def set_communicator(world, rank, size, kcommsize=None):
"""Communicator inilialized."""
# wcomm is always set to world
wcomm = world
if kcommsize is None or kcommsize == size or size == 1:
# By default, only use parallization in kpoints
# then kcomm is set to world communicator
# and wS is not parallelized
kcomm = world
wScomm = serial_comm
else:
# If use wS parallization for storage of spectral function
# then new kpoint and wS communicator are generated
assert kcommsize != size
r0 = (rank // kcommsize) * kcommsize
ranks = np.arange(r0, r0 + kcommsize)
kcomm = world.new_communicator(ranks)
# wS comm generated
r0 = rank % kcommsize
ranks = np.arange(r0, r0+size, kcommsize)
wScomm = world.new_communicator(ranks)
return kcomm, wScomm, wcomm
def set_communicator(world, rank, size, kcommsize=None):
"""Communicator inilialized."""
# wcomm is always set to world
wcomm = world
if kcommsize is None or kcommsize == size or size == 1:
# By default, only use parallization in kpoints
# then kcomm is set to world communicator
# and wS is not parallelized
kcomm = world
wScomm = serial_comm
else:
# If use wS parallization for storage of spectral function
# then new kpoint and wS communicator are generated
assert kcommsize != size
r0 = (rank // kcommsize) * kcommsize
ranks = np.arange(r0, r0 + kcommsize)
kcomm = world.new_communicator(ranks)
# wS comm generated
r0 = rank % kcommsize
ranks = np.arange(r0, r0 + size, kcommsize)
wScomm = world.new_communicator(ranks)
return kcomm, wScomm, wcomm
def main():
from gpaw.grid_descriptor import GridDescriptor
from gpaw.mpi import world
serial = world.new_communicator([world.rank])
# Generator which must run on all ranks
gen = np.random.RandomState(0)
# This one is just used by master
gen_serial = np.random.RandomState(17)
maxsize = 5
for i in range(1):
N1_c = gen.randint(1, maxsize, 3)
N2_c = gen.randint(1, maxsize, 3)
gd1 = GridDescriptor(N1_c, N1_c)
gd2 = GridDescriptor(N2_c, N2_c)
serial_gd1 = gd1.new_descriptor(comm=serial)
serial_gd2 = gd2.new_descriptor(comm=serial)
a1_serial = serial_gd1.empty()
a1_serial.flat[:] = gen_serial.rand(a1_serial.size)
if world.rank == 0:
print('r0: a1 serial', a1_serial.ravel())
a1 = gd1.empty()
a1[:] = -1
grid2grid(world, serial_gd1, gd1, a1_serial, a1)
print(world.rank, 'a1 distributed', a1.ravel())
world.barrier()
a2 = gd2.zeros()
a2[:] = -2
grid2grid(world, gd1, gd2, a1, a2)
print(world.rank, 'a2 distributed', a2.ravel())
world.barrier()
#grid2grid(world, gd2, gd2_serial
gd1 = GridDescriptor(N1_c, N1_c * 0.2)
#serialgd = gd2.new_descriptor(
a1 = gd1.empty()
a1.flat[:] = gen.rand(a1.size)
#print a1
grid2grid(world, gd1, gd2, a1, a2)
def test(xc, tol=5e-10):
N_c = np.array([10, 6, 4])
# This test is totally serial.
gd = GridDescriptor(N_c,
N_c * 0.2,
pbc_c=(1, 0, 1),
comm=world.new_communicator([world.rank]))
actual_n = N_c - (1 - gd.pbc_c)
gen = np.random.RandomState(17)
n_sg = gd.zeros(2)
n_sg[:] = gen.rand(*n_sg.shape)
#sigma_xg = gd.zeros(3)
#sigma_xg[:] = gen.random.rand(*sigma_xg.shape)
if hasattr(xc, 'libvdwxc'):
xc._nspins = 2
xc.initialize_backend(gd)
v_sg = gd.zeros(2)
E = xc.calculate(gd, n_sg, v_sg)
print('E', E)
dn = 1e-6
all_indices = itertools.product(range(2), range(1, actual_n[0], 2),
range(0, actual_n[1], 2),
range(0, actual_n[2], 2))
for testindex in all_indices:
n1_sg = n_sg.copy()
n2_sg = n_sg.copy()
v = v_sg[testindex] * gd.dv
n1_sg[testindex] -= dn
n2_sg[testindex] += dn
E1 = xc.calculate(gd, n1_sg, v_sg.copy())
E2 = xc.calculate(gd, n2_sg, v_sg.copy())
dedn = 0.5 * (E2 - E1) / dn
err = abs(dedn - v)
print('{}{} v={} fd={} err={}'.format(xc.name, list(testindex), v,
dedn, err))
assert err < tol, err
B = parsize_bands # number of blocks
G = 120 # number of grid points (G x G x G)
N = 2000 # number of bands
h = 0.2 # grid spacing
a = h * G # side length of box
M = N // B # number of bands per block
assert M * B == N
D = world.size // B # number of domains
assert D * B == world.size
# Set up communicators:
r = world.rank // D * D
domain_comm = world.new_communicator(np.arange(r, r + D))
band_comm = world.new_communicator(np.arange(world.rank % D, world.size, D))
# Set up grid descriptor:
gd = GridDescriptor((G, G, G), (a, a, a), True, domain_comm, parsize)
# Random wave functions:
np.random.seed(world.rank)
psit_mG = np.random.uniform(-0.5, 0.5, size=(M,) + tuple(gd.n_c))
if world.rank == 0:
print 'Size of wave function array:', psit_mG.shape
# Send and receive buffers:
send_mG = gd.empty(M)
recv_mG = gd.empty(M)
from gpaw.fd_operators import Gradient
import numpy as np
from gpaw.grid_descriptor import GridDescriptor
from gpaw.mpi import world
if world.size > 4:
# Grid is so small that domain decomposition cannot exceed 4 domains
assert world.size % 4 == 0
group, other = divmod(world.rank, 4)
ranks = np.arange(4 * group, 4 * (group + 1))
domain_comm = world.new_communicator(ranks)
else:
domain_comm = world
gd = GridDescriptor((8, 1, 1), (8.0, 1.0, 1.0), comm=domain_comm)
a = gd.zeros()
dadx = gd.zeros()
a[:, 0, 0] = np.arange(gd.beg_c[0], gd.end_c[0])
gradx = Gradient(gd, v=0)
print a.itemsize, a.dtype, a.shape
print dadx.itemsize, dadx.dtype, dadx.shape
gradx.apply(a, dadx)
# a = [ 0. 1. 2. 3. 4. 5. 6. 7.]
#
# da
# -- = [-2.5 1. 1. 1. 1. 1. 1. -2.5]
# dx
dadx = gd.collect(dadx, broadcast=True)
assert dadx[3, 0, 0] == 1.0 and np.sum(dadx[:, 0, 0]) == 0.0
niter_tolerance = 0
if world.size >= 3:
calc = GPAW(kpts=[6, 6, 1],
spinpol=True,
parallel={'domain': world.size},
txt='H-a.txt')
H.set_calculator(calc)
e1 = H.get_potential_energy()
niter1 = calc.get_number_of_iterations()
assert H.get_calculator().wfs.kd.comm.size == 1
equal(e1, -2.23708481, energy_tolerance)
if world.rank < 3:
comm = world.new_communicator(np.array([0, 1, 2]))
H.set_calculator(
GPAW(kpts=[6, 6, 1],
spinpol=True,
communicator=comm,
txt='H-b.txt'))
e2 = H.get_potential_energy()
assert H.get_calculator().wfs.kd.comm.size == 3
equal(e1, e2, 5e-9)
else:
comm = world.new_communicator(np.array(range(3, world.size)))
H.set_calculator(
GPAW(kpts=[6, 6, 1],
spinpol=True,
communicator=comm,
txt='H-b2.txt'))
cell=(3.5, 3.5, 4. + 2 / 3.),
pbc=True)
# Only a short, non-converged calcuation
conv = {'eigenstates': 1.24, 'energy': 2e-1, 'density': 1e-1}
calc = GPAW(h=0.30,
kpts=(1, 1, 3),
setups={'Na': '1'},
nbands=3,
convergence=conv)
atoms.set_calculator(calc)
e0 = atoms.get_potential_energy()
wf0 = calc.get_pseudo_wave_function(2, 1, 1, broadcast=True)
# Write the restart file(s)
for mode in modes:
calc.write('tmp.%s' % mode, 'all')
del calc
# Now read with single process
comm = world.new_communicator(np.array((rank, )))
for mode in modes:
calc = GPAW('tmp.%s' % mode, communicator=comm)
wf1 = calc.get_pseudo_wave_function(2, 1, 1)
diff = np.abs(wf0 - wf1)
assert (np.all(diff < 1e-12))
world.barrier()
if rank == 0:
for mode in modes:
os.remove('tmp.%s' % mode)
#!/usr/bin/env python
import numpy as np
from gpaw import debug, dry_run
from gpaw.mpi import world, serial_comm, _Communicator, \
SerialCommunicator, DryRunCommunicator
even_comm = world.new_communicator(np.arange(0, world.size, 2))
if world.size > 1:
odd_comm = world.new_communicator(np.arange(1, world.size, 2))
else:
odd_comm = None
if world.rank % 2 == 0:
assert odd_comm is None
comm = even_comm
else:
assert even_comm is None
comm = odd_comm
hasmpi = False
try:
import _gpaw
hasmpi = hasattr(_gpaw, 'Communicator')
except ImportError, AttributeError:
pass
assert world.parent is None
assert comm.parent is world
if hasmpi:
assert comm.parent.get_c_object() is world.get_c_object()
niter_tolerance = 0
if world.size >= 3:
calc = GPAW(kpts=[6, 6, 1],
spinpol=True,
parallel={'domain': world.size},
txt='H-a.txt')
H.set_calculator(calc)
e1 = H.get_potential_energy()
niter1 = calc.get_number_of_iterations()
assert H.get_calculator().wfs.kpt_comm.size == 1
equal(e1, -2.23708481, energy_tolerance)
if world.rank < 3:
comm = world.new_communicator(np.array([0, 1, 2]))
H.set_calculator(GPAW(kpts=[6, 6, 1],
spinpol=True,
communicator=comm,
txt='H-b.txt'))
e2 = H.get_potential_energy()
assert H.get_calculator().wfs.kpt_comm.size == 3
equal(e1, e2, 5e-9)
else:
comm = world.new_communicator(np.array(range(3, world.size)))
H.set_calculator(GPAW(kpts=[6, 6, 1],
spinpol=True,
communicator=comm,
txt='H-b2.txt'))
e2 = H.get_potential_energy()
if "EON_CLIENT_STANDALONE" in os.environ:
os.environ["EON_NUMBER_OF_CLIENTS"] = "1"
if "EON_NUMBER_OF_CLIENTS" not in os.environ:
sys.stderr.write("you must set the env var EON_NUMBER_OF_CLIENTS\n")
sys.exit(1)
clients = int(os.environ["EON_NUMBER_OF_CLIENTS"])
potential_group_size = potentials / clients
my_client_rank = client_ranks[potential_ranks.index(rank) /
potential_group_size]
#print "pot: rank: %i my_client_rank: %i" % (world.rank, my_client_rank)
for i in xrange(clients):
s = potential_group_size
new_comm = world.new_communicator(
numpy.array(potential_ranks[i * s:i * s + s], dtype='i'))
if new_comm != None:
my_comm = new_comm
first_time = True
nforce_calls = 0
performance_log = ""
while True:
nforce_calls += 1
natoms = numpy.array((0, ), 'i')
if my_comm.rank == 0:
world.receive(natoms, my_client_rank, tag=0)
my_comm.broadcast(natoms, 0)
atomic_numbers = numpy.zeros(natoms, 'i')
positions = numpy.zeros(3 * natoms, 'd')
print '-----------'
if Eref is not None:
Eerr = abs(E - Eref)
assert Eerr < 1e-8, 'Bad E: err=%f; parallel=%s' % (Eerr, parallel)
if Fref is not None:
Ferr = np.abs(F - Fref).max()
assert Ferr < 1e-6, 'Bad F: err=%f; parallel=%s' % (Ferr, parallel)
return E, F
# First calculate reference energy and forces E and F
#
# If we want to really dumb things down, enable this to force an
# entirely serial calculation:
if 0:
serial = world.new_communicator([0])
E = 0.0
F = np.zeros((len(system), 3))
if world.rank == 0:
E, F = calculate({}, serial)
E = world.sum(E)
world.sum(F)
else:
# Normally we'll just do it in parallel;
# that case is covered well by other tests, so we can probably trust it
E, F = calculate({}, world)
def check(parallel):
return calculate(parallel, comm=world, Eref=E, Fref=F)
assert world.size in [1, 2, 4, 8], ('Number of CPUs %d not supported'
from ase.build import molecule
from gpaw import GPAW
from gpaw.wavefunctions.pw import PW
from gpaw.mpi import world
a = molecule('H', pbc=1)
a.center(vacuum=2)
comm = world.new_communicator([world.rank])
e0 = 0.0
a.calc = GPAW(mode=PW(250), communicator=comm, txt=None)
e0 = a.get_potential_energy()
e0 = world.sum(e0) / world.size
a.calc = GPAW(mode=PW(250),
eigensolver='rmm-diis',
basis='szp(dzp)',
txt='%d.txt' % world.size)
e = a.get_potential_energy()
f = a.get_forces()
assert abs(e - e0) < 7e-5, abs(e - e0)
assert abs(f).max() < 1e-10, abs(f).max()
potential_ranks.append(i)
if "EON_CLIENT_STANDALONE" in os.environ:
os.environ["EON_NUMBER_OF_CLIENTS"] = "1"
if "EON_NUMBER_OF_CLIENTS" not in os.environ:
sys.stderr.write("you must set the env var EON_NUMBER_OF_CLIENTS\n");
sys.exit(1)
clients = int(os.environ["EON_NUMBER_OF_CLIENTS"])
potential_group_size = potentials/clients
my_client_rank = client_ranks[potential_ranks.index(rank)/potential_group_size]
#print "pot: rank: %i my_client_rank: %i" % (world.rank, my_client_rank)
for i in xrange(clients):
s = potential_group_size
new_comm = world.new_communicator(numpy.array(potential_ranks[i*s:i*s+s], dtype='i'))
if new_comm != None:
my_comm = new_comm
first_time = True
nforce_calls = 0
performance_log = ""
while True:
nforce_calls += 1
natoms = numpy.array((0,), 'i')
if my_comm.rank == 0:
world.receive(natoms, my_client_rank, tag=0)
my_comm.broadcast(natoms, 0)
atomic_numbers = numpy.zeros(natoms, 'i')
positions = numpy.zeros(3*natoms, 'd')
from __future__ import print_function
import numpy as np
from ase.lattice import bulk
from ase.dft.kpoints import monkhorst_pack
from ase.parallel import paropen
from gpaw import GPAW, PW
from gpaw.mpi import size, rank, world, serial_comm
from gpaw.xc.tools import vxc
from gpaw.xc.hybridg import HybridXC
mgo = bulk('MgO', 'rocksalt', a=4.189)
if rank < 3:
comm = world.new_communicator(np.arange(min(3, size)))
else:
comm = world.new_communicator(np.array((rank, )))
if 1:
mgo.calc = GPAW(mode=PW(500),
parallel=dict(band=1),
idiotproof=False,
communicator=comm,
setups={'Mg': '2'},
convergence={'eigenstates': 5.e-9},
kpts=monkhorst_pack((2, 2, 2)) + 0.25)
mgo.get_potential_energy()
if rank < 3:
mgo.calc.write('mgo', 'all')
else:
mgo.calc.write('dummy_%d' % rank, 'all')
world.barrier()
B = parsize_bands # number of blocks
G = 120 # number of grid points (G x G x G)
N = 2000 # number of bands
h = 0.2 # grid spacing
a = h * G # side length of box
M = N // B # number of bands per block
assert M * B == N
D = world.size // B # number of domains
assert D * B == world.size
# Set up communicators:
r = world.rank // D * D
domain_comm = world.new_communicator(np.arange(r, r + D))
band_comm = world.new_communicator(np.arange(world.rank % D, world.size, D))
# Set up grid descriptor:
gd = GridDescriptor((G, G, G), (a, a, a), True, domain_comm, parsize)
# Random wave functions:
np.random.seed(world.rank)
psit_mG = np.random.uniform(-0.5, 0.5, size=(M, ) + tuple(gd.n_c))
if world.rank == 0:
print 'Size of wave function array:', psit_mG.shape
# Send and receive buffers:
send_mG = gd.empty(M)
recv_mG = gd.empty(M)
from ase.structure import molecule
from gpaw import GPAW
from gpaw.wavefunctions.pw import PW
from gpaw.mpi import world
a = molecule('H', pbc=1)
a.center(vacuum=2)
comm = world.new_communicator([0])
e0 = 0.0
if world.rank == 0:
a.calc = GPAW(mode=PW(250),
communicator=comm,
txt=None)
e0 = a.get_potential_energy()
e0 = world.sum(e0)
a.calc = GPAW(mode=PW(250),
eigensolver='rmm-diis',
basis='szp(dzp)',
txt='%d.txt' % world.size)
e = a.get_potential_energy()
f = a.get_forces()
assert abs(e - e0) < 7e-5, abs(e - e0)
assert abs(f).max() < 1e-10, abs(f).max()
from ase.parallel import parprint as pp
from gpaw import GPAW, PW, restart
from gpaw.response.df import DielectricFunction
from gpaw.mpi import world
from gpaw.version import version
from ase.lattice import bulk
system = Graphene(symbol="C", latticeconstant={"a": 2.45, "c": 1.0}, size=(1, 1, 1))
system.pbc = (1, 1, 0)
system.center(axis=2, vacuum=4.0)
nkpts = 5
communicator = world.new_communicator(np.array([world.rank]))
gpwname = "dump.graphene.gpw"
if world.rank == 0:
calc = GPAW(
mode="pw",
kpts=(nkpts, nkpts, 1),
communicator=communicator,
xc="oldLDA",
nbands=len(system) * 6,
txt="gpaw.graphene.txt",
)
system.set_calculator(calc)
system.get_potential_energy()
calc.write(gpwname, mode="all")
from __future__ import print_function
import numpy as np
from ase.lattice import bulk
from ase.dft.kpoints import monkhorst_pack
from ase.parallel import paropen
from gpaw import GPAW, PW
from gpaw.mpi import size, rank, world, serial_comm
from gpaw.xc.tools import vxc
from gpaw.xc.hybridg import HybridXC
mgo = bulk('MgO', 'rocksalt', a=4.189)
if rank < 3:
comm = world.new_communicator(np.arange(min(3, size)))
else:
comm = world.new_communicator(np.array((rank,)))
if 1:
mgo.calc = GPAW(mode=PW(500),
parallel=dict(band=1),
idiotproof=False,
communicator=comm,
setups={'Mg': '2'},
convergence={'eigenstates': 5.e-9},
kpts=monkhorst_pack((2, 2, 2)) + 0.25)
mgo.get_potential_energy()
if rank < 3:
mgo.calc.write('mgo', 'all')
else:
mgo.calc.write('dummy_%d' % rank, 'all')
world.barrier()
( 0, d*sqrt(3./4.), d/2.)],
magmoms=[1.0, 1.0, 1.0],
cell=(3.5, 3.5, 4.+2/3.),
pbc=True)
# Only a short, non-converged calcuation
conv = {'eigenstates': 1.24, 'energy':2e-1, 'density':1e-1}
calc = GPAW(h=0.30, kpts=(1,1,3),
setups={'Na': '1'},
nbands=3, convergence=conv)
atoms.set_calculator(calc)
e0 = atoms.get_potential_energy()
wf0 = calc.get_pseudo_wave_function(2, 1, 1, broadcast=True)
# Write the restart file(s)
for mode in modes:
calc.write('tmp.%s' % mode, 'all')
del calc
# Now read with single process
comm = world.new_communicator(np.array((rank,)))
for mode in modes:
calc = GPAW('tmp.%s' % mode, communicator=comm)
wf1 = calc.get_pseudo_wave_function(2, 1, 1)
diff = np.abs(wf0 - wf1)
assert(np.all(diff < 1e-12))
world.barrier()
if rank == 0:
for mode in modes:
os.remove('tmp.%s' % mode)
a = 2.5
H = Atoms('H', cell=[a, a, a], pbc=True)
energy_tolerance = 0.00006
niter_tolerance = 0
if world.size >= 3:
calc = GPAW(kpts=[6, 6, 1],
spinpol=True,
parallel={'domain': world.size},
txt='H-a.txt')
H.set_calculator(calc)
e1 = H.get_potential_energy()
niter1 = calc.get_number_of_iterations()
assert H.get_calculator().wfs.kpt_comm.size == 1
equal(e1, -2.23708481, energy_tolerance)
equal(niter1, 16, niter_tolerance)
comm = world.new_communicator(np.array([0, 1, 2]))
if world.rank < 3:
H.set_calculator(
GPAW(kpts=[6, 6, 1],
spinpol=True,
communicator=comm,
txt='H-b.txt'))
e2 = H.get_potential_energy()
assert H.get_calculator().wfs.kpt_comm.size == 3
equal(e1, e2, 1e-11)
from ase.parallel import parprint as pp
from gpaw import GPAW
from gpaw.response.df import DielectricFunction
from gpaw.mpi import world
system = Graphene(symbol='C',
latticeconstant={'a': 2.45,'c': 1.0},
size=(1,1,1))
system.pbc = (1, 1, 0)
system.center(axis=2, vacuum=4.0)
nkpts = 5
communicator = world.new_communicator(np.array([world.rank]))
gpwname = 'dump.graphene.gpw'
if world.rank == 0:
calc = GPAW(mode='pw',
kpts=(nkpts, nkpts, 1),
communicator=communicator,
xc='oldLDA',
nbands=len(system) * 6,
txt='gpaw.graphene.txt')
system.set_calculator(calc)
system.get_potential_energy()
calc.write(gpwname, mode='all')
world.barrier()
from ase.structure import molecule
from gpaw import GPAW
from gpaw.wavefunctions.pw import PW
from gpaw.mpi import world
a = molecule('H', pbc=1)
a.center(vacuum=2)
comm = world.new_communicator([world.rank])
e0 = 0.0
a.calc = GPAW(mode=PW(250),
communicator=comm,
txt=None)
e0 = a.get_potential_energy()
e0 = world.sum(e0) / world.size
a.calc = GPAW(mode=PW(250),
eigensolver='rmm-diis',
basis='szp(dzp)',
txt='%d.txt' % world.size)
e = a.get_potential_energy()
f = a.get_forces()
assert abs(e - e0) < 7e-5, abs(e - e0)
assert abs(f).max() < 1e-10, abs(f).max()
from gpaw.fd_operators import Gradient
import numpy as np
from gpaw.grid_descriptor import GridDescriptor
from gpaw.mpi import world
if world.size > 4:
# Grid is so small that domain decomposition cannot exceed 4 domains
assert world.size % 4 == 0
group, other = divmod(world.rank, 4)
ranks = np.arange(4*group, 4*(group+1))
domain_comm = world.new_communicator(ranks)
else:
domain_comm = world
gd = GridDescriptor((8, 1, 1), (8.0, 1.0, 1.0), comm=domain_comm)
a = gd.zeros()
dadx = gd.zeros()
a[:, 0, 0] = np.arange(gd.beg_c[0], gd.end_c[0])
gradx = Gradient(gd, v=0)
print a.itemsize, a.dtype, a.shape
print dadx.itemsize, dadx.dtype, dadx.shape
gradx.apply(a, dadx)
# a = [ 0. 1. 2. 3. 4. 5. 6. 7.]
#
# da
# -- = [-2.5 1. 1. 1. 1. 1. 1. -2.5]
# dx
dadx = gd.collect(dadx, broadcast=True)
assert dadx[3, 0, 0] == 1.0 and np.sum(dadx[:, 0, 0]) == 0.0
from gpaw.test import equal
a = 2.5
H = Atoms('H', cell=[a, a, a], pbc=True)
energy_tolerance = 0.00006
niter_tolerance = 0
if world.size >= 3:
calc = GPAW(kpts=[6, 6, 1],
spinpol=True,
parallel={'domain': world.size},
txt='H-a.txt')
H.set_calculator(calc)
e1 = H.get_potential_energy()
niter1 = calc.get_number_of_iterations()
assert H.get_calculator().wfs.kpt_comm.size == 1
equal(e1, -2.23708481, energy_tolerance)
equal(niter1, 16, niter_tolerance)
comm = world.new_communicator(np.array([0, 1, 2]))
if world.rank < 3:
H.set_calculator(GPAW(kpts=[6, 6, 1],
spinpol=True,
communicator=comm,
txt='H-b.txt'))
e2 = H.get_potential_energy()
assert H.get_calculator().wfs.kpt_comm.size == 3
equal(e1, e2, 1e-11)
if Eref is not None:
Eerr = abs(E - Eref)
assert Eerr < 1e-8, 'Bad E: err=%f; parallel=%s' % (Eerr, parallel)
if Fref is not None:
Ferr = np.abs(F - Fref).max()
assert Ferr < 1e-6, 'Bad F: err=%f; parallel=%s' % (Ferr, parallel)
return E, F
# First calculate reference energy and forces E and F
#
# If we want to really dumb things down, enable this to force an
# entirely serial calculation:
if 0:
serial = world.new_communicator([0])
E = 0.0
F = np.zeros((len(system), 3))
if world.rank == 0:
E, F = calculate({}, serial)
E = world.sum(E)
world.sum(F)
else:
# Normally we'll just do it in parallel;
# that case is covered well by other tests, so we can probably trust it
E, F = calculate({}, world)
def check(parallel):
return calculate(parallel, comm=world, Eref=E, Fref=F)
from gpaw.matrix import Matrix
from gpaw.mpi import world
N = 6
if world.rank < 2:
comm = world.new_communicator([0, 1])
else:
comm = world.new_communicator([2, 3])
A0 = Matrix(N, N, dist=(comm, 2, 1))
A0.array[:] = world.rank
A = Matrix(N, N, dist=(world, 2, 2, 2))
A0.redist(A)
world.barrier()
print(A.array)
A0.array[:] = 117
A.redist(A0, 0)
print(A0.array)
client_ranks[k] = i
k += 1
elif process_types[i] == 2:
if first_potential_rank == None:
first_potential_rank = i
potential_ranks[j] = i
j += 1
my_potential_rank = world.rank - first_potential_rank
my_client_rank = client_ranks[my_potential_rank / potential_group_size]
print "pot: rank: %i my_client_rank: %i" % (world.rank, my_client_rank)
for i in xrange(clients):
s = potential_group_size
new_comm = world.new_communicator(potential_ranks[i * s:i * s + s])
if new_comm != None:
my_comm = new_comm
first_time = True
while True:
natoms = numpy.array((0, ), 'i')
if my_comm.rank == 0:
world.receive(natoms, my_client_rank, tag=0)
my_comm.broadcast(natoms, 0)
atomic_numbers = numpy.zeros(natoms, 'i')
positions = numpy.zeros(3 * natoms, 'd')
cell = numpy.zeros(9, 'd')
pbc = numpy.array((0, ), 'i')
if my_comm.rank == 0:
client_ranks[k] = i
k += 1
elif process_types[i] == 2:
if first_potential_rank == None:
first_potential_rank = i
potential_ranks[j] = i
j += 1
my_potential_rank = world.rank-first_potential_rank
my_client_rank = client_ranks[my_potential_rank/potential_group_size]
print "pot: rank: %i my_client_rank: %i" % (world.rank, my_client_rank)
for i in xrange(clients):
s = potential_group_size
new_comm = world.new_communicator(potential_ranks[i*s:i*s+s])
if new_comm != None:
my_comm = new_comm
first_time = True
while True:
natoms = numpy.array((0,), 'i')
if my_comm.rank == 0:
world.receive(natoms, my_client_rank, tag=0)
my_comm.broadcast(natoms, 0)
atomic_numbers = numpy.zeros(natoms, 'i')
positions = numpy.zeros(3*natoms, 'd')
cell = numpy.zeros(9, 'd')
pbc = numpy.array((0,), 'i')
if my_comm.rank == 0: