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 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 iteration(self):
if mpi.rank == mpi.root:
self.load_samples()
mpi.scatter(self.rbuf.npats, self.nbuf.npats)
mpi.scatter(self.rbuf.x, self.nbuf.x)
self.infer_coefficients()
self.compute_phi_gradient()
if mpi.rank == mpi.root:
self.update_phi()
self.update_eta()
def parallelRunTest(self):
#decide on roots
roots = [0,0,0]
roots = [int(mpi.procs / 3), 0, int(mpi.procs / 2) ]
nprocs = mpi.procs
#values to be scattered
list1 = []
list2 = []
longList = []
tuple1 = ()
string1 = ""
for x in range(nprocs):
list1 += [nprocs - x]
list2 += [ "fOo", x, ( 8,str(x*x) )]
tuple1 += (2*x, 2*x + 1)
string1 += "fOo for" + str(x%10)
for i in range(1024):
longList += [ 500-4*i - 10*x, "K" ]
#do scatters
results = [0,0,0, 0,0,0, 0,0,0]
results[0] = mpi.scatter( list1, roots[0])
results[1] = mpi.scatter( list2, roots[0] )
results[2] = mpi.scatter( tuple1, roots[0] )
results[3] = mpi.scatter( string1,roots[0])
results[4] = mpi.scatter( longList, roots[0] )
#correct answers
correctAnswers = [0,0,0, 0,0,0, 0,0,0]
for x in range(5):
correctAnswers[x] = []
correctAnswers[0] = [nprocs - mpi.rank]
correctAnswers[1] = list2[ mpi.rank*3: mpi.rank*3 + 3]
correctAnswers[2] = (2*mpi.rank, 2*mpi.rank+1)
correctAnswers[3] = "fOo for"+str(mpi.rank%10)
correctAnswers[4] = longList[2048*mpi.rank: 2048*(mpi.rank+1)]
for x in range(5):
if results[x] != correctAnswers[x]:
failString = "scatter failed on test "+str(x)
failString += " and process " + str(mpi.rank) + "\n"
failString += "Scatter result was " + str(results[x])
failString += " and it should be "+ str(correctAnswers[x])
self.fail( failString);
return
def parallelRunTest(self):
#decide on roots
roots = [0, 0, 0]
roots = [int(mpi.procs / 3), 0, int(mpi.procs / 2)]
nprocs = mpi.procs
#values to be scattered
list1 = []
list2 = []
longList = []
tuple1 = ()
string1 = ""
for x in range(nprocs):
list1 += [nprocs - x]
list2 += ["fOo", x, (8, str(x * x))]
tuple1 += (2 * x, 2 * x + 1)
string1 += "fOo for" + str(x % 10)
for i in range(1024):
longList += [500 - 4 * i - 10 * x, "K"]
#do scatters
results = [0, 0, 0, 0, 0, 0, 0, 0, 0]
results[0] = mpi.scatter(list1, roots[0])
results[1] = mpi.scatter(list2, roots[0])
results[2] = mpi.scatter(tuple1, roots[0])
results[3] = mpi.scatter(string1, roots[0])
results[4] = mpi.scatter(longList, roots[0])
#correct answers
correctAnswers = [0, 0, 0, 0, 0, 0, 0, 0, 0]
for x in range(5):
correctAnswers[x] = []
correctAnswers[0] = [nprocs - mpi.rank]
correctAnswers[1] = list2[mpi.rank * 3:mpi.rank * 3 + 3]
correctAnswers[2] = (2 * mpi.rank, 2 * mpi.rank + 1)
correctAnswers[3] = "fOo for" + str(mpi.rank % 10)
correctAnswers[4] = longList[2048 * mpi.rank:2048 * (mpi.rank + 1)]
for x in range(5):
if results[x] != correctAnswers[x]:
failString = "scatter failed on test " + str(x)
failString += " and process " + str(mpi.rank) + "\n"
failString += "Scatter result was " + str(results[x])
failString += " and it should be " + str(correctAnswers[x])
self.fail(failString)
return
def scatter_test(comm, generator, kind, root):
if comm.rank == root:
print ("Scattering %s from root %d..." % (kind, root)),
if comm.rank == root:
values = list()
for p in range(0, comm.size):
values.append(generator(p))
result = mpi.scatter(comm, values, root = root)
else:
result = mpi.scatter(comm, root = root);
assert result == generator(comm.rank)
if comm.rank == root: print "OK."
return
def scatter_test(comm, generator, kind, root):
if comm.rank == root:
print("Scattering %s from root %d..." % (kind, root)),
if comm.rank == root:
values = list()
for p in range(0, comm.size):
values.append(generator(p))
result = mpi.scatter(comm, values, root=root)
else:
result = mpi.scatter(comm, root=root)
assert result == generator(comm.rank)
if comm.rank == root: print("OK.")
return
newphi += dphi
newpsi += dpsi
z.append([newphi, newpsi])
z.append([phiF, psiF])
print "\nI0: ",
print z
else:
z = []
#if (mpi.rank == 0):
# z = mpi.bcast(z)
#else:
# z = mpi.bcast()
#
#z_p = z[mpi.rank]
z_p = mpi.scatter(z)[0]
print z_p
import sys
sys.exit(0)
ff.params['HarmonicDihedral'] = {'kbias':[kappa, kappa],
'dihedralnum':[PHI-1, PSI-1],
'angle':[z_p[0], z_p[1]]}
dt = 1.0
kappaincr = (1000.-40.)/100000.
for iter in range(0, 2000): # NUMBER OF FTSM ITERATIONS
#for workpt in range(0, numpoints): # LOOPING OVER POINTS
if (iter >= 10001 and iter <= 110000):
kappa += kappaincr
import mpi, sys, os, string
if mpi.rank == 0:
sequences = sys.argv[1:]
else:
sequences = []
local_sequences = mpi.scatter(sequences)
result = []
for sequence in local_sequences:
cmd = "java -Djava.awt.headless=true -cp FoldingServer.jar foldingServer.FoldingServer -c " + sequence
for line in os.popen(cmd).readlines():
if line.find(":") >= 0:
message = str(mpi.rank) + ";" + sequence + ";" + line.rstrip("\n")
result.append(message)
all = mpi.gather(result)
if mpi.rank == 0:
for result in all:
print result
import sys, os
import Numeric
import mpi
if __name__=="__main__":
rank,size = mpi.init()
if(size >= 2):
print "testing scatter on",size,"processors..."
else:
print "unable to run test on",size,"processors!"
print "please rerun on 2 or more processors."
sys.exit()
print "\n"
print "allocating test data:"
data = 0
if(rank==0):
data = Numeric.array("abcdefghijklmnopqrst",Numeric.Character)
print "scattering data:"
mydata = mpi.scatter(data, 10, mpi.MPI_CHAR, 10, mpi.MPI_CHAR,
0, mpi.MPI_COMM_WORLD)
print "scattered data:",mydata
mpi.barrier(mpi.MPI_COMM_WORLD)
mpi.finalize()
newphi += dphi
newpsi += dpsi
z.append([newphi, newpsi])
z.append([phiF, psiF])
print "\nI0: ",
print z
else:
z = []
#if (mpi.rank == 0):
# z = mpi.bcast(z)
#else:
# z = mpi.bcast()
#
#z_p = z[mpi.rank]
z_p = mpi.scatter(z)[0]
print z_p
import sys
sys.exit(0)
ff.params['HarmonicDihedral'] = {
'kbias': [kappa, kappa],
'dihedralnum': [PHI - 1, PSI - 1],
'angle': [z_p[0], z_p[1]]
}
dt = 1.0
kappaincr = (1000. - 40.) / 100000.
for iter in range(0, 2000): # NUMBER OF FTSM ITERATIONS
#for workpt in range(0, numpoints): # LOOPING OVER POINTS
if (iter >= 10001 and iter <= 110000):
kappa += kappaincr
