def __init__(self, input, db='ram', chains=2):
try:
mec = client.MultiEngineClient()
except:
p = subprocess.Popen('ipcluster -n %d'%proc, shell=True)
p.wait()
mec = client.MultiEngineClient()
# Check everything is alright.
nproc = len(mec.get_ids())
assert chains <= nproc
Sampler.__init__(self, input, db=db)
# Import the individual models in each process
#mec.pushModule(input)
proc = range(chains)
try:
mec.execute('import %s as input'%input.__name__, proc)
except:
mec.execute( 'import site' , proc)
mec.execute( 'site.addsitedir( ' + `os.getcwd()` + ' )' , proc)
mec.execute( 'import %s as input; reload(input)'%input.__name__, proc)
# Instantiate Sampler instances in each process
mec.execute('from pymc import MCMC', proc)
#mec.execute('from pymc.database.parallel import Database')
#for i in range(nproc):
# mec.execute(i, 'db = Database(%d)'%i)
mec.execute("S = MCMC(input, db='txt')", proc)
self.mec = mec
self.proc = proc
def __init__(self, input, db='ram', chains=2):
try:
mec = client.MultiEngineClient()
except:
p = subprocess.Popen('ipcluster -n %d' % proc, shell=True)
p.wait()
mec = client.MultiEngineClient()
# Check everything is alright.
nproc = len(mec.get_ids())
assert chains <= nproc
Sampler.__init__(self, input, db=db)
# Import the individual models in each process
#mec.pushModule(input)
proc = range(chains)
try:
mec.execute('import %s as input' % input.__name__, proc)
except:
mec.execute('import site', proc)
mec.execute('site.addsitedir( ' + ` os.getcwd() ` + ' )', proc)
mec.execute('import %s as input; reload(input)' % input.__name__,
proc)
# Instantiate Sampler instances in each process
mec.execute('from pymc import MCMC', proc)
#mec.execute('from pymc.database.parallel import Database')
#for i in range(nproc):
# mec.execute(i, 'db = Database(%d)'%i)
mec.execute("S = MCMC(input, db='txt')", proc)
self.mec = mec
self.proc = proc
def check(self):
from pymc import Sampler
from pymc.examples import trans_dimensional
M = Sampler(trans_dimensional)
M.sample(5000,0,10,verbose=False)
M.plot()
class test_AdaptativeMetropolis(NumpyTestCase):
S = Sampler(AMmodel, 'ram')
S.sample(10000)
print S.A.trace(burn=5000, thin=50)
def check(self):
from pymc import Sampler
from pymc.examples import trans_dimensional
M = Sampler(trans_dimensional)
M.sample(5000, 0, 10, verbose=False)
M.plot()
