def split(nxpe, nype, path="data", output="./", informat="nc", outformat=None):
"""Split restart files across NXPE x NYPE processors.
Returns True on success
"""
if outformat == None:
outformat = informat
mxg = 2
myg = 2
npes = nxpe * nype
if npes <= 0:
print "ERROR: Negative or zero number of processors"
return False
if path == output:
print "ERROR: Can't overwrite restart files"
return False
file_list = glob.glob(os.path.join(path, "BOUT.restart.*."+informat))
nfiles = len(file_list)
if nfiles == 0:
print "ERROR: No restart files found"
return False
# Read old processor layout
f = DataFile(os.path.join(path, file_list[0]))
# Get list of variables
var_list = f.list()
if len(var_list) == 0:
print "ERROR: No data found"
return False
old_npes = f.read('NPES')
old_nxpe = f.read('NXPE')
if nfiles != old_npes:
print "WARNING: Number of restart files inconsistent with NPES"
print "Setting nfiles = " + str(old_npes)
nfiles = old_npes
if old_npes % old_nxpe != 0:
print "ERROR: Old NPES is not a multiple of old NXPE"
return False
old_nype = old_npes / old_nxpe
if nype % old_nype != 0:
print "SORRY: New nype must be a multiple of old nype"
return False
if nxpe % old_nxpe != 0:
print "SORRY: New nxpe must be a multiple of old nxpe"
return False
# Get dimension sizes
old_mxsub = 0
old_mysub = 0
mz = 0
for v in var_list:
if f.ndims(v) == 3:
s = f.size(v)
old_mxsub = s[0] - 2*mxg
old_mysub = s[1] - 2*myg
mz = s[2]
break
f.close()
# Calculate total size of the grid
nx = old_mxsub * old_nxpe
ny = old_mysub * old_nype
print "Grid sizes: ", nx, ny, mz
# Create the new restart files
for mype in range(npes):
# Calculate X and Y processor numbers
pex = mype % nxpe
pey = int(mype / nxpe)
old_pex = int(pex / xs)
old_pey = int(pey / ys)
old_x = pex % xs
old_y = pey % ys
# Old restart file number
old_mype = old_nxpe * old_pey + old_pex
# Calculate indices in old restart file
xmin = old_x*mxsub
xmax = xmin + mxsub - 1 + 2*mxg
ymin = old_y*mysub
ymax = ymin + mysub - 1 + 2*myg
print "New: "+str(mype)+" ("+str(pex)+", "+str(pey)+")"
print " => "+str(old_mype)+" ("+str(old_pex)+", "+str(old_pey)+") : ("+str(old_x)+", "+str(old_y)+")"
def redistribute(npes, path="data", nxpe=None, output=".", informat=None, outformat=None, mxg=2, myg=2):
"""Resize restart files across NPES processors.
Does not check if new processor arrangement is compatible with the branch cuts. In this respect restart.split is safer. However, BOUT++ checks the topology during initialisation anyway so this is not too serious.
Parameters
----------
npes : int
number of processors for the new restart files
path : string, optional
location of old restart files
nxpe : int, optional
number of processors to use in the x-direction (determines split: npes = nxpe * nype). Default is None which uses the same algorithm as BoutMesh (but without topology information) to determine a suitable value for nxpe.
output : string, optional
location to save new restart files
informat : string, optional
specify file format of old restart files (must be a suffix understood by DataFile, e.g. 'nc'). Default uses the format of the first 'BOUT.restart.*' file listed by glob.glob.
outformat : string, optional
specify file format of new restart files (must be a suffix understood by DataFile, e.g. 'nc'). Default is to use the same as informat.
Returns
-------
True on success
"""
if npes <= 0:
print("ERROR: Negative or zero number of processors")
return False
if path == output:
print("ERROR: Can't overwrite restart files")
return False
if informat == None:
file_list = glob.glob(os.path.join(path, "BOUT.restart.*"))
else:
file_list = glob.glob(os.path.join(path, "BOUT.restart.*."+informat))
nfiles = len(file_list)
# Read old processor layout
f = DataFile(file_list[0])
# Get list of variables
var_list = f.list()
if len(var_list) == 0:
print("ERROR: No data found")
return False
old_npes = f.read('NPES')
old_nxpe = f.read('NXPE')
old_nype = int(old_npes/old_nxpe)
if nfiles != old_npes:
print("WARNING: Number of restart files inconsistent with NPES")
print("Setting nfiles = " + str(old_npes))
nfiles = old_npes
if nfiles == 0:
print("ERROR: No restart files found")
return False
informat = file_list[0].split(".")[-1]
if outformat == None:
outformat = informat
old_mxsub = 0
old_mysub = 0
mz = 0
for v in var_list:
if f.ndims(v) == 3:
s = f.size(v)
old_mxsub = s[0] - 2*mxg
if old_mxsub < 0:
if s[0] == 1:
old_mxsub = 1
mxg = 0
elif s[0] == 3:
old_mxsub = 1
mxg = 1
else:
print("Number of x points is wrong?")
return False
old_mysub = s[1] - 2*myg
if old_mysub < 0:
if s[1] == 1:
old_mysub = 1
myg = 0
elif s[1] == 3:
old_mysub = 1
myg = 1
else:
print("Number of y points is wrong?")
return False
mz = s[2]
break
# Calculate total size of the grid
nx = old_mxsub * old_nxpe
ny = old_mysub * old_nype
print("Grid sizes: ", nx, ny, mz)
if nxpe == None: # Copy algorithm from BoutMesh for selecting nxpe
ideal = sqrt(float(nx) * float(npes) / float(ny)) # Results in square domain
for i in range(1,npes+1):
if npes%i == 0 and nx%i == 0 and int(nx/i) >= mxg and ny%(npes/i) == 0:
# Found an acceptable value
# Warning: does not check branch cuts!
if nxpe==None or abs(ideal - i) < abs(ideal - nxpe):
nxpe = i # Keep value nearest to the ideal
if nxpe == None:
print("ERROR: could not find a valid value for nxpe")
return False
nype = int(npes/nxpe)
outfile_list = []
for i in range(npes):
outpath = os.path.join(output, "BOUT.restart."+str(i)+"."+outformat)
outfile_list.append(DataFile(outpath, write=True, create=True))
infile_list = []
for i in range(old_npes):
inpath = os.path.join(path, "BOUT.restart."+str(i)+"."+outformat)
infile_list.append(DataFile(inpath))
old_mxsub = int(nx/old_nxpe)
old_mysub = int(ny/old_nype)
mxsub = int(nx/nxpe)
mysub = int(ny/nype)
for v in var_list:
ndims = f.ndims(v)
#collect data
if ndims == 0:
#scalar
data = f.read(v)
elif ndims == 2:
data = numpy.zeros( (nx+2*mxg,ny+2*nyg) )
for i in range(old_npes):
ix = i%old_nxpe
iy = int(i/old_nxpe)
ixstart = mxg
if ix == 0:
ixstart = 0
ixend = -mxg
if ix == old_nxpe-1:
ixend = 0
iystart = myg
if iy == 0:
iystart = 0
iyend = -myg
if iy == old_nype-1:
iyend = 0
data[ix*old_mxsub+ixstart:(ix+1)*old_mxsub+2*mxg+ixend, iy*old_mysub+iystart:(iy+1)*old_mysub+2*myg+iyend] = infile_list[i].read(v)[ixstart:old_mxsub+2*mxg+ixend, iystart:old_mysub+2*myg+iyend]
elif ndims == 3:
data = numpy.zeros( (nx+2*mxg,ny+2*myg,mz) )
for i in range(old_npes):
ix = i%old_nxpe
iy = int(i/old_nxpe)
ixstart = mxg
if ix == 0:
ixstart = 0
ixend = -mxg
if ix == old_nxpe-1:
ixend = 0
iystart = myg
if iy == 0:
iystart = 0
iyend = -myg
if iy == old_nype-1:
iyend = 0
data[ix*old_mxsub+ixstart:(ix+1)*old_mxsub+2*mxg+ixend, iy*old_mysub+iystart:(iy+1)*old_mysub+2*myg+iyend, :] = infile_list[i].read(v)[ixstart:old_mxsub+2*mxg+ixend, iystart:old_mysub+2*myg+iyend, :]
else:
print("ERROR: variable found with unexpected number of dimensions,",ndims,v)
return False
# write data
for i in range(npes):
ix = i%nxpe
iy = int(i/nxpe)
outfile = outfile_list[i]
if v == "NPES":
outfile.write(v,npes)
elif v == "NXPE":
outfile.write(v,nxpe)
elif ndims == 0:
# scalar
outfile.write(v,data)
elif ndims == 2:
# Field2D
outfile.write(v,data[ix*mxsub:(ix+1)*mxsub+2*mxg, iy*mysub:(iy+1)*mysub+2*myg])
elif ndims == 3:
# Field3D
outfile.write(v,data[ix*mxsub:(ix+1)*mxsub+2*mxg, iy*mysub:(iy+1)*mysub+2*myg, :])
else:
print("ERROR: variable found with unexpected number of dimensions,",f.ndims(v))
f.close()
for infile in infile_list:
infile.close()
for outfile in outfile_list:
outfile.close()
return True
else:
print ("Please respond with 'yes' or 'no' "\
"(or 'y' or 'n').\n")
# Loop means more than one variable can be loaded
# Perhaps better implemented as a function
c = 0
while c == 0:
# An iterator to loop over all of the variables in the file
it = f.handle.variables.__iter__()
print 'Variable Number' + '\t' + 'Name' + '\t' + '\t' + 'Dims.'
# For all variables in the file, print the identifier in
# the dictionary, its name and the number of dimensions
for i in range(np.shape(f.handle.variables.keys())[0]):
print str(i) + '\t' + f.handle.variables.keys()[i] + '\t' + '\t' + str(np.shape(f.size(it.next()))[0])
print '\n' + 'Variable number to load?'
v = raw_input()
print 'Importing variable : ' + f.handle.variables.keys()[v]
# If the variable has 4D data, recommend slicing it up
if np.shape(f.size(f.handle.variables.keys()[v]))[0] == 4:
print 'Time slices (-1 for all), Range=', t
# Takes the Max and Min slice range from the user, places into list
# that's passed to the collect routine later
tind = [int(raw_input('min: ')), int(raw_input('max: '))]
# If the minimum or maximum lie outside the range, just choose everything
# This is probably not ideal
if np.min(tind) < 0 or np.max(tind) > t[1]:
def redistribute(npes, path="data", nxpe=None, output=".", informat=None, outformat=None, mxg=2, myg=2):
"""Resize restart files across NPES processors.
Does not check if new processor arrangement is compatible with the branch cuts. In this respect restart.split is safer. However, BOUT++ checks the topology during initialisation anyway so this is not too serious.
Parameters
----------
npes : int
number of processors for the new restart files
path : string, optional
location of old restart files
nxpe : int, optional
number of processors to use in the x-direction (determines split: npes = nxpe * nype). Default is None which uses the same algorithm as BoutMesh (but without topology information) to determine a suitable value for nxpe.
output : string, optional
location to save new restart files
informat : string, optional
specify file format of old restart files (must be a suffix understood by DataFile, e.g. 'nc'). Default uses the format of the first 'BOUT.restart.*' file listed by glob.glob.
outformat : string, optional
specify file format of new restart files (must be a suffix understood by DataFile, e.g. 'nc'). Default is to use the same as informat.
Returns
-------
True on success
"""
if npes <= 0:
print("ERROR: Negative or zero number of processors")
return False
if path == output:
print("ERROR: Can't overwrite restart files")
return False
if informat == None:
file_list = glob.glob(os.path.join(path, "BOUT.restart.*"))
else:
file_list = glob.glob(os.path.join(path, "BOUT.restart.*."+informat))
nfiles = len(file_list)
# Read old processor layout
f = DataFile(file_list[0])
# Get list of variables
var_list = f.list()
if len(var_list) == 0:
print("ERROR: No data found")
return False
old_npes = f.read('NPES')
old_nxpe = f.read('NXPE')
old_nype = int(old_npes/old_nxpe)
if nfiles != old_npes:
print("WARNING: Number of restart files inconsistent with NPES")
print("Setting nfiles = " + str(old_npes))
nfiles = old_npes
if nfiles == 0:
print("ERROR: No restart files found")
return False
informat = file_list[0].split(".")[-1]
if outformat == None:
outformat = informat
old_mxsub = 0
old_mysub = 0
mz = 0
for v in var_list:
if f.ndims(v) == 3:
s = f.size(v)
old_mxsub = s[0] - 2*mxg
if old_mxsub < 0:
if s[0] == 1:
old_mxsub = 1
mxg = 0
elif s[0] == 3:
old_mxsub = 1
mxg = 1
else:
print("Number of x points is wrong?")
return False
old_mysub = s[1] - 2*myg
if old_mysub < 0:
if s[1] == 1:
old_mysub = 1
myg = 0
elif s[1] == 3:
old_mysub = 1
myg = 1
else:
print("Number of y points is wrong?")
return False
mz = s[2]
break
# Calculate total size of the grid
nx = old_mxsub * old_nxpe
ny = old_mysub * old_nype
print("Grid sizes: ", nx, ny, mz)
if nxpe == None: # Copy algorithm from BoutMesh for selecting nxpe
ideal = sqrt(float(nx) * float(npes) / float(ny)) # Results in square domain
for i in range(1,npes+1):
if npes%i == 0 and nx%i == 0 and int(nx/i) >= mxg and ny%(npes/i) == 0:
# Found an acceptable value
# Warning: does not check branch cuts!
if nxpe==None or abs(ideal - i) < abs(ideal - nxpe):
nxpe = i # Keep value nearest to the ideal
if nxpe == None:
print("ERROR: could not find a valid value for nxpe")
return False
nype = int(npes/nxpe)
outfile_list = []
for i in range(npes):
outpath = os.path.join(output, "BOUT.restart."+str(i)+"."+outformat)
outfile_list.append(DataFile(outpath, write=True, create=True))
infile_list = []
for i in range(old_npes):
inpath = os.path.join(path, "BOUT.restart."+str(i)+"."+outformat)
infile_list.append(DataFile(inpath))
old_mxsub = int(nx/old_nxpe)
old_mysub = int(ny/old_nype)
mxsub = int(nx/nxpe)
mysub = int(ny/nype)
for v in var_list:
ndims = f.ndims(v)
#collect data
if ndims == 0:
#scalar
data = f.read(v)
elif ndims == 2:
data = numpy.zeros( (nx+2*mxg,ny+2*nyg) )
for i in range(old_npes):
ix = i%old_nxpe
iy = int(i/old_nxpe)
ixstart = mxg
if ix == 0:
ixstart = 0
ixend = -mxg
if ix == old_nxpe-1:
ixend = 0
iystart = myg
if iy == 0:
iystart = 0
iyend = -myg
if iy == old_nype-1:
iyend = 0
data[ix*old_mxsub+ixstart:(ix+1)*old_mxsub+2*mxg+ixend, iy*old_mysub+iystart:(iy+1)*old_mysub+2*myg+iyend] = infile_list[i].read(v)[ixstart:old_mxsub+2*mxg+ixend, iystart:old_mysub+2*myg+iyend]
elif ndims == 3:
data = numpy.zeros( (nx+2*mxg,ny+2*myg,mz) )
for i in range(old_npes):
ix = i%old_nxpe
iy = int(i/old_nxpe)
ixstart = mxg
if ix == 0:
ixstart = 0
ixend = -mxg
if ix == old_nxpe-1:
ixend = 0
iystart = myg
if iy == 0:
iystart = 0
iyend = -myg
if iy == old_nype-1:
iyend = 0
data[ix*old_mxsub+ixstart:(ix+1)*old_mxsub+2*mxg+ixend, iy*old_mysub+iystart:(iy+1)*old_mysub+2*myg+iyend, :] = infile_list[i].read(v)[ixstart:old_mxsub+2*mxg+ixend, iystart:old_mysub+2*myg+iyend, :]
else:
print("ERROR: variable found with unexpected number of dimensions,",ndims,v)
return False
# write data
for i in range(npes):
ix = i%nxpe
iy = int(i/nxpe)
outfile = outfile_list[i]
if v == "NPES":
outfile.write(v,npes)
elif v == "NXPE":
outfile.write(v,nxpe)
elif ndims == 0:
# scalar
outfile.write(v,data)
elif ndims == 2:
# Field2D
outfile.write(v,data[ix*mxsub:(ix+1)*mxsub+2*mxg, iy*mysub:(iy+1)*mysub+2*myg])
elif ndims == 3:
# Field3D
outfile.write(v,data[ix*mxsub:(ix+1)*mxsub+2*mxg, iy*mysub:(iy+1)*mysub+2*myg, :])
else:
print("ERROR: variable found with unexpected number of dimensions,",f.ndims(v))
f.close()
for infile in infile_list:
infile.close()
for outfile in outfile_list:
outfile.close()
return True
