def syncAndApply(self):
if mpi.rank == 0:
self.dataLock.acquire(
) # this lock probably isn't necessary yet
try:
for i in range(len(self.cursorObjects)):
self.cursors[i] = self.cursorObjects[i][0].getPos()
except:
traceback.print_exc()
finally:
self.dataLock.release()
if mpi.rank == 0:
resultCursors = mpi.bcast(self.cursors)
else:
self.resultCursors = mpi.bcast()
if mpi.rank != 0:
for i in range(len(self.cursorObjects)):
if len(self.resultCursors) > i:
# access: cursorObjects[i][localcopies]
for j in range(len(self.cursorObjects[i])
): # set for each local copy
self.cursorObjects[i][j].setPos(
self.resultCursors[i][0],
self.resultCursors[i][1])
def iteration(self):
mpi.bcast(self.phi)
mpi.scatter(self.rootbufs.x, self.nodebufs.x)
self.infer_coefficients()
self.learn_basis()
if self.t > 0 and self.t % self.update_coefficient_statistics_interval == 0:
self.update_coefficient_statistics()
def syncAndApply(self):
tmpQueue = None
if mpi.rank == 0:
self.dataLock.acquire() # this lock probably isn't necessary
try:
tmpQueue = self.queue
self.queue = []
except:
traceback.print_exc()
finally:
self.dataLock.release()
if mpi.rank == 0 and len(tmpQueue) > 0:
print "Bcasting:", tmpQueue
#print "mpi barrier", mpi.rank
#mpi.barrier()
#print "bcast:", mpi.rank
if mpi.rank == 0:
resultQueue = mpi.bcast(tmpQueue)
else:
resultQueue = mpi.bcast()
if len(resultQueue) > 0:
print "Bcasting recv:", resultQueue, mpi.rank
for panningObj in self.panningObjects:
for result in resultQueue:
x = int((result[0] - self.lastX) * self.width)
y = int((result[1] - self.lastY) * self.height)
print "panning, ", mpi.rank, ":", x, y
panningObj.pan(x, y)
self.lastX = result[0]
self.lastY = result[1]
def parallelRunTest(self):
if mpi.rank == 0:
st = "Hello World!!"
recvSt = mpi.bcast(st)
if recvSt != "Hello World!!":
self.fail("bcast test failed on short string")
longStr = ""
for i in range(2048):
longStr += "Foo"
longStr += str(i)
recvSt = mpi.bcast(longStr)
if recvSt != longStr:
self.fail( "bcast test failed on long string")
else:
recvSt = mpi.bcast()
if recvSt != "Hello World!!":
self.fail("Received incorrect string in broadcast")
longStr = ""
for i in range(2048):
longStr += "Foo"
longStr += str(i)
recvSt = mpi.bcast( )
if recvSt != longStr:
self.fail( "bcast test failed on long string")
return
def syncAndApply(self):
tmpQueue = None
if mpi.rank == 0:
self.dataLock.acquire() # this lock probably isn't necessary
try:
tmpQueue = self.queue
self.queue = []
except:
traceback.print_exc()
finally:
self.dataLock.release()
if mpi.rank == 0 and len(tmpQueue) > 0:
print "Bcasting:", tmpQueue
#print "mpi barrier", mpi.rank
#mpi.barrier()
#print "bcast:", mpi.rank
if mpi.rank == 0:
resultQueue = mpi.bcast(tmpQueue)
else:
resultQueue = mpi.bcast()
if len(resultQueue) > 0:
print "Bcasting recv:", resultQueue, mpi.rank
for panningObj in self.panningObjects:
for result in resultQueue:
x = int((result[0] - self.lastX) * self.width)
y = int((result[1] - self.lastY) * self.height)
print "panning, ", mpi.rank, ":", x, y
panningObj.pan( x, y)
self.lastX = result[0]
self.lastY = result[1]
def do_M_step(self, ess_list):
# CPU 0
if mpi.rank==0:
mus=zeros((self.node_size,1), 'd')
kappas=zeros(self.node_size, 'd')
ess_r, ess_w=ess_list.pop()
for i in range(0, len(ess_list)):
r, w=ess_list[i]
ess_r+=r
ess_w+=w
for i in range(0, self.node_size):
r=ess_r[i]
w=ess_w[i]
norm_r=norm(r)
print "do_M_step (%i): r=%s, w=%s, norm_r=%s" % (i,r,w,norm_r)
if w == 0:
print "WARNING: There is no data to estimate mu and kappa from"
kappas[i]=self.kappas[i]
mus[i]=self.mus[i]
else:
mu_coords=r/norm_r
kappas[i]=estimate_kappa(w,r,mu_coords)
mus[i]=to_radian(mu_coords)
vm_list, samplers=self._make_vm_list(mus, kappas, self.node_size)
self.mus, self.kappas, self.vm_list, self.samplers=\
mpi.bcast((mus, kappas, vm_list, samplers))
# Other CPUs
else:
self.mus, self.kappas, self.vm_list, self.samplers=mpi.bcast()
self.ess_list=[self._get_empty_ess()]
def iteration(self):
mpi.bcast(self.phi)
mpi.scatter(self.rootbufs.x, self.nodebufs.x)
self.infer_coefficients()
self.learn_basis()
if self.t > 0 and self.t % self.update_coefficient_statistics_interval == 0:
self.update_coefficient_statistics()
def parallelRunTest(self):
if mpi.rank == 0:
st = "Hello World!!"
recvSt = mpi.bcast(st)
if recvSt != "Hello World!!":
self.fail("bcast test failed on short string")
longStr = ""
for i in range(2048):
longStr += "Foo"
longStr += str(i)
recvSt = mpi.bcast(longStr)
if recvSt != longStr:
self.fail("bcast test failed on long string")
else:
recvSt = mpi.bcast()
if recvSt != "Hello World!!":
self.fail("Received incorrect string in broadcast")
longStr = ""
for i in range(2048):
longStr += "Foo"
longStr += str(i)
recvSt = mpi.bcast()
if recvSt != longStr:
self.fail("bcast test failed on long string")
return
def raw_input(self, prompt=""):
"""
On the master node:
1). Write a prompt and read a line.
2). Broadcast the Line or Terminate
3). Broadcast the Line
a). First, get the length of the line and broadcast it
b). Broadcast the line data itself
4). Terminate
a). If the user types the control sequence to exit
EOFError is raised.
b). Catch EOFError and broadcast length, this time broadcasting negative
c). All nodes check for length < 0 and raise an EOFError.
"""
if( self.rank == 0 ):
try:
data = raw_input(prompt)
except EOFError:
length = mpi.bcast( -1, 1, mpi.MPI_INT, 0, mpi.MPI_COMM_WORLD )
self.write("\n")
raise
length = mpi.bcast( len(data), 1, mpi.MPI_INT, 0, mpi.MPI_COMM_WORLD )
data = mpi.bcast(data,length[0], mpi.MPI_CHAR, 0, mpi.MPI_COMM_WORLD )
else:
length = mpi.bcast( 0, 1, mpi.MPI_INT, 0, mpi.MPI_COMM_WORLD )
if (length[0] < 0):
raise EOFError
data = mpi.bcast("",length[0], mpi.MPI_CHAR, 0, mpi.MPI_COMM_WORLD )
s = ""
for e in data:
s += "".join(e)
return s
def _globalValue(self, i, method):
dom = self.domainForID(i)
result = None
if rank == dom:
j = self.globalIDs[i]
result = method(j)
mpi.bcast(result, dom)
return result
def wrapped_method(self, *args, **kwargs):
mpi.bcast((expression, args, kwargs))
# local execution
ret = method(self, *args, **kwargs)
# get return values from all cpus
ret = mpi.gather(ret)
if not init:
# filter object creation which must not return
return ret
def meshScales(xnodes, xmin, xmax):
nx = len(xnodes)
xsort = list(xnodes)
xsort.sort()
dx = ([(0.5 * (xsort[i + 1] + xsort[i]) - 0.5 * (xsort[i] + xsort[i - 1]))
for i in xrange(1, nx - 1)] + [0.5 * (xsort[0] + xsort[1]) - xmin] +
[xmax - 0.5 * (xsort[-2] + xsort[-1])])
dxmin = mpi.bcast(0.5 * min(dx))
dxmax = mpi.bcast(0.5 * max(dx))
return dxmin, dxmax
def main( local_comm ):
name = "test"
local_rank = mpi.comm_rank( local_comm )
local_size = mpi.comm_size( local_comm )
print "%s (%s,%s): creating root communicator!"%(name,local_rank,local_size)
sys.stdout.flush()
if local_rank == 0:
tmp_comm = mpi.comm_split( mpi.MPI_COMM_WORLD, 5, 0 )
print "%s (%s,%s): joined root communicator %s"%(name,local_rank,local_size,tmp_comm)
sys.stdout.flush()
ncomponents = mpi.comm_size( tmp_comm )
else:
tmp_comm = mpi.comm_split( mpi.MPI_COMM_WORLD, 6, 0 )
print "%s (%s,%s): Joined non-root communicator %s"%(name,local_rank,local_size,tmp_comm)
sys.stdout.flush()
ncomponents = 0
print "%s (%s,%s): Distributing root communicator!"%(name,local_rank,local_size)
ncomponents = mpi.bcast( ncomponents, 1, mpi.MPI_INT, 0, local_comm )
ncomponents = ncomponents[0]
print "%s (%s,%s): Distributed root communicator!"%(name,local_rank,local_size)
# Get total number of components and distribute to every node:
# ncomponents = mpi.allreduce( ncomponents, 1, mpi.MPI_INT, mpi.MPI_SUM, root_comm )
#print "%s (%s,%s): Root Comm = %s"%(name,local_rank,local_size,root_comm)
#ncomponents = mpi.comm_size( root_comm )
print "%s(%s,%s): ncomponents = %s"%(name, local_rank, local_size, ncomponents )
def randomDistribute3d(thisDomain, # domain ID to be calculated
nDomains, # total number of domains
nNodesGlobal, # global number of nodes in this nodelist
xyzRangeTotal): # total simulation volume
assert thisDomain >= 0 and thisDomain < nDomains
assert nDomains > 0
import random
g = random.Random()
globalNodeIDs = []
nodePositions = []
for globalNodeID in xrange(0, nNodesGlobal):
mpi.barrier()
domain0 = g.randint(0, nDomains - 1)
domain = mpi.bcast(domain0)
if domain == thisDomain:
globalNodeIDs.append(globalNodeID)
nodePositions.append(Vector3d(g.uniform(xyzRangeTotal[0][0],
xyzRangeTotal[1][0]),
g.uniform(xyzRangeTotal[0][1],
xyzRangeTotal[1][1]),
g.uniform(xyzRangeTotal[0][2],
xyzRangeTotal[1][2])))
assert len(globalNodeIDs) == len(nodePositions)
assert mpi.allreduce(len(globalNodeIDs), mpi.SUM) == nNodesGlobal
return globalNodeIDs, nodePositions
def randomDistribute(
thisDomain, # domain ID to be calculated
nDomains, # total number of domains
nNodesGlobal, # global number of nodes in this nodelist
xRangeTotal): # total simulation volume
assert thisDomain >= 0 and thisDomain < nDomains
assert nDomains > 0
import random
g = random.Random()
globalNodeIDs = []
xNodePositions = []
dxNodes = (xRangeTotal[1] - xRangeTotal[0]) / nNodesGlobal
for globalNodeID in xrange(0, nNodesGlobal):
mpi.barrier()
domain0 = g.randint(0, nDomains - 1)
domain = mpi.bcast(domain0)
if domain == thisDomain:
globalNodeIDs.append(globalNodeID)
xNodePositions.append(xRangeTotal[0] +
(globalNodeID + 0.5) * dxNodes)
assert len(globalNodeIDs) == len(xNodePositions)
assert mpi.allreduce(len(globalNodeIDs), mpi.SUM) == nNodesGlobal
return globalNodeIDs, xNodePositions
def checkHashConsistency(myHashes, sharedIDs, allowEmptyComm):
msg = "ok"
myHashSet = set(myHashes)
for sendProc in xrange(numDomains):
theirHashSet = mpi.bcast(myHashSet, root=sendProc)
if sendProc != mpi.rank:
commonHashes = myHashSet.intersection(theirHashSet)
if len(commonHashes) > 0 and (not sendProc in neighborDomains):
msg = "Missed a neighbor domain : %i %i : %i" % (
mpi.rank, sendProc, len(commonHashes))
elif len(commonHashes) == 0 and (
sendProc in neighborDomains) and not allowEmptyComm:
msg = "Erroneously communicating between domains : %i %i" % (
mpi.rank, sendProc)
elif len(commonHashes) > 0:
k = neighborDomains.index(sendProc)
if len(commonHashes) != len(sharedIDs[k]):
msg = "Size of shared elements does not match: %i %i : %i %i" % (
mpi.rank, sendProc, len(commonHashes),
len(sharedIDs[k]))
else:
sharedHashes = set([myHashes[i] for i in sharedIDs[k]])
if sharedHashes != commonHashes:
msg = ("Set of common hashes does not match: " +
str(sharedHashes) + " != " +
str(commonHashes))
msg = allReduceMsg(msg)
if msg != "ok":
return msg
return msg
def set_cpd(self, new_cpd=None):
if mpi.rank==0:
assert(not new_cpd is None)
cpd=normalize_cpd(new_cpd)
# Get rid of very small values that lead to log overflow
cpd=clip(cpd, _MIN_TRANSITION, 1000)
# Calculate log(cpd) for speed reasons
log_cpd=log(cpd)
cum_cpd=cumsum(cpd, -1)
# Avoid bisect errors
cum_cpd[...,-1]=2.0
self.cpd, self.log_cpd, self.cum_cpd=mpi.bcast((cpd, log_cpd, cum_cpd))
if __debug__:
self._test_cpd(self.cpd, self.cpd_shape)
else:
self.cpd, self.log_cpd, self.cum_cpd=mpi.bcast()
def __init__(self, skip_checks=True):
import mpi
if mpi.rank == 0:
finder.__init__(self, skip_checks)
else:
finder.__init__(self, skip_checks, False)
self._syspath, self._cache = mpi.bcast((self._syspath, self._cache))
def __init__(self,skip_checks=True):
import mpi
if mpi.rank == 0:
finder.__init__(self,skip_checks)
else:
finder.__init__(self,skip_checks,False)
self._syspath,self._cache = mpi.bcast((self._syspath,self._cache))
def set_cpd(self, new_cpd=None):
if mpi.rank == 0:
assert (not new_cpd is None)
cpd = normalize_cpd(new_cpd)
# Get rid of very small values that lead to log overflow
cpd = clip(cpd, _MIN_TRANSITION, 1000)
# Calculate log(cpd) for speed reasons
log_cpd = log(cpd)
cum_cpd = cumsum(cpd, -1)
# Avoid bisect errors
cum_cpd[..., -1] = 2.0
self.cpd, self.log_cpd, self.cum_cpd = mpi.bcast(
(cpd, log_cpd, cum_cpd))
if __debug__:
self._test_cpd(self.cpd, self.cpd_shape)
else:
self.cpd, self.log_cpd, self.cum_cpd = mpi.bcast()
def randomString():
l = range(20)
random.shuffle(l)
result = ""
for x in l:
result += str(x)
result = mpi.bcast(result, 0)
return result
def allReduceMsg(msg):
if msg == "ok":
badProc = numDomains
else:
badProc = rank
badProc = mpi.allreduce(badProc, mpi.MIN)
if badProc != numDomains:
msg = mpi.bcast(msg, root=badProc)
return msg
def __init__(self,
fileName, # Name of the file
meshName, # Name of mesh variable in file
rho0, # Initial mass density
serialFile = True, # Should this be treated as a serial file or broken up in parallel?
nNodePerh = 2.01, # number of nodes per smoothing scale
SPH = False, # Force round H tensors
scale = 1.0): # Optionally scale the coordinates by some factor
self.x, self.y, self.z, self.m, self.H = [], [], [], [], []
self.rho0 = rho0
if rank == 0 or (not serialFile):
# Read the file to a set of positions, volumes, and H's.
pos = vector_of_Vector3d()
vol = vector_of_double()
H = vector_of_SymTensor3d()
readSiloPolyMesh(fileName, meshName, pos, vol, H)
print "Read %i points from %s." % (len(pos), fileName)
assert len(pos) == len(vol) == len(H)
self.x = [scale * x.x for x in pos]
self.y = [scale * x.y for x in pos]
self.z = [scale * x.z for x in pos]
self.m = [scale**3 * x*rho0 for x in vol]
self.H = [x/scale for x in H]
self.x = mpi.bcast(self.x, root=0)
self.y = mpi.bcast(self.y, root=0)
self.z = mpi.bcast(self.z, root=0)
self.m = mpi.bcast(self.m, root=0)
self.H = mpi.bcast(self.H, root=0)
# Initialize the base class, which will break up the serial node distribution
# for parallel cases if required.
NodeGeneratorBase.__init__(self, serialFile,
self.x, self.y, self.z, self.m, self.H)
# If SPH has been specified, make sure the H tensors are round.
if SPH:
self.makeHround()
return
def gatherarray(a, root=0, othersempty=0, bcast=0):
if not lparallel: return a
# --- First check if input can be converted to an array
isinputok = 1
try:
if type(a) in [type(0.), type(0)]:
a = array([a])
else:
a = array(a)
except:
isinputok = 0
# --- Make sure the input is ok on all of the processors
isinputok = globalmin(isinputok)
# --- If any returned an error, then all exit (to avoid a deadlock)
if not isinputok:
print "Object could not be converted to an array"
return None
# --- Now, actually gather the array.
# --- The check of whether the result is ok may not be needed.
try:
result = gather(a, root)
isinputok = 1
except:
isinputok = 0
# --- Make sure again that the input is ok on all of the processors
isinputok = globalmin(isinputok)
if not isinputok:
print "Error in gather object"
if type(a) == ArrayType: print "Object has shape ", shape(a)
return None
# --- All processors but root simply return either the input argument
# --- or an empty array unless the result is to be broadcast
if me != root and not bcast:
if othersempty: return zeros(len(shape(a)) * [0], a.typecode())
else: return a
# --- Root processor reshapes the data, removing the first dimension
# --- Do it bit by bit since the data passed by the other processors may
# --- not be all the same size.
if me == root:
newlen = 0
for i in range(npes):
newlen = newlen + shape(result[i])[0]
newshape = list(shape(result[0]))
newshape[0] = newlen
newresult = zeros(newshape, a.typecode())
i1 = 0
for i in range(npes):
i2 = i1 + shape(result[i])[0]
newresult[i1:i2, ...] = result[i]
i1 = i2
else:
newresult = 0
if bcast: newresult = mpi.bcast(newresult, root)
return newresult
def restoreState(self, cacheFileName):
def readNodeData(f, iproc):
pos = f.readObject("proc%06i/pos" % iproc)
m = f.readObject("proc%06i/m" % iproc)
H = f.readObject("proc%06i/H" % iproc)
vol = f.readObject("proc%06i/vol" % iproc)
surface = f.readObject("proc%06i/surface" % iproc)
return pos, m, H, vol, surface
if cacheFileName is None:
return False
if os.path.splitext(cacheFileName) != ".silo":
cacheFileName += ".silo"
result = False
if mpi.rank == 0:
result = (cacheFileName and os.path.exists(cacheFileName))
result = mpi.bcast(result, root=0)
if result:
print "Restoring MedialGenerator state from %s" % cacheFileName
if mpi.rank == 0:
f = SiloFileIO(cacheFileName, Read)
numGeneratingProcs = f.readObject("numGeneratingProcs")
# Decide how to divide the generating domains between our current processes.
n0 = numGeneratingProcs / mpi.procs
remainder = numGeneratingProcs % mpi.procs
for iproc in xrange(mpi.procs):
if iproc >= numGeneratingProcs:
imin, imax = 0, 0
else:
imin = iproc * n0 + min(iproc, remainder)
imax = imin + n0
if iproc < remainder:
imax += 1
pos, m, H, vol, surface = [], [], [], [], []
for igenproc in xrange(imin, imax):
posi, mi, Hi, voli, surfacei = readNodeData(
f, igenproc)
pos += posi
m += mi
H += Hi
vol += voli
surface += surfacei
if iproc == 0:
self.pos, self.m, self.H, self.vol, self.surface = pos, m, H, vol, surface
else:
mpi.send((pos, m, H, vol, surface), dest=iproc)
f.close()
else:
self.pos, self.m, self.H, self.vol, self.surface = mpi.recv(
source=0)[0]
return result
def setUp(self):
global itest
self.testext = "Random%s_%idomain" % (randomString(), mpi.procs)
eos = GammaLawGasMKS(5.0/3.0, 1.0)
self.nodes = makeFluidNodeList("test nodes %i" % itest, eos,
numInternal = nperdomain,
nPerh = 2.01,
hmin = 1.0e-5,
hmax = 0.3)
itest += 1
self.pos = self.nodes.positions()
self.H = self.nodes.Hfield()
# Figure out the domain bounding volumes.
dxproc = (x1 - x0)/nxproc
dyproc = (y1 - y0)/nxproc
ixproc = rank % nxproc
iyproc = rank / nxproc
xminproc = Vector(x0 + ixproc*dxproc, y0 + iyproc*dyproc)
xmaxproc = Vector(x0 + (ixproc + 1)*dxproc, y0 + (iyproc + 1)*dyproc)
# Randomly seed the generators. We choose from random cells in order
# to keep nodes from getting too close together.
xynodes_all = []
occupiedCells = set()
for k in xrange(n):
i = rangen.randint(0, ncell)
while i in occupiedCells:
i = rangen.randint(0, ncell)
ix = i % nxcell
iy = i / nxcell
xynodes_all.append(Vector((ix + 0.5)*dxcell, (iy + 0.5)*dycell))
occupiedCells.add(i)
assert len(occupiedCells) == n
xynodes_all = mpi.bcast(xynodes_all)
xynodes = [v for v in xynodes_all if testPointInBox(v, xminproc, xmaxproc)]
dxavg = (x1 - x0)/nx
dyavg = (y1 - y0)/ny
self.dxmin = dxavg
assert mpi.allreduce(len(xynodes), mpi.SUM) == n
# Now we can set the node conditions.
self.nodes.numInternalNodes = len(xynodes)
for i in xrange(len(xynodes)):
self.pos[i] = xynodes[i]
self.H[i] = SymTensor(1.0/(2.0*dxavg), 0.0,
0.0, 1.0/(2.0*dyavg))
self.nodes.neighbor().updateNodes()
# Fix up the H's.
iterateThoseHs(self.nodes)
return
def setUp(self):
nxperdomain = nx / numDomains
eos = GammaLawGasMKS(5.0 / 3.0, 1.0)
self.nodes = makeFluidNodeList("test nodes",
eos,
numInternal=nxperdomain,
nPerh=2.01)
pos = self.nodes.positions()
H = self.nodes.Hfield()
# Generate initial positions, and split them up between domains appropriately.
gap = 0.9
dxavg = (x1 - x0 - gap) / nx
xnodes = [x0 + (i + 0.5) * dxavg for i in xrange(nx / 2)] + [
0.5 * (x0 + x1 + gap) + (i + 0.5) * dxavg for i in xrange(nx / 2)
]
xnodes.sort()
self.dxmin, self.dxmax = meshScales(xnodes, x0, x1)
for proc in xrange(numDomains):
xnodes[proc * nxperdomain:(proc + 1) * nxperdomain] = mpi.bcast(
xnodes[proc * nxperdomain:(proc + 1) * nxperdomain])
xnodes = xnodes[rank * nxperdomain:(rank + 1) * nxperdomain]
assert len(xnodes) == nxperdomain
assert mpi.allreduce(len(xnodes), mpi.SUM) == nx
# We now have the positions for each domain appropriately divided, so shuffle
# the local positions.
#random.shuffle(xnodes)
# Now we can set the node conditions.
for i in xrange(nxperdomain):
pos[i] = Vector(xnodes[i])
H[i] = SymTensor(1.0 / (2.0 * dxavg))
self.nodes.neighbor().updateNodes()
# Iterate the H tensors to somthing reasonable.
db = DataBase()
db.appendNodeList(self.nodes)
for bc in bclist:
bc.setAllGhostNodes(db)
for bc in bclist:
bc.finalizeGhostBoundary()
db = DataBase()
db.appendNodeList(self.nodes)
vecbound = vector_of_Boundary()
for bc in bclist:
vecbound.append(bc)
WT = TableKernel(BSplineKernel(), 1000)
smooth = SPHSmoothingScale()
iterateIdealH(db, vecbound, WT, smooth)
return
def __import_module__(partname, fqname, parent):
try:
return sys.modules[fqname]
except KeyError:
pass
fp = None # module's file
pathname = None # module's location
stuff = None # tuple of (suffix,mode,type) for the module
ierror = False # are we propagating an import error from rank 0?
# Start with the lookup on rank 0. The other processes will be waiting
# on a broadcast, so we need to send one even if we're bailing out due
# to an import error.
if mpi.rank == 0:
try:
fp, pathname, stuff = imp.find_module(partname,
parent and parent.__path__)
except ImportError:
ierror = True
return None
finally:
pathname,stuff,ierror = mpi.bcast((pathname,stuff,ierror))
else:
pathname,stuff,ierror = mpi.bcast((pathname,stuff,ierror))
if ierror:
return None
# If imp.find_module returned an open file to rank 0, then we should
# open the corresponding file for this process too.
if stuff and stuff[1]:
fp = open(pathname,stuff[1])
try:
m = imp.load_module(fqname, fp, pathname, stuff)
finally:
if fp: fp.close()
if parent:
setattr(parent, partname, m)
return m
def __import_module__(partname, fqname, parent):
try:
return sys.modules[fqname]
except KeyError:
pass
fp = None # module's file
pathname = None # module's location
stuff = None # tuple of (suffix,mode,type) for the module
ierror = False # are we propagating an import error from rank 0?
# Start with the lookup on rank 0. The other processes will be waiting
# on a broadcast, so we need to send one even if we're bailing out due
# to an import error.
if mpi.rank == 0:
try:
fp, pathname, stuff = imp.find_module(partname, parent
and parent.__path__)
except ImportError:
ierror = True
return None
finally:
pathname, stuff, ierror = mpi.bcast((pathname, stuff, ierror))
else:
pathname, stuff, ierror = mpi.bcast((pathname, stuff, ierror))
if ierror:
return None
# If imp.find_module returned an open file to rank 0, then we should
# open the corresponding file for this process too.
if stuff and stuff[1]:
fp = open(pathname, stuff[1])
try:
m = imp.load_module(fqname, fp, pathname, stuff)
finally:
if fp: fp.close()
if parent:
setattr(parent, partname, m)
return m
def integrate(self, rectangles, function):
# equivalent to mpi.WORLD.bcast(n,0) or rather a
# C call to MPI_Bcast(MPI_COMM_WORLD,n,0,&status)
n = mpi.bcast(rectangles)
h = 1.0/n
sum = 0.0
for i in range(mpi.rank+1,n+1,mpi.procs):
x = h * (i-0.5)
sum = sum + function(x)
myAnswer = h * sum
answer = mpi.allreduce(myAnswer,mpi.SUM)
return answer
def integrate(self, rectangles, function):
# equivalent to mpi.WORLD.bcast(n,0) or rather a
# C call to MPI_Bcast(MPI_COMM_WORLD,n,0,&status)
n = mpi.bcast(rectangles)
h = 1.0 / n
sum = 0.0
for i in range(mpi.rank + 1, n + 1, mpi.procs):
x = h * (i - 0.5)
sum = sum + function(x)
myAnswer = h * sum
answer = mpi.allreduce(myAnswer, mpi.SUM)
return answer
def fromLabel(
cls,
fileName, # Name of Abaqus file.
materialLabel, # Name of the material we're generating from in the file
elsetLabel, # Name of the element set we're generating from in the file
serialFile=True, # Should this be treated as a serial file or broken up in parallel?
nNodePerh=2.01, # number of nodes per smoothing scale
SPH=False, # Force round H tensors
scale=1.0): # Optionally scale the coordinates by some factor
"""Construct an Abaqus NodeGenerator for a single element set."""
lines = []
vertices = {}
if rank == 0 or (not serialFile):
f = open(fileName, "r")
lines = f.readlines()
f.close()
# Find and read the vertex coordinates.
iline = 0
while (iline < len(lines) and lines[iline][:5] != "*NODE"):
iline += 1
if iline == len(lines):
raise RuntimeError, "Unable to find *NODE specification in %s" % fileName
iline += 1
while lines[iline][0] != "*":
stuff = lines[iline].split(",")
assert len(stuff) == 4
i = int(stuff[0])
xi, yi, zi = (float(stuff[j]) for j in xrange(1, 4))
vertices[i] = scale * Vector(xi, yi, zi)
iline += 1
print "AbaqusNodeGenerator : Read %i vertices from file %s" % (
len(vertices), fileName)
lines = mpi.bcast(lines, root=0)
vertices = mpi.bcast(vertices, root=0)
return cls(lines, vertices, materialLabel, elsetLabel, serialFile,
nNodePerh, SPH, scale)
def checkConsistentCommInfo(myHashes, sharedIDs):
msg = "ok"
positions = [
quantizedPosition(hashi, xmin, xmax) for hashi in myHashes
]
for sendProc in xrange(numDomains):
numChecks = mpi.bcast(len(neighborDomains), root=sendProc)
assert mpi.allreduce(numChecks,
mpi.MIN) == mpi.allreduce(numChecks, mpi.MAX)
for k in xrange(numChecks):
if rank == sendProc:
ksafe = k
else:
ksafe = 0
recvProc = mpi.bcast(neighborDomains[ksafe], root=sendProc)
recvHashes = mpi.bcast([myHashes[i] for i in sharedIDs[ksafe]],
root=sendProc)
recvPos = mpi.bcast([positions[i] for i in sharedIDs[ksafe]],
root=sendProc)
if rank == recvProc:
assert sendProc in neighborDomains
kk = neighborDomains.index(sendProc)
assert kk < len(sharedIDs)
if not ([myHashes[i]
for i in sharedIDs[kk]] == recvHashes):
msg = (
"Shared indices don't match %i %i\n %s != %s\n %s\n %s"
% (rank, sendProc,
str([myHashes[i]
for i in sharedIDs[kk]]), recvHashes, [
str(positions[i])
for i in sharedIDs[kk]
], [str(xi) for xi in recvPos]))
msg = allReduceMsg(msg)
if msg != "ok":
return msg
return msg
def parallelRunTest(self):
# -----------------------------------------------
# See if we can broadcast a python object
# -----------------------------------------------
original = [1,2,3]
if mpi.rank == 0:
result = mpi.bcast(original)
else:
result = mpi.bcast(None)
if original != result:
self.fail('Bcast of pickled list fails')
# -----------------------------------------------
# See if we can broadcast an advanced python object
# -----------------------------------------------
if mpi.rank == 0:
val = something(33)
else:
val = None
received = mpi.bcast(val)
if received.x != 33:
self.fail('Bcast fails with advanced object')
return
def syncAndApply(self):
if mpi.rank == 0:
self.dataLock.acquire() # this lock probably isn't necessary yet
try:
for i in range(len(self.cursorObjects)):
self.cursors[i] = self.cursorObjects[i][0].getPos()
except:
traceback.print_exc()
finally:
self.dataLock.release()
if mpi.rank == 0:
resultCursors = mpi.bcast(self.cursors)
else:
self.resultCursors = mpi.bcast()
if mpi.rank != 0:
for i in range(len(self.cursorObjects)):
if len(self.resultCursors) > i:
# access: cursorObjects[i][localcopies]
for j in range(len(self.cursorObjects[i])): # set for each local copy
self.cursorObjects[i][j].setPos( self.resultCursors[i][0], self.resultCursors[i][1])
def parallelRunTest(self):
# -----------------------------------------------
# See if we can broadcast a python object
# -----------------------------------------------
original = [1, 2, 3]
if mpi.rank == 0:
result = mpi.bcast(original)
else:
result = mpi.bcast(None)
if original != result:
self.fail('Bcast of pickled list fails')
# -----------------------------------------------
# See if we can broadcast an advanced python object
# -----------------------------------------------
if mpi.rank == 0:
val = something(33)
else:
val = None
received = mpi.bcast(val)
if received.x != 33:
self.fail('Bcast fails with advanced object')
return
def parallelRunTest(self):
myList = [ 0,0,0,0,0,0 ]
myList[0] = 42
myList[1] = "Hello"
myList[2] = ["Another list", 2]
myList[3] = ("A tuple", 2)
myList[4] = 4+5j
myList[5] = 3.14159
for x in range(6):
mpi.barrier()
z = mpi.bcast( myList[x],0 )
if z != myList[x]:
self.fail( "Broadcast test 2 failed on test " + str(x))
return
def parallelRunTest(self):
myList = [0, 0, 0, 0, 0, 0]
myList[0] = 42
myList[1] = "Hello"
myList[2] = ["Another list", 2]
myList[3] = ("A tuple", 2)
myList[4] = 4 + 5j
myList[5] = 3.14159
for x in range(6):
mpi.barrier()
z = mpi.bcast(myList[x], 0)
if z != myList[x]:
self.fail("Broadcast test 2 failed on test " + str(x))
return
def VFSurfaceGenerator(filename,
rho,
nx,
nNodePerh=2.01,
SPH=False,
scaleFactor=1.0,
refineFactor=0,
rejecter=None):
surface = None
if mpi.rank == 0:
surface = readPolyhedronOBJ(filename)
if refineFactor != 0:
surface = refinePolyhedron(surface, refineFactor)
if scaleFactor != 1.0:
surface *= scaleFactor
surface = mpi.bcast(surface, 0)
return PolyhedralSurfaceGenerator(surface, rho, nx, nNodePerh, SPH,
rejecter)
def __init__(self,
serialInitialization,
*vars):
if serialInitialization:
ntot = len(vars[0])
minGlobalID, maxGlobalID = self.globalIDRange(ntot)
self.globalIDs = range(minGlobalID, maxGlobalID)
self._cullVars(minGlobalID, maxGlobalID, *vars)
else:
ntot = 0
for proc in xrange(mpi.procs):
if mpi.rank == proc:
self.globalIDs = range(ntot, ntot + len(vars[0]))
ntot += mpi.bcast(len(vars[0]), proc)
return
def plotPolygonalMesh(mesh, persist=False):
polylocal = []
for izone in xrange(mesh.numZones):
zone = mesh.zone(izone)
polylocal.append([mesh.node(i).position() for i in zone.nodeIDs])
polylocal[-1].append(polylocal[-1][0])
assert len(polylocal) == mesh.numZones
p = generateNewGnuPlot(persist)
for sendProc in xrange(mpi.procs):
polys = mpi.bcast(polylocal, root=sendProc)
for poly in polys:
p.replot(
Gnuplot.Data([x.x for x in poly], [x.y for x in poly],
with_="lines lt %i lw 2" % 1,
title=None,
inline=True))
return p
def readField2String(materialName, fieldName, file):
delimiter = "$"
result = ""
if mpi.rank == 0:
found = False
for line in file:
vals = line.split(delimiter)
if vals[0][0] != "#":
if (vals[0] == materialName and vals[1] == fieldName):
n = int(vals[2])
result = vals[3:-1]
assert len(result) == n
found = True
break
if not found:
raise ValueError, "Unable to find %s %s" % (materialName,
fieldName)
result = mpi.bcast(result, 0)
return result
def __call__(self, x, y, z, m, H):
n = len(x)
assert len(y) == n
assert len(z) == n
assert len(m) == n
assert len(H) == n
# We'll take advantage of any available parallelism to split
# up the containment testing. The following algorithm is borrowed
# from NodeGeneratorBase to divvy up the ID range.
ndomain0 = n / mpi.procs
remainder = n % mpi.procs
assert remainder < mpi.procs
ndomain = ndomain0
if mpi.rank < remainder:
ndomain += 1
imin = mpi.rank * ndomain0 + min(mpi.rank, remainder)
imax = imin + ndomain
# Check our local range of IDs.
xloc, yloc, zloc, mloc, Hloc = [], [], [], [], []
localIndices = [
i for i in xrange(imin, imax) if self.accept(x[i], y[i], z[i])
]
# Now cull to the interior values.
xnew, ynew, znew, mnew, Hnew = [], [], [], [], []
for iproc in xrange(mpi.procs):
otherIndices = mpi.bcast(localIndices, iproc)
for i in otherIndices:
xnew.append(x[i])
ynew.append(y[i])
znew.append(z[i])
mnew.append(m[i])
Hnew.append(H[i])
# That's it.
return xnew, ynew, znew, mnew, Hnew
def testArrayDouble(self):
gamma = mpi.bcast( [9.9,3.3,4.4],3,mpi.MPI_DOUBLE,0,mpi.MPI_COMM_WORLD )
self.assertEqual( Numeric.array([9.9,3.3,4.4],'d'), gamma )
from os import system, getpid, environ
from subprocess import Popen
from nodefactory import createNode
from util import *
stop = False
node = None
goingdown = False
if size > 1:
if rank == 0:
stop = runningCheck()
stop = bcast( stop )
if not stop:
try:
node = createNode('mpi')
except:
displayExcept()
print 'fatal error creating node %d' % rank
stop = True
stop = bcast( stop )
if not stop:
def initialize_phi(self, *dims): self.phi = np.empty(basis_dims) if self.phi is None else self.phi mpi.bcast(self.phi)
plot "pingpong.plt" using 1:2 title "pyMPI" with linespoints, "pingpong.plt" using 1:4 title "C" with linespoints
"""
# Randomly split into senders and receivers
if mpi.rank == 0:
import random
ranks = list(range(mpi.size))
random.shuffle(ranks)
half = mpi.size/2
senders = ranks[:half]
receivers = ranks[half:half*2]
dead = ranks[half*2:]
sendmap = dict(zip(senders,receivers))
recvmap = dict(zip(receivers,senders))
mpi.bcast(sendmap)
mpi.bcast(recvmap)
mpi.bcast(dead)
else:
sendmap = mpi.bcast()
recvmap = mpi.bcast()
dead = mpi.bcast()
runs = 10
k = 25
# Log file
fd = open('pingpong_%d.plt'%mpi.size,'w')
fd.write('# %s\n'%asctime())
fd.write('# %d processors\n'%mpi.size)
def step(self, phi0, a, X):
if mpi.rank == mpi.root:
self.update(phi0, a, X)
mpi.bcast(phi0, mpi.root)
def on_disconnect(self):
logger.info('Client is disconnected: closing server')
server.close()
mpi.bcast(('return', None, None))
def run_server(port, settings):
server = None
if mpi.size == 1:
class PodService(rpyc.Service):
def on_disconnect(self):
logger.info('Client is disconnected: closing server')
server.close()
class exposed_Pod(Pod):
pass
logger.info('Creating poder on %s:%i', socket.gethostname(), port)
server = ThreadedServer(PodService, port=port, auto_register = False,
protocol_config={'allow_public_attrs' : True})
server.start()
else:
if mpi.myid == 0:
# Master serves, it holds a PodMPI instance as opposed to the slaves.
class PodService(rpyc.Service):
def on_disconnect(self):
logger.info('Client is disconnected: closing server')
server.close()
mpi.bcast(('return', None, None))
class exposed_Pod(PodMPI):
pass
logger.info('Creating poder on %s:%i', socket.gethostname(), port)
server = ThreadedServer(PodService, port=port,
auto_register = False,
protocol_config={'allow_public_attrs' : True})
server.start()
else:
# Slaves work with instances of Pod.
#
# Slaves scenario:
# * on the first loop occurence, they create a Pod object named 'pod',
# * then on subsequent loop occurences, they call a pod method and bind its return value to the variable 'ret'.
#
# In the body of the loop, a python expression is dynamically executed. The expression is formed of a stub and function's arguments. The stub contains a function name with a variable assignment (like 'ret = pod.dump'). The positional and optionnal arguments are passed to the named function in the stub.
#
# One loop occurence goes as follows:
# * wait for an expression from master node,
# * execute the expression
# * then return the expression's left hand side (if any) to master.
# local namespace scope for using exec,
# it keeps track of the already created variables over multiple loop iterations
scope = {}
while True:
(expression, args, kwargs) = mpi.bcast()
# logger.info(expression)
# logger.info(args)
# logger.info(kwargs)
if expression == 'return':
# TODO: how to tell exec it's in a function?
return
scope.update(locals())
exec expression in globals(), scope
mpi.gather(scope.get('ret'))
def testSingleChar(self):
sigma = mpi.bcast( 'g', 1, mpi.MPI_CHAR, 0, mpi.MPI_COMM_WORLD )
self.assertEqual( Numeric.array(['g'],'c'), sigma )
def testNil1(self):
nil1 = mpi.bcast( Numeric.zeros(0,Numeric.Int32), 1, mpi.MPI_INT, 0, mpi.MPI_COMM_WORLD )
self.assertEqual( [0], nil1 )
def testSingleFloat(self):
sigma = mpi.bcast( 7.7, 1, mpi.MPI_FLOAT, 0, mpi.MPI_COMM_WORLD )
self.assertEqual( Numeric.array([7.7],'f'), sigma)
def testSingleInt(self):
sigma = mpi.bcast( 7, 1, mpi.MPI_INT, 0, mpi.MPI_COMM_WORLD )
self.assertEqual( Numeric.array([7],'i'), sigma )
def testSingleDouble(self):
sigma = mpi.bcast( 7.7, 1, mpi.MPI_DOUBLE, 0, mpi.MPI_COMM_WORLD )
self.assertEqual( Numeric.array([7.7],'d'), sigma)
def testArrayChar(self):
gamma = mpi.bcast( ['i','c','d'],3,mpi.MPI_CHAR,0,mpi.MPI_COMM_WORLD )
self.assertEqual( Numeric.array(['i','c','d'],'c'), gamma )
def testArrayInt(self):
gamma = mpi.bcast( [9,3,4],3,mpi.MPI_INT,0,mpi.MPI_COMM_WORLD )
self.assertEqual( Numeric.array([9,3,4],'i'), gamma )
def testArrayFloat(self):
gamma = mpi.bcast( [9.9,3.3,4.4],3,mpi.MPI_FLOAT,0,mpi.MPI_COMM_WORLD )
self.assertEqual( Numeric.array([9.9,3.3,4.4],'f'), gamma )
def main():
if sys.argv[-1].startswith("usefs="): sys.argv = sys.argv[:-1] # remove the runpar fileserver info
(options,args) = parse_command_line()
if not options.nolog and (not mpi or (mpi and mpi.rank==0)): EMAN.appinit(sys.argv)
inputParm = EMAN.ccmlInputParm()
sf = EMAN.XYData()
if options.sfFileName != "" :
readsf = sf.readFile(options.sfFileName)
if ((readsf == -1) and (options.verbose > 0)) :
print "The file of scattering factor does NOT exist"
inputParm.scateringFactor = sf
startNumOfRawImages = options.startNumOfRawImages
#endNumOfRawImages = options.endNumOfRawImages
refImageFileName = args[-1]
numOfRefImages = options.numOfRefImages
solutionFile = options.solutionFile
# write log info to .emanlog file so that eman program can browse the history
if not options.nolog and (not mpi or (mpi and mpi.rank==0)):
pid = EMAN.LOGbegin(sys.argv)
for f in args[0:-1]: EMAN.LOGInfile(pid,f)
EMAN.LOGReffile(pid,args[-1])
if options.solutionFile: EMAN.LOGOutfile(pid,options.solutionFile)
if options.listFile: EMAN.LOGOutfile(pid,options.listFile)
if options.mrcSolutionFile: EMAN.LOGOutfile(pid,options.mrcSolutionFile)
inputParm.sym = options.sym
inputParm.FFTOverSampleScale = options.FFTOverSampleScale
inputParm.pftStepSize = options.pftStepSize
inputParm.deltaR = options.deltaR
inputParm.RMin = options.RMin
inputParm.RMax = options.RMax
inputParm.searchMode = options.searchMode
inputParm.scalingMode = options.scalingMode
inputParm.residualMode = options.residualMode
inputParm.weightMode = options.weightMode
# inputParm.rawImageFN will be set later
inputParm.refImagesFN = refImageFileName
inputParm.rawImageIniParmFN = options.rawImageIniParmFN
inputParm.rawImagePhaseCorrected = options.phasecorrected
inputParm.maxNumOfRun = options.maxNumOfRun
inputParm.zScoreCriterion = options.zScoreCriterion
inputParm.residualCriterion = options.residualCriterion
inputParm.solutionCenterDiffCriterion = options.solutionCenterDiffCriterion
inputParm.solutionOrientationDiffCriterion = options.solutionOrientationDiffCriterion/180.0*pi
inputParm.maxNumOfIteration = options.maxNumOfIteration
inputParm.numOfRandomJump = options.numOfRandomJump
inputParm.numOfFastShrink = options.numOfFastShrink
inputParm.numOfStartConfigurations = options.numOfStartConfigurations
inputParm.orientationSearchRange = options.orientationSearchRange/180.0*pi
inputParm.centerSearchRange = options.centerSearchRange
inputParm.numOfRefImages = options.numOfRefImages
inputParm.refEulerConvention = options.refEulerConvention
#maskR = options.maskR
#if (maskR<=0): maskR = refImageSizeY/2
inputParm.verbose = options.verbose
verbose = options.verbose
#verboseSolution = options.verboseSolution
updataHeader = options.updataHeader
solutionFile = options.solutionFile
mrcSolutionFile = options.mrcSolutionFile
iniCenterOrientationMode = options.iniCenterOrientationMode
refCenterOrientationMode = options.refCenterOrientationMode
rawImages = []
if not mpi or (mpi and mpi.rank==0):
for imgfile in args[0:-1]:
imgnum = EMAN.fileCount(imgfile)[0]
for i in range(imgnum): rawImages.append((imgfile, i))
if mpi: rawImages = mpi.bcast(rawImages)
endNumOfRawImages = options.endNumOfRawImages
if endNumOfRawImages <=0 or endNumOfRawImages > len(rawImages):
endNumOfRawImages = len(rawImages)
numRawImages = endNumOfRawImages - startNumOfRawImages
if mpi:
ptclset = range(startNumOfRawImages + mpi.rank, endNumOfRawImages, mpi.size)
else:
ptclset = range(startNumOfRawImages, endNumOfRawImages)
solutions = []
rMask = options.rMask #mask size is given
if options.rMask <= 0 : rMask = refImageSizeY/2 #mask size = half image size
rMask1 = options.rMask1 #output tnf mask size is given
if options.rMask1 <= 0 : rMask1 = rMask #output tnf mask size = half image size
inputParm.rMask = rMask
inputParm.rMask1 = rMask1
rawImage = EMAN.EMData()
rawImage.getEuler().setSym(inputParm.sym) #set the symmetry of the raw partile
inputParm.rawImageFN = rawImages[0][0] #give the initial raw particle filename
print "start to prepare------"
rawImage.crossCommonLineSearchPrepare(inputParm) #prepare, create pseudo PFT of ref images
print "end to prepare------"
inputParm.rawImage = rawImage
#for rawImgSN in ptclset:
for index in range(len(ptclset)):
rawImgSN = ptclset[index]
inputParm.rawImageFN = rawImages[rawImgSN][0]
inputParm.thisRawImageSN = rawImages[rawImgSN][1]
if mpi: print "rank %d: %d in %d-%d (%d in %d-%d)" % (mpi.rank, rawImgSN, startNumOfRawImages, endNumOfRawImages, index, 0, len(ptclset))
#rawImage.readImage(rawImages[rawImgSN][0], rawImages[rawImgSN][1])
#rawImage.applyMask(rMask, 6) #apply mask type 6 [edge mean value] to raw image, center will be image center
#rawImage.getEuler().setSym("icos")
#if rawImage.hasCTF() == 1:
#ctfParm = rawImage.getCTF()
#inputParm.zScoreCriterion = options.zScoreCriterion + atan(abs(ctfParm[0])-1.5)/(pi/4) +0.59 #adjust zScore criterion -0.6 --> +1.2, 1.5, 2.0
#inputParm.numOfRefImages = int(min(numOfRefImages, max(numOfRefImages*exp(-(abs(ctfParm[0])/2.0-0.15))+0.5, 5.0))) # adjust maxNumOfRun, the min is 2
inputParm.thisRawImageSN = rawImgSN
solutionCenterDiffCriterion = inputParm.solutionCenterDiffCriterion
solutionOrientationDiffCriterion = inputParm.solutionOrientationDiffCriterion
#initialize Center And Orientation by ont of the following modes
if iniCenterOrientationMode == "iniparmfile" :
inputParm.initializeCenterAndOrientationFromIniParmFile() # need to set "refEulerConvention"
elif iniCenterOrientationMode == "headerfile" :
inputParm.initializeCenterAndOrientationFromParticle() # need to set "refEulerConvention"
else :
inputParm.initializeCenterAndOrientationFromRandom() # default is random orientation and physical center
#set the refence Center And Orientation by ont of the following modes
if refCenterOrientationMode == "iniparmfile" : inputParm.setRefCenterAndOrientationFromIniParmFile() # need to set "refEulerConvention"
elif refCenterOrientationMode == "headerfile" : inputParm.setRefCenterAndOrientationFromParticle() # need to set "refEulerConvention"
else : inputParm.setRefCenterAndOrientationFromInitializedParms() # default is copy the initial center and orientation
rawImage.crossCommonLineSearchReadRawParticle(inputParm) #create pseudo PFT of raw image
maxNumOfRun = inputParm.maxNumOfRun
outputParmList = []
numOfRun = 0
passAllConsistencyCriteria = 0
while (numOfRun < maxNumOfRun) or (len(outputParmList) < 2):
if (iniCenterOrientationMode != "iniparmfile") and (iniCenterOrientationMode != "headerfile") :
inputParm.initializeCenterAndOrientationFromRandom() # default is random orientation and physical center
if (refCenterOrientationMode != "iniparmfile") and (refCenterOrientationMode != "headerfile") :
inputParm.setRefCenterAndOrientationFromInitializedParms() # default is copy the initial center and orientation
numOfRun = numOfRun + 1
print "numOfRun = ", numOfRun
############################################################################
############ execute cross common line search for reference ################
############################################################################
outputParm = rawImage.crossCommonLineSearch(inputParm)
############################################################################
# pass criteria check
outputParmList.append(outputParm) #if passed criteria, e.g. zscore, residualThreshold, etc
############################################################################
outputParmList.sort(lambda x, y: cmp(x.residual, y.residual))
############################################################################
########################## consistency check ###############################
############################################################################
#passConsistencyCriteria = 0
finalOutputParmList = []
lowestResidualList = []
lengthOfList = len(outputParmList)
if lengthOfList < 2 : continue
for i in range(lengthOfList-1):
thisOutputParm = outputParmList[i]
numOfPairsPassConsistencyCheck = 0
for j in range(i+1,lengthOfList):
refOutputParm = outputParmList[j]
tmpOutputParm = EMAN.ccmlOutputParm() #create a new output parm object
tmpOutputParm.rawImageSN = thisOutputParm.rawImageSN #copy all paramenters
tmpOutputParm.residual = thisOutputParm.residual
tmpOutputParm.sigma = thisOutputParm.sigma
tmpOutputParm.verbose = thisOutputParm.verbose
tmpOutputParm.zScore = thisOutputParm.zScore
tmpOutputParm.zScoreCriterion = thisOutputParm.zScoreCriterion
tmpOutputParm.passAllCriteria = 0
tmpOutputParm.setCalculatedCenterAndOrientation(thisOutputParm.cx,thisOutputParm.cy,thisOutputParm.q)
tmpOutputParm.setRefCenterAndOrientation(refOutputParm.cx, refOutputParm.cy, refOutputParm.q)
tmpOutputParm.calculateDifferenceWithRefParm() #calculated the difference
centerDiff = tmpOutputParm.centerDiff
orientationDiff = tmpOutputParm.orientationDiff
##### FLIP CASE : if no consistency found, try flip this orientation
if ((centerDiff > solutionCenterDiffCriterion) or (orientationDiff > solutionOrientationDiffCriterion)) :
quatFlip = EMAN.Quaternion(refOutputParm.q.getEuler().alt(), refOutputParm.q.getEuler().az(), refOutputParm.q.getEuler().phi()+pi)
tmpOutputParm.setRefCenterAndOrientation(refOutputParm.cx, refOutputParm.cy, quatFlip)
tmpOutputParm.calculateDifferenceWithRefParm() #calculated the difference
centerDiff = tmpOutputParm.centerDiff
orientationDiff = tmpOutputParm.orientationDiff
tmpOutputParm.setRefCenterAndOrientation(refOutputParm.cx, refOutputParm.cy, refOutputParm.q) #set back the exact orientation of reference
#Save the configurations with lowest residuals
if (i<3) and (j==i+1) : lowestResidualList.append(tmpOutputParm)
#make the good/answers list
if ((centerDiff < solutionCenterDiffCriterion) and (orientationDiff < solutionOrientationDiffCriterion)) :
numOfPairsPassConsistencyCheck += 1
if numOfPairsPassConsistencyCheck == 1 : #save to the final list
tmpOutputParm.passAllCriteria = 1
finalOutputParmList.append(tmpOutputParm)
if i==0 and numOfPairsPassConsistencyCheck >= options.numConsistentRun: #if the first one, check whether it has 3 pair of consistencies
passAllConsistencyCriteria = 1
break
if i>0 : break #if not the first one, find one pair of consistency, then break
#no break here, just for saving all possible solutions
if passAllConsistencyCriteria and len(finalOutputParmList) >= options.numConsistentRun: break #if 3 consistent pair orientations were found, then stop
rawImage.crossCommonLineSearchReleaseParticle(inputParm) # release the memory related to this raw particle
# if no consistency found, keep the lowest ones as output
if len(finalOutputParmList) == 0 : finalOutputParmList = lowestResidualList
for i in range(len(finalOutputParmList)) :
if passAllConsistencyCriteria : finalOutputParmList[i].passAllCriteria = 1
else : finalOutputParmList[i].passAllCriteria = 0
if options.solutionFile:
for i in range(len(finalOutputParmList)) : finalOutputParmList[i].outputResult(solutionFile)
outputParm = finalOutputParmList[0] #just use the lowest residual as regular output
if outputParm.passAllCriteria: passfail = "pass"
else: passfail = "fail"
print "Final result: euler=%g\t%g\t%g\tcenter=%g\t%g\tresidue=%g\t%s" % (outputParm.alt*180/pi, outputParm.az*180/pi, outputParm.phi*180/pi, outputParm.cx, outputParm.cy, outputParm.residual, passfail)
if options.scoreFile:
rawImage.readImage(rawImages[rawImgSN][0], rawImages[rawImgSN][1], 1) # read header only
if rawImage.hasCTF():
defocus = rawImage.getCTF()[0]
else:
defocus = 0
solution = (rawImages[rawImgSN][0], rawImages[rawImgSN][1], outputParm.alt, outputParm.az, outputParm.phi, \
outputParm.cx, outputParm.cy, defocus, outputParm.residual, outputParm.passAllCriteria)
solutions.append( solution )
sys.stdout.flush()
rawImage.crossCommonLineSearchFinalize(inputParm) #finalize, i.e. delete memories
if mpi:
if options.verbose:
print "rank %d: done and ready to output" % (mpi.rank)
sys.stdout.flush()
mpi.barrier()
#print "rank %d: %s" % (mpi.rank, solutions)
if mpi.rank==0:
for r in range(1,mpi.size):
msg, status = mpi.recv(source = r, tag = r)
solutions += msg
def ptcl_cmp(x, y):
eq = cmp(x[0], y[0])
if not eq: return cmp(x[1],y[1])
else: return eq
solutions.sort(ptcl_cmp)
else:
mpi.send(solutions, 0, tag = mpi.rank)
if not mpi or (mpi and mpi.rank==0):
if options.scoreFile:
sFile = open(options.scoreFile, "w")
sFile.write("#LST\n")
for i in solutions:
if i[-1]:
sFile.write("%d\t%s\tdefocus=%g\tresidual=%g\n" % (i[1], i[0], i[7], i[8]))
sFile.close()
if options.listFile:
lFile = open(options.listFile, "w")
lFile.write("#LST\n")
for i in solutions:
if i[-1]:
lFile.write("%d\t%s\t%g\t%g\t%g\t%g\t%g\n" % (i[1], i[0], i[2]*180.0/pi, i[3]*180.0/pi, i[4]*180.0/pi, i[5], i[6]))
lFile.close()
if options.mrcSolutionFile:
outFile = open(options.mrcSolutionFile, "w")
for i in solutions:
if i[-1]:
#rawImage.readImage(i[0], i[1], 1)
rawImage.readImage(i[0], i[1])
thisEu = EMAN.Euler(i[2], i[3], i[4])
thisEu.convertToMRCAngle()
alt = thisEu.alt_MRC()*180.0/pi
az = thisEu.az_MRC()*180.0/pi
phi = thisEu.phi_MRC()*180.0/pi
cx = i[5]
cy = i[6]
dx = cx - rawImage.xSize()/2
dy = cy - rawImage.ySize()/2
rawImage.applyMask(rMask1,6,dx,dy,0) #apply mask type 4 [outside=0] to raw image, center will be the solved center
#tnfFileName = "%s-%d.tnf" % (os.path.basename(os.path.splitext(rawImages[rawImgSN][0])[0]), rawImages[rawImgSN][1])
prefix = os.path.dirname(options.mrcSolutionFile).replace(" ", "")
if prefix != "" : prefix = prefix + "/"
tnfFileName = "%s%s-%d.tnf" % (prefix,os.path.basename(os.path.splitext(i[0])[0]), i[1])
rawFFT = rawImage.doFFT()
rawFFT.writeImage(tnfFileName,0) #tnf file no header information, it is a pure FFT of raw image file
outFile.write("%s\n" % (os.path.abspath(tnfFileName)))
outFile.write(" %d, %.4f, %.4f, %.4f, %.4f, %.4f, 0.0\n" % (0, alt, az, phi, cy, cx))
outFile.close()
if updataHeader:
for i in solutions:
rawImage.readImage(i[0], i[1], 1)
if options.verbose:
cx = rawImage.get_center_x()
cy = rawImage.get_center_y()
alt = rawImage.alt()
az = rawImage.az()
phi = rawImage.phi()
print "Update header: %s %d\t%7.5f %7.5f %7.2f %7.2f %7.2f => %7.5f %7.5f %7.2f %7.2f %7.2f" % \
(i[0], i[1], alt*180.0/pi, az*180.0/pi, phi*180.0/pi, cx, cy, i[2]*180.0/pi, i[3]*180.0/pi, i[4]*180.0/pi, i[5], i[6])
rawImage.setRAlign(i[2], i[3], i[4])
rawImage.set_center_x(i[5])
rawImage.set_center_y(i[6])
imgtype = EMAN.EMData.ANY
rawImage.writeImage(i[0], i[1], imgtype, 1)
if not options.nolog and (not mpi or (mpi and mpi.rank==0)): EMAN.LOGend()
