def test_test2(self):
"""
Apply the laplacian finite difference operator to clt
"""
f = cdms2.open(cdat_info.get_prefix() + '/sample_data/clt.nc', 'r')
cltVar = f['clt']
# global sizes
nLat, nLon = cltVar.shape[1:]
# local rank and number of procs
rk = MPI.COMM_WORLD.Get_rank()
sz = MPI.COMM_WORLD.Get_size()
# compute domain decomposition
decomp = CubeDecomp(sz, (nLat, nLon))
# number of processors along each axis
npLat, npLon = None, None
# list of slices
slab = decomp.getSlab(rk)
dc = decomp.getDecomp()
if dc is not None:
npLat, npLon = dc
if rk == 0:
print ''
print 'lat x lon sizes : %d x %d ' % (nLat, nLon)
print 'lat x lon domain decomp: %d x %d ' % (npLat, npLon)
else:
if rk == 0:
print 'No uniform decomp could be found for %d procs' % sz
sys.exit(1)
# starting/ending indices for local domain
iLatBeg, iLatEnd = slab[0].start, slab[0].stop
iLonBeg, iLonEnd = slab[1].start, slab[1].stop
# now read local domain data for time 0
clt = cltVar[0, iLatBeg:iLatEnd, iLonBeg:iLonEnd]
# make halo available to other procs
numGhosts = 1
clt.exposeHalo(ghostWidth=numGhosts)
# compute the star Laplacian in the interior, this does not require
# any communication
# laplacian = 4*clt[j, i] - clt[j+1, i] - clt[j-1, i] - clt[j, i+1] - clt[j, i-1]
# data domain
laplaceClt = 4 * clt[:]
# local neighbor contributions, no communication
laplaceClt[1:, :] -= clt[0:-1, :]
laplaceClt[0:-1, :] -= clt[1:, :]
laplaceClt[:, 1:] -= clt[:, 0:-1]
laplaceClt[:, 0:-1] -= clt[:, 1:]
# now compute and fill in the halo
# find the procs to the north, east, south, and west. This call will
# return None if there is no neighbor.
noProc = decomp.getNeighborProc(rk, (1, 0), periodic=(False, True))
soProc = decomp.getNeighborProc(rk, (-1, 0), periodic=(False, True))
eaProc = decomp.getNeighborProc(rk, (0, 1), periodic=(False, True))
weProc = decomp.getNeighborProc(rk, (0, -1), periodic=(False, True))
# correct at north/south poles where zero flux condition applies
if noProc is None:
laplaceClt[-1, :] -= clt[-1, :]
if soProc is None:
laplaceClt[0, :] -= clt[0, :]
# fetch the remote data in the halo of the neighboring processor. When
# the first argument is None, this amounts to a no-op (zero data are
# returned. Note that side refers to the neighbour domain. For instance,
# the data to the west of the local domain correspond to the east halo
# on the neighbouring processor.
weCltData = clt.fetchHaloData(weProc, side=(0, +1))
eaCltData = clt.fetchHaloData(eaProc, side=(0, -1))
soCltData = clt.fetchHaloData(soProc, side=(+1, 0))
noCltData = clt.fetchHaloData(noProc, side=(-1, 0))
# finish the operator
weSlc = clt.getHaloEllipsis(side=(0, -1))
eaSlc = clt.getHaloEllipsis(side=(0, +1))
soSlc = clt.getHaloEllipsis(side=(-1, 0))
noSlc = clt.getHaloEllipsis(side=(+1, 0))
laplaceClt[weSlc] -= weCltData
laplaceClt[eaSlc] -= eaCltData
if soProc is not None:
laplaceClt[soSlc] -= soCltData
if noProc is not None:
laplaceClt[noSlc] -= noCltData
if True:
laplaceClt0 = numpy.zeros(cltVar.shape[1:], cltVar.dtype)
# gather the data on proc 0
laplaceClt0List = MPI.COMM_WORLD.gather(laplaceClt, root=0)
checksum = 0
if rk == 0:
for proc in range(sz):
slab = decomp.getSlab(proc)
iLatBeg, iLatEnd = slab[0].start, slab[0].stop
iLonBeg, iLonEnd = slab[1].start, slab[1].stop
laplaceClt0[iLatBeg:iLatEnd, iLonBeg:iLonEnd] = \
laplaceClt0List[proc]
checksum = laplaceClt0.sum()
print 'checksum = %20.15g' % checksum
if False:
# plot
lat = cltVar.getLatitude()
lon = cltVar.getLongitude()
latmin, latmax = lat[:].min(), lat[:].max()
lonmin, lonmax = lon[:].min(), lon[:].max()
mp = Basemap(llcrnrlat=latmin,
urcrnrlat=latmax,
llcrnrlon=lonmin,
urcrnrlon=lonmax,
projection='cyl',
resolution='l')
mp.pcolor(lon[:], lat[:], laplaceClt0)
mp.colorbar()
mp.drawcoastlines()
pylab.title('Laplacian of clt')
# checks
self.assertLess(abs(checksum), 1.e-3)
# clean up
clt.freeHalo()
def test_test2(self):
"""
Apply the laplacian finite difference operator to clt
"""
f = cdms2.open(cdat_info.get_prefix() + '/sample_data/clt.nc', 'r')
cltVar = f['clt']
# global sizes
nLat, nLon = cltVar.shape[1:]
# local rank and number of procs
rk = MPI.COMM_WORLD.Get_rank()
sz = MPI.COMM_WORLD.Get_size()
# compute domain decomposition
decomp = CubeDecomp(sz, (nLat, nLon))
# number of processors along each axis
npLat, npLon = None, None
# list of slices
slab = decomp.getSlab(rk)
dc = decomp.getDecomp()
if dc is not None:
npLat, npLon = dc
if rk == 0:
print ''
print 'lat x lon sizes : %d x %d ' % (nLat, nLon)
print 'lat x lon domain decomp: %d x %d ' % (npLat, npLon)
else:
if rk == 0:
print 'No uniform decomp could be found for %d procs' % sz
sys.exit(1)
# starting/ending indices for local domain
iLatBeg, iLatEnd = slab[0].start, slab[0].stop
iLonBeg, iLonEnd = slab[1].start, slab[1].stop
# now read local domain data for time 0
clt = cltVar[0, iLatBeg:iLatEnd, iLonBeg:iLonEnd]
# make halo available to other procs
numGhosts = 1
clt.exposeHalo(ghostWidth = numGhosts)
# compute the star Laplacian in the interior, this does not require
# any communication
# laplacian = 4*clt[j, i] - clt[j+1, i] - clt[j-1, i] - clt[j, i+1] - clt[j, i-1]
# data domain
laplaceClt = 4 * clt[:]
# local neighbor contributions, no communication
laplaceClt[1: , :] -= clt[0:-1,:]
laplaceClt[0:-1, :] -= clt[1: ,:]
laplaceClt[:, 1: ] -= clt[:,0:-1]
laplaceClt[:, 0:-1] -= clt[:,1: ]
# now compute and fill in the halo
# find the procs to the north, east, south, and west. This call will
# return None if there is no neighbor.
noProc = decomp.getNeighborProc(rk, ( 1, 0), periodic = (False, True))
soProc = decomp.getNeighborProc(rk, (-1, 0), periodic = (False, True))
eaProc = decomp.getNeighborProc(rk, ( 0, 1), periodic = (False, True))
weProc = decomp.getNeighborProc(rk, ( 0, -1), periodic = (False, True))
# correct at north/south poles where zero flux condition applies
if noProc is None:
laplaceClt[-1,:] -= clt[-1,:]
if soProc is None:
laplaceClt[0,:] -= clt[0,:]
# fetch the remote data in the halo of the neighboring processor. When
# the first argument is None, this amounts to a no-op (zero data are
# returned. Note that side refers to the neighbour domain. For instance,
# the data to the west of the local domain correspond to the east halo
# on the neighbouring processor.
weCltData = clt.fetchHaloData(weProc, side=(0, +1))
eaCltData = clt.fetchHaloData(eaProc, side=(0, -1))
soCltData = clt.fetchHaloData(soProc, side=(+1, 0))
noCltData = clt.fetchHaloData(noProc, side=(-1, 0))
# finish the operator
weSlc = clt.getHaloEllipsis(side=(0, -1))
eaSlc = clt.getHaloEllipsis(side=(0, +1))
soSlc = clt.getHaloEllipsis(side=(-1, 0))
noSlc = clt.getHaloEllipsis(side=(+1, 0))
laplaceClt[weSlc] -= weCltData
laplaceClt[eaSlc] -= eaCltData
if soProc is not None:
laplaceClt[soSlc] -= soCltData
if noProc is not None:
laplaceClt[noSlc] -= noCltData
if True:
laplaceClt0 = numpy.zeros(cltVar.shape[1:], cltVar.dtype)
# gather the data on proc 0
laplaceClt0List = MPI.COMM_WORLD.gather(laplaceClt, root = 0)
checksum = 0
if rk == 0:
for proc in range(sz):
slab = decomp.getSlab(proc)
iLatBeg, iLatEnd = slab[0].start, slab[0].stop
iLonBeg, iLonEnd = slab[1].start, slab[1].stop
laplaceClt0[iLatBeg:iLatEnd, iLonBeg:iLonEnd] = \
laplaceClt0List[proc]
checksum = laplaceClt0.sum()
print 'checksum = %20.15g' % checksum
if False:
# plot
lat = cltVar.getLatitude()
lon = cltVar.getLongitude()
latmin, latmax = lat[:].min(), lat[:].max()
lonmin, lonmax = lon[:].min(), lon[:].max()
mp = Basemap(llcrnrlat = latmin, urcrnrlat = latmax,
llcrnrlon = lonmin, urcrnrlon = lonmax,
projection = 'cyl', resolution = 'l')
mp.pcolor(lon[:], lat[:], laplaceClt0)
mp.colorbar()
mp.drawcoastlines()
pylab.title('Laplacian of clt')
# checks
self.assertLess(abs(checksum), 1.e-3)
# clean up
clt.freeHalo()
def getDomainDecomp(nprocs,sizes):
latPrimeNumbers = getPrimeFactors(sizes[0])
lonPrimeNumbers = getPrimeFactors(sizes[1])
lonPrimeNumbers.reverse()
for plat in latPrimeNumbers:
for plon in lonPrimeNumbers:
if plat * plon == nprocs:
return [plat, plon]
return None, None
nLat,nLon = clt.shape[1:]
rk = MPI.COMM_WORLD.Get_rank()
sz = MPI.COMM_WORLD.Get_size()
decomp = CubeDecomp(sz, (nLat,nLon))
npLat,npLon = decomp.getDecomp()
slab = decomp.getSlab(rk)
print 'SLAB:',slab,type(slab)
if npLat is None or npLon is None:
print 'could not find a domain decomp for this number of procs'
sys.exit(1)
if rk == 0:
print 'domain decomp: ', npLat, ' x ', npLon
iLatBeg , iLatEnd = slab[0].start, slab[0].stop
iLonBeg , iLonEnd = slab[1].start, slab[1].stop
print '[%d] sub-domain slab: %d:%d, %d:%d dims %d x %d size: %d' % (rk, iLatBeg, iLatEnd, iLonBeg, iLatEnd, iLatEnd - iLatBeg, iLonEnd - iLonBeg, (iLatEnd - iLatBeg)*(iLonEnd - iLonBeg))