self.comm.Iprobe(source=self.parent_rank, tag=T.REDUCE):
# we are not root, check if parent sent us a message
# receive message from parent and set flag to start reduce
self.comm.recv(source=self.parent_rank, tag=T.REDUCE)
start_reduce = True
# it is critical that we don't start a reduce if we are in cleanup
# phase because we may have already started the non-blocking barrier
# just send an invalid message back to parent
if start_reduce and cleanup:
# avoid starting a reduce
start_reduce = False
# if we have parent, send invalid msg
if self.parent_rank != MPI.PROC_NULL:
self.reduce_status = G.MSG_INVALID
self.comm.send(self.reduce_buf, self.parent_rank, T.REDUCE)
if start_reduce:
# set flag to indicate we have a reduce outstanding
# and initiate state for a fresh reduction
self.reduce_time_last = time_now
self.reduce_outstanding = True
self.reduce_replies = 0
self.reduce_status = G.MSG_VALID
self.reduce_buf['status'] = G.MSG_VALID
# invoke callback to get input data
if hasattr(self.task, "reduce_init"):
self.task.reduce_init(self.reduce_buf)
# sent message to each child
for child in self.child_ranks:
self.comm.send(None, child, T.REDUCE)
@staticmethod
def exit(code):
MPI.Finalize()
sys.exit(code)
class Circle:
def __init__(self,
name="Circle",
split="equal",
k=2,
dbname=None,
resume=False):
random.seed() # use system time to seed
self.comm = MPI.COMM_WORLD
self.comm.Set_name(name)
self.size = self.comm.Get_size()
self.rank = self.comm.Get_rank()
self.host = MPI.Get_processor_name()
self.pid = os.getpid()
self.d = {"rank": "rank %s" % self.rank}
self.logger = getLogger(__name__)
self.split = split
self.dbname = dbname
self.resume = resume
self.reduce_time_interval = G.reduce_interval
self.task = None
self.abort = False
self.requestors = []
# counters
self.work_requested = 0
self.work_processed = 0
self.work_request_received = 0
self.workreq_outstanding = False
self.workreq_rank = None
# reduction
self.reduce_enabled = False
self.reduce_time_last = MPI.Wtime()
self.reduce_outstanding = False
self.reduce_replies = 0
self.reduce_buf = {}
self.reduce_status = None
# periodic report
self.report_enabled = False
self.report_interval = 60
self.report_last = MPI.Wtime()
self.report_processed = 0
# barriers
self.barrier_started = False
self.barrier_up = False # flag to indicate barrier sent to parent
self.barrier_replies = 0
self.workdir = os.getcwd()
if not G.tempdir:
G.tempdir = os.path.join(os.getcwd(),
(".pcircle" + utils.timestamp()))
G.tempdir = self.comm.bcast(G.tempdir)
if not os.path.exists(G.tempdir):
try:
os.mkdir(G.tempdir)
except OSError:
pass
# token
self.token = Token(self)
# tree init
self.k = k
self.parent_rank = MPI.PROC_NULL
self.child_ranks = [] # [MPI.PROC_NULL] * k is too much C
self.children = 0
# compute rank of parent if we have one
if self.rank > 0:
self.parent_rank = (self.rank - 1) // k
# identify ranks of what would be leftmost and rightmost children
left = self.rank * k + 1
right = self.rank * k + k
# if we have at least one child
# compute number of children and list of child ranks
if left < self.size:
# adjust right child in case we don't have a full set of k
if right >= self.size:
right = self.size - 1
# compute number of children and the list
self.children = right - left + 1
for i in range(self.children):
self.child_ranks.append(left + i)
self.logger.debug("parent: %s, children: %s" %
(self.parent_rank, self.child_ranks),
extra=self.d)
# workq init
# TODO: compare list vs. deque
# 3 possible workq: workq, workq_buf(locates in memory, used when pushing to or retrieving from database )
self.workq = deque()
# workq buffer
self.workq_buf = deque()
# flag that indicates database is used for workq
self.use_store = False
if G.resume:
self.workq_init(self.dbname, G.resume)
self.logger.debug("Circle initialized", extra=self.d)
def finalize(self, cleanup=True):
if cleanup and hasattr(self, "workq_db"):
self.workq_db.cleanup()
if os.path.exists(G.tempdir) and cleanup:
try:
shutil.rmtree(G.tempdir)
except:
pass
def workq_init(self, dbname=None, resume=False):
# NOTE: the db filename and its rank is seprated with "-"
# we rely on this to separate, so the filename itself (within our control)
# should not use dash ... the default is to use "." for sepration
# Yes, this is very fragile, hopefully we will fix this later
if G.resume == True:
self.dbname = os.path.join(
self.workdir, ".pcp_workq.%s.%s.db" % (G.rid, self.rank))
if os.path.exists(self.dbname):
self.workq_db = DbStore(self.dbname, G.resume)
else:
if dbname is None:
self.dbname = os.path.join(G.tempdir, "workq-%s" % self.rank)
else:
self.dbname = os.path.join(G.tempdir,
"%s.workq-%s" % (dbname, self.rank))
self.workq_db = DbStore(self.dbname, resume=G.resume)
# after task(fcp) creation, push works in workq_buf into workq_db
def push_remaining_buf(self):
if len(self.workq_buf) > 0:
self.workq_db.mput(self.workq_buf)
self.workq_db.clear()
def next_proc(self):
""" Note next proc could return rank of itself """
if self.size == 1:
return MPI.PROC_NULL
else:
return random.randint(0, self.size - 1)
def workq_info(self):
s = "has %s items in work queue\n" % self.qsize
return s
def qsize(self):
qsize = len(self.workq) + len(self.workq_buf)
if hasattr(self, "workq_db"):
qsize += len(self.workq_db)
return qsize
def begin(self, task):
""" entry point to work """
self.task = task
self.task.create()
self.comm.barrier()
self.loop()
self.cleanup()
if self.report_enabled:
self.do_periodic_report(prefix="Circle final report")
self.comm.barrier()
if self.qsize() != 0:
pprint("Rank %s workq.len = %s" % (self.rank, self.qsize()))
pprint(self.__dict__)
sys.stdout.flush()
self.comm.Abort(1)
def loop(self):
""" central loop to finish the work """
while True:
# check if we shall do report
cur_time = MPI.Wtime()
if self.report_enabled and (cur_time - self.report_last >
self.report_interval):
self.report_last = cur_time
self.do_periodic_report()
# check for and service requests
self.workreq_check()
if self.reduce_enabled:
self.reduce_check()
if self.qsize() == 0:
self.request_work()
# if I have work, and no abort signal, process one
if self.qsize() > 0 and not self.abort:
self.task.process()
self.work_processed += 1
else:
status = self.token.check_for_term()
if status == G.TERMINATE:
break
def enq(self, work):
if work is None:
self.logger.warn("enq work item is None", extra=self.d)
return
if len(self.workq) < G.memitem_threshold:
self.workq.append(work)
return
else:
self.workq_buf.append(work)
if len(self.workq_buf) == G.DB_BUFSIZE:
if self.use_store == False:
self.workq_init(self.dbname, G.resume)
self.use_store = True
self.workq_db.mput(self.workq_buf)
self.workq_buf.clear()
def preq(self, work):
self.workq.appendleft(work)
def setq(self, q):
self.workq = q
def deq(self):
# deque a work starting from workq, then from workq_buf, then from workq_db
if len(self.workq) > 0:
return self.workq.pop()
elif len(self.workq_buf) > 0:
return self.workq_buf.pop()
elif hasattr(self, "workq_db") and len(self.workq_db) > 0:
#read a batch of works into memory
workq, objs_size = self.workq_db.mget(G.memitem_threshold)
self.workq = deque(workq)
self.workq_db.mdel(G.memitem_threshold, objs_size)
if len(self.workq) > 0:
return self.workq.pop()
else:
return None
def barrier_start(self):
self.barrier_started = True
def barrier_test(self):
if not self.barrier_started:
return False
# check if we have received message from all children
if self.barrier_replies < self.children:
# still waiting for barries from children
st = MPI.Status()
flag = self.comm.Iprobe(MPI.ANY_SOURCE, T.BARRIER, st)
if flag:
child = st.Get_source()
self.comm.recv(source=child, tag=T.BARRIER)
self.barrier_replies += 1
# if we have not sent a message to our parent, and we
# have received a message from all of our children (or we have no children)
# send a message to our parent
if not self.barrier_up and self.barrier_replies == self.children:
if self.parent_rank != MPI.PROC_NULL:
self.comm.send(None, self.parent_rank, T.BARRIER)
# transition to state where we're waiting for parent
# to notify us that the barrier is complete
self.barrier_up = True
# wait for message to come back down from parent to mark end of barrier
complete = False
if self.barrier_up:
if self.parent_rank != MPI.PROC_NULL:
# check for message from parent
flag = self.comm.Iprobe(self.parent_rank, T.BARRIER)
if flag:
self.comm.recv(source=self.parent_rank, tag=T.BARRIER)
# mark barrier as complete
complete = True
else:
# we have no parent, we must be root
# so mark the barrier complete
complete = True
# barrier is complete, send messages to children if any and return true
if complete:
for child in self.child_ranks:
self.comm.send(None, dest=child, tag=T.BARRIER)
# reset state for another barrier
self.barrier_started = False
self.barrier_up = False
self.barrier_replies = 0
return True
# barrier still not complete
return False
def bcast_abort(self):
self.abort = True
buf = G.ABORT
for i in range(self.size):
if (i != self.rank):
self.comm.send(buf, dest=i, tag=T.WORK_REQUEST)
self.logger.warn("abort message sent to %s" % i, extra=self.d)
def cleanup(self):
while True:
# start non-block barrier if we have no outstanding items
if not self.reduce_outstanding and \
not self.workreq_outstanding and \
self.token.send_req == MPI.REQUEST_NULL:
self.barrier_start()
# break the loop when non-blocking barrier completes
if self.barrier_test():
break
# send no work message for any work request that comes in
self.workreq_check(cleanup=True)
# clean up any outstanding reduction
if self.reduce_enabled:
self.reduce_check(cleanup=True)
# recv any incoming work reply messages
self.request_work(cleanup=True)
# check and recv any incoming token
self.token.check_and_recv()
# if we have an outstanding token, check if it has been recv'ed
# I don't think this is needed as there seem no side effect
if self.token.send_req != MPI.REQUEST_NULL:
if self.token.send_req.Test():
self.token.send_req = MPI.REQUEST_NULL
def workreq_check(self, cleanup=False):
""" for any process that sends work request message:
add the process to the requester list
if my work queue is not empty:
distribute the work evenly
else:
send "no work" message to each requester
reset the requester list to empty
"""
while True:
st = MPI.Status()
ret = self.comm.Iprobe(source=MPI.ANY_SOURCE,
tag=T.WORK_REQUEST,
status=st)
if not ret: # no work request, break out the loop
break
# we have work request message
rank = st.Get_source()
buf = self.comm.recv(source=rank, tag=T.WORK_REQUEST, status=st)
if buf == G.ABORT:
self.logger.warn("Abort request from rank %s" % rank,
extra=self.d)
self.abort = True
self.send_no_work(rank)
return
else:
self.logger.debug("receive work request from requestor [%s]" %
rank,
extra=self.d)
# add rank to requesters
self.requestors.append(rank)
# out of while loop
if not self.requestors:
return
else:
# first combine workq and work_buf, both of them are in memory
if len(self.workq_buf) > 0:
self.workq.extend(self.workq_buf)
self.workq_buf.clear()
# if in-memory workq is empty, get a batch of works from database
if len(self.workq) == 0 and hasattr(self, "workq_db"):
if len(self.workq_db) > 0:
workq, objs_size = self.workq_db.mget(G.memitem_threshold)
self.workq = deque(workq)
self.workq_db.mdel(G.memitem_threshold, objs_size)
self.logger.debug(
"have %s requesters, with %s work items in queue" %
(len(self.requestors), len(self.workq)),
extra=self.d)
# have work requesters
if self.qsize() == 0 or cleanup:
for rank in self.requestors:
self.send_no_work(rank)
else:
# we do have work
self.send_work_to_many()
self.requestors = []
def spread_counts(self, rcount, wcount):
"""
@rcount: # of requestors
@wcount: # of work items
@return: spread it evenly among all requesters
case 1: wcount == rcount:
base = 0
extra = wcount
each requestor get 1
case 2: wcount < rcount:
base = 0
extra = wcount
first "wcount" requester get 1
case 3: wcount > rcount:
is it possible?
"""
if self.split != "equal":
raise NotImplementedError
base = wcount // (rcount + 1) # leave self a base number of works
extra = wcount - base * (rcount + 1)
assert extra <= rcount
sizes = [base] * rcount
for i in range(extra):
sizes[i] += 1
return sizes
def send_no_work(self, rank):
""" send no work reply to someone requesting work"""
buf = {G.KEY: G.ABORT} if self.abort else {G.KEY: G.ZERO}
r = self.comm.isend(buf, dest=rank, tag=T.WORK_REPLY)
r.wait()
self.logger.debug("Send no work reply to %s" % rank, extra=self.d)
def send_work_to_many(self):
rcount = len(self.requestors)
wcount = len(self.workq)
sizes = self.spread_counts(rcount, wcount)
self.logger.debug("requester count: %s, work count: %s, spread: %s" %
(rcount, wcount, sizes),
extra=self.d)
for idx, dest in enumerate(self.requestors):
self.send_work(dest, sizes[idx])
def send_work(self, rank, witems):
"""
@dest - the rank of requester
@count - the number of work to send
"""
if witems <= 0:
self.send_no_work(rank)
return
# for termination detection
if (rank < self.rank) or (rank == self.token.src):
self.token.proc = G.BLACK
buf = None
# based on if it is memory or store-based
# we have different ways of constructing buf
sliced = list(itertools.islice(self.workq, 0, witems))
buf = {G.KEY: witems, G.VAL: sliced}
self.comm.send(buf, dest=rank, tag=T.WORK_REPLY)
self.logger.debug("%s work items sent to rank %s" % (witems, rank),
extra=self.d)
# remove (witems) of work items
# for DbStotre, all we need is a number, not the actual objects
# for KVStore, we do need the object list for its key value
# the "size" is a bit awkward use - we know the size after we do mget()
# however, it is not readily available when we do mdel(), so we keep
# previous data and pass it back in to save us some time.
#
for i in range(witems):
self.workq.popleft()
def request_work(self, cleanup=False):
if self.workreq_outstanding:
st = MPI.Status()
reply = self.comm.Iprobe(source=self.work_requested_rank,
tag=T.WORK_REPLY,
status=st)
if reply:
self.work_receive(self.work_requested_rank)
# flip flag to indicate we no longer waiting for reply
self.workreq_outstanding = False
# else:
# self.logger.debug("has req outstanding, dest = %s, no reply" %
# self.work_requested_rank, extra = self.d)
elif not cleanup:
# send request
dest = self.next_proc()
if dest == self.rank or dest == MPI.PROC_NULL:
# have no one to ask, we are done
return
buf = G.ABORT if self.abort else G.MSG
# blocking send
self.logger.debug("send work request to rank %s : %s" %
(dest, G.str[buf]),
extra=self.d)
self.comm.send(buf, dest, T.WORK_REQUEST)
self.workreq_outstanding = True
self.work_requested_rank = dest
def work_receive(self, rank):
""" when incoming work reply detected """
buf = self.comm.recv(source=rank, tag=T.WORK_REPLY)
if buf[G.KEY] == G.ABORT:
self.logger.debug("receive abort signal", extra=self.d)
self.abort = True
return
elif buf[G.KEY] == G.ZERO:
self.logger.debug("receive no work signal", extra=self.d)
return
else:
assert type(buf[G.VAL]) == list
self.workq.extend(buf[G.VAL])
def reduce(self, buf):
# copy data from user buffer
self.reduce_buf = copy(buf)
def reduce_check(self, cleanup=False):
"""
initiate and progress a reduce operation at specified interval,
ensure progress of reduction in background, stop reduction if cleanup flag is True
"""
if self.reduce_outstanding:
# if we have outstanding reduce, check message from children
# otherwise, check whether we should start new reduce
for child in self.child_ranks:
if self.comm.Iprobe(source=child, tag=T.REDUCE):
# receive message from child
# 'status' element is G.MSG_VALID or not
# the rest is opaque
inbuf = self.comm.recv(source=child, tag=T.REDUCE)
self.reduce_replies += 1
self.logger.debug("client data from %s: %s" %
(child, inbuf),
extra=self.d)
if inbuf['status'] == G.MSG_INVALID:
self.reduce_status = False
else:
self.reduce_status = True
# invoke user's callback to reduce user data
if hasattr(self.task, "reduce"):
self.task.reduce(self.reduce_buf, inbuf)
# check if we have gotten replies from all children
if self.reduce_replies == self.children:
# all children replied
# add our own contents to reduce buffer
# send message to parent if we have one
if self.parent_rank != MPI.PROC_NULL:
self.comm.send(self.reduce_buf, self.parent_rank, T.REDUCE)
else:
# we are the root, print results if we have valid data
if self.reduce_status and hasattr(self.task,
"reduce_report"):
self.task.reduce_report(self.reduce_buf)
# invoke callback on root to deliver final results
if hasattr(self.task, "reduce_finish"):
self.task.reduce_finish(self.reduce_buf)
# disable flag to indicate we got what we want
self.reduce_outstanding = False
else:
# we don't have an outstanding reduction
# determine if a new reduce should be started
# only bother checking if we think it is about time or
# we are in cleanup mode
start_reduce = False
time_now = MPI.Wtime()
time_next = self.reduce_time_last + self.reduce_time_interval
if time_now >= time_next or cleanup:
if self.parent_rank == MPI.PROC_NULL:
# we are root, kick it off
start_reduce = True
elif self.comm.Iprobe(source=self.parent_rank, tag=T.REDUCE):
# we are not root, check if parent sent us a message
# receive message from parent and set flag to start reduce
self.comm.recv(source=self.parent_rank, tag=T.REDUCE)
start_reduce = True
# it is critical that we don't start a reduce if we are in cleanup
# phase because we may have already started the non-blocking barrier
# just send an invalid message back to parent
if start_reduce and cleanup:
# avoid starting a reduce
start_reduce = False
# if we have parent, send invalid msg
if self.parent_rank != MPI.PROC_NULL:
self.reduce_status = G.MSG_INVALID
self.comm.send(self.reduce_buf, self.parent_rank, T.REDUCE)
if start_reduce:
# set flag to indicate we have a reduce outstanding
# and initiate state for a fresh reduction
self.reduce_time_last = time_now
self.reduce_outstanding = True
self.reduce_replies = 0
self.reduce_status = G.MSG_VALID
self.reduce_buf['status'] = G.MSG_VALID
# invoke callback to get input data
if hasattr(self.task, "reduce_init"):
self.task.reduce_init(self.reduce_buf)
# sent message to each child
for child in self.child_ranks:
self.comm.send(None, child, T.REDUCE)
def do_periodic_report(self, prefix="Circle report"):
delta = self.work_processed - self.report_processed
rate = int(delta / self.report_interval)
self.report_processed = self.work_processed
s = "\n%s on [rank: %s %s/%s] at %s\n" % \
(prefix, self.rank, self.host, self.pid, time.strftime("%Y-%m-%d %H:%M:%S"))
s += "\t{:<20}{:<10,}{:5}{:<20}{:<12,}\n".format(
"work queue size:", len(self.workq), "|", "work processed:",
self.work_processed)
s += "\t{:<20}{:<10,}{:5}{:<20}{:<10}\n".format(
"work delta:", delta, "|", "rate:", "%s /s" % rate)
print(s)
@staticmethod
def exit(code):
MPI.Finalize()
sys.exit(code)
class Test(unittest.TestCase):
""" Unit test for Circle """
def setUp(self):
dbname = "/tmp/test.db"
if os.path.exists(dbname):
os.remove(dbname)
self.db = DbStore(dbname)
self.db.put(FileItem("/tmp"))
self.db.put(FileItem("/tmp/1"))
self.db.put(FileItem("/tmp/2"))
def tearDown(self):
self.db.cleanup()
def test_dbstore_put(self):
self.assertEquals(self.db.size(), 3)
def test_dbstore_pop(self):
self.db.pop()
self.assertEquals(self.db.size(), 2)
self.db.pop()
self.db.pop()
self.assertEquals(self.db.size(), 0)
# what happens when db is empty?
self.db.pop()
self.assertEquals(self.db.size(), 0)
def test_dbstore_mput(self):
objs = [FileItem("/1/2"), FileItem("/3/4")]
self.db.mput(objs)
self.assertEquals(self.db.size(), 5)
def test_dbstore_mdel(self):
self.db.mdel(3)
self.assertEquals(self.db.size(), 0)
class Test(unittest.TestCase):
""" Unit test for Circle """
def setUp(self):
dbname = "/tmp/test.db"
if os.path.exists(dbname):
os.remove(dbname)
self.db = DbStore(dbname)
self.db.put(FileItem("/tmp"))
self.db.put(FileItem("/tmp/1"))
self.db.put(FileItem("/tmp/2"))
def tearDown(self):
self.db.cleanup()
def test_dbstore_put(self):
self.assertEquals(self.db.size(), 3)
def test_dbstore_pop(self):
self.db.pop()
self.assertEquals(self.db.size(), 2)
self.db.pop()
self.db.pop()
self.assertEquals(self.db.size(), 0)
# what happens when db is empty?
self.db.pop()
self.assertEquals(self.db.size(), 0)
def test_dbstore_mput(self):
objs = [FileItem("/1/2"), FileItem("/3/4")]
self.db.mput(objs)
self.assertEquals(self.db.size(), 5)
def test_dbstore_mdel(self):
self.db.mdel(3)
self.assertEquals(self.db.size(), 0)
