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simplify examples #42

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77 changes: 23 additions & 54 deletions examples/collective_write.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,16 +31,12 @@
32 400 x 400 x 200 6.67 45.72
"""

import sys, os, argparse, inspect
import sys, os, argparse
import numpy as np
from mpi4py import MPI
import pnetcdf

NDIMS = 3
NUM_VARS = 10

def parse_help(comm):
rank = comm.Get_rank()
def parse_help():
help_flag = "-h" in sys.argv or "--help" in sys.argv
if help_flag and rank == 0:
help_text = (
Expand All @@ -54,21 +50,22 @@ def parse_help(comm):
print(help_text)
return help_flag

def print_info(info_used):
print("MPI hint: cb_nodes =", info_used.Get("cb_nodes"))
print("MPI hint: cb_buffer_size =", info_used.Get("cb_buffer_size"))
print("MPI hint: striping_factor =", info_used.Get("striping_factor"))
print("MPI hint: striping_unit =", info_used.Get("striping_unit"))
def pnetcdf_io(filename, file_format, length):
# number of dimensions
NDIMS = 3
# number of variables
NUM_VARS = 10

def pnetcdf_io(comm, filename, file_format, length):
rank = comm.Get_rank()
nprocs = comm.Get_size()
if verbose and rank == 0:
print("Number of variables = ", NUM_VARS)
print("Number of dimensions = ", NDIMS)

starts = np.zeros(NDIMS, dtype=np.int32)
counts = np.zeros(NDIMS, dtype=np.int32)
gsizes = np.zeros(NDIMS, dtype=np.int32)
buf = []

# calculate local subarray access pattern
psizes = MPI.Compute_dims(nprocs, NDIMS)
starts[0] = rank % psizes[0]
starts[1] = (rank // psizes[1]) % psizes[1]
Expand All @@ -87,20 +84,12 @@ def pnetcdf_io(comm, filename, file_format, length):
for j in range(bufsize):
buf[i][j] = rank * i + 123 + j

comm.Barrier()
write_timing = MPI.Wtime()

# Create the file using file clobber mode
try:
f = pnetcdf.File(filename = filename, \
mode = 'w', \
format = file_format, \
comm = comm, \
info = None)
except OSError as e:
print("Error at {}:{} ncmpi_create() file {} ({})".format(__file__,inspect.currentframe().f_back.f_lineno, filename, e))
comm.Abort()
exit(1)
f = pnetcdf.File(filename = filename,
mode = 'w',
format = file_format,
comm = comm,
info = None)

# Define dimensions
dims = []
Expand All @@ -127,34 +116,14 @@ def pnetcdf_io(comm, filename, file_format, length):
# Close the file
f.close()

write_timing = MPI.Wtime() - write_timing

# calculate write amount across all processes in total
write_size = bufsize * NUM_VARS * np.dtype(np.int32).itemsize
sum_write_size = comm.reduce(write_size, MPI.SUM, root=0)
max_write_timing = comm.reduce(write_timing, MPI.MAX, root=0)

if rank == 0 and verbose:
subarray_size = (bufsize * np.dtype(np.int32).itemsize) / 1048576.0
print_info(info_used)
print("Local array size {} x {} x {} integers, size = {:.2f} MB".format(length, length, length, subarray_size))
sum_write_size /= 1048576.0
print("Global array size {} x {} x {} integers, write size = {:.2f} GB".format(gsizes[0], gsizes[1], gsizes[2], sum_write_size/1024.0))

write_bw = sum_write_size / max_write_timing
print(" procs Global array size exec(sec) write(MB/s)")
print("------- ------------------ --------- -----------")
print(" {:4d} {:4d} x {:4d} x {:4d} {:8.2f} {:10.2f}\n".format(nprocs, gsizes[0], gsizes[1], gsizes[2], max_write_timing, write_bw))


if __name__ == "__main__":

verbose = True
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
nprocs = comm.Get_size()

if parse_help(comm):
if parse_help():
MPI.Finalize()
sys.exit(1)

Expand All @@ -168,25 +137,25 @@ def pnetcdf_io(comm, filename, file_format, length):
parser.add_argument("-l", help="Size of each dimension of the local array\n")
args = parser.parse_args()

file_format = None
length = 10

if args.q: verbose = False
verbose = False if args.q else True

file_format = None
if args.k:
kind_dict = {'1':None, '2':"NETCDF3_64BIT_OFFSET", '5':"NETCDF3_64BIT_DATA"}
kind_dict = {'1':None, '2':"NC_64BIT_OFFSET", '5':"NC_64BIT_DATA"}
file_format = kind_dict[args.k]

length = 10
if args.l and int(args.l) > 0:
length = int(args.l)

filename = args.dir

if verbose and rank == 0:
print("{}: example of collective writes".format(os.path.basename(__file__)))

# Run I/O
try:
pnetcdf_io(comm, filename, file_format, length)
pnetcdf_io(filename, file_format, length)
except BaseException as err:
print("Error: type:", type(err), str(err))
raise
Expand Down
13 changes: 8 additions & 5 deletions examples/create_open.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,11 +34,12 @@ def parse_help():
return help_flag

def pnetcdf_io(filename):
if verbose and rank == 0:
print("{}: example of file create and open".format(os.path.basename(__file__)))

# create a new file using file clobber mode, i.e. flag "-w"
f = pnetcdf.File(filename=filename, mode = 'w', comm=comm, info=None)
f = pnetcdf.File(filename = filename,
mode = 'w',
comm = comm,
info = None)

# close the file
f.close()
Expand All @@ -51,7 +52,6 @@ def pnetcdf_io(filename):


if __name__ == "__main__":
verbose = True
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
nprocs = comm.Get_size()
Expand All @@ -68,10 +68,13 @@ def pnetcdf_io(filename):
parser.add_argument("-q", help="Quiet mode (reports when fail)", action="store_true")
args = parser.parse_args()

if args.q: verbose = False
verbose = False if args.q else True

filename = args.dir

if verbose and rank == 0:
print("{}: example of file create and open".format(os.path.basename(__file__)))

try:
pnetcdf_io(filename)
except BaseException as err:
Expand Down
17 changes: 14 additions & 3 deletions examples/fill_mode.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,10 +63,14 @@ def pnetcdf_io(filename):
NX = 4

if verbose and rank == 0:
print("{}: example of setting fill mode".format(os.path.basename(__file__)))
print("Y dimension size = ", NY)
print("X dimension size = ", NX)

# create a new file using clobber "w" mode
f = pnetcdf.File(filename=filename, mode = 'w', comm=comm, info=None)
f = pnetcdf.File(filename = filename,
mode = 'w',
comm = comm,
info = None)

# the global array is NY * (NX * nprocs)
global_ny = NY
Expand Down Expand Up @@ -131,8 +135,11 @@ def pnetcdf_io(filename):

# write to the 2nd record
rec_var.put_var_all(buf, start = starts, count = counts)

# close file
f.close()


if __name__ == "__main__":
verbose = True

Expand All @@ -152,10 +159,14 @@ def pnetcdf_io(filename):
parser.add_argument("-q", help="Quiet mode (reports when fail)", action="store_true")

args = parser.parse_args()
if args.q: verbose = False

verbose = False if args.q else True

filename = args.dir

if verbose and rank == 0:
print("{}: example of setting fill mode".format(os.path.basename(__file__)))

try:
pnetcdf_io(filename)
except BaseException as err:
Expand Down
47 changes: 29 additions & 18 deletions examples/flexible_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -89,14 +89,21 @@ def pnetcdf_io(filename, file_format):
NY = 5
NX = 5
NZ = 5
ghost_len = 3

if verbose and rank == 0:
print("{}: example of using flexible APIs".format(os.path.basename(__file__)))
print("Z dimension size = ", NZ)
print("Y dimension size = ", NY)
print("X dimension size = ", NX)

# number of cells at both end of each dimension
ghost_len = 3

# Create the file
f = pnetcdf.File(filename=filename, mode = 'w', format = file_format, comm=comm, info=None)
f = pnetcdf.File(filename = filename,
mode = 'w',
format = file_format,
comm = comm,
info = None)

# Define dimensions
dim_z = f.def_dim("Z", NZ*nprocs)
Expand Down Expand Up @@ -146,9 +153,9 @@ def pnetcdf_io(filename, file_format):
buf_zy.fill(-1)

# read using flexible API
var_zy.get_var_all(buf_zy, start = starts, \
count = counts, \
bufcount = 1, \
var_zy.get_var_all(buf_zy, start = starts,
count = counts,
bufcount = 1,
buftype = subarray)

# check contents of the get buffer
Expand All @@ -171,7 +178,10 @@ def pnetcdf_io(filename, file_format):
array_of_sizes = np.array([NY + 2 * ghost_len, NX + 2 * ghost_len])
array_of_subsizes = np.array([NY, NX])
array_of_starts = np.array([ghost_len, ghost_len])
subarray = MPI.DOUBLE.Create_subarray(array_of_sizes, array_of_subsizes, array_of_starts, order=MPI.ORDER_C)
subarray = MPI.DOUBLE.Create_subarray(array_of_sizes,
array_of_subsizes,
array_of_starts,
order=MPI.ORDER_C)
subarray.Commit()

# initialize write user buffer
Expand All @@ -181,9 +191,9 @@ def pnetcdf_io(filename, file_format):
counts = np.array([NY, NX])

# calling a blocking flexible write API
req_id = var_yx.iput_var(buf_yx, start = starts, \
count = counts, \
bufcount = 1, \
req_id = var_yx.iput_var(buf_yx, start = starts,
count = counts,
bufcount = 1,
buftype = subarray)

# commit posted pending nonblocking requests
Expand All @@ -198,9 +208,9 @@ def pnetcdf_io(filename, file_format):
buf_yx.fill(-1)

# calling a blocking flexible read API
req_id = var_yx.iget_var(buf_yx, start = starts, \
count = counts, \
bufcount = 1, \
req_id = var_yx.iget_var(buf_yx, start = starts,
count = counts,
bufcount = 1,
buftype=subarray)

# commit posted pending nonblocking requests
Expand All @@ -227,7 +237,6 @@ def pnetcdf_io(filename, file_format):


if __name__ == "__main__":
verbose = True
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
nprocs = comm.Get_size()
Expand All @@ -245,16 +254,18 @@ def pnetcdf_io(filename, file_format):
parser.add_argument("-k", help="File format: 1 for CDF-1, 2 for CDF-2, 5 for CDF-5")
args = parser.parse_args()

file_format = None

if args.q: verbose = False
verbose = False if args.q else True

file_format = None
if args.k:
kind_dict = {'1':None, '2':"NETCDF3_64BIT_OFFSET", '5':"NETCDF3_64BIT_DATA"}
kind_dict = {'1':None, '2':"NC_64BIT_OFFSET", '5':"NC_64BIT_DATA"}
file_format = kind_dict[args.k]

filename = args.dir

if verbose and rank == 0:
print("{}: example of using flexible APIs".format(os.path.basename(__file__)))

try:
pnetcdf_io(filename, file_format)
except BaseException as err:
Expand Down
15 changes: 10 additions & 5 deletions examples/get_info.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,7 @@ def parse_help():
print(help_text)
return help_flag


def print_info(info_used):
nkeys = info_used.Get_nkeys()
print("MPI File Info: nkeys =", nkeys)
Expand All @@ -60,11 +61,13 @@ def print_info(info_used):


def pnetcdf_io(filename):
if verbose and rank == 0:
print("{}: example of getting MPI-IO hints".format(os.path.basename(__file__)))

# create a new file using clobber "w" mode
f = pnetcdf.File(filename=filename, mode = 'w', file_format = "NETCDF3_64BIT_DATA", comm=comm, info=None)
f = pnetcdf.File(filename=filename,
mode = 'w',
file_format = "NC_64BIT_DATA",
comm=comm,
info=None)

# exit the define mode
f.enddef()
Expand All @@ -82,7 +85,6 @@ def pnetcdf_io(filename):


if __name__ == "__main__":
verbose = True
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
nprocs = comm.Get_size()
Expand All @@ -99,10 +101,13 @@ def pnetcdf_io(filename):
parser.add_argument("-q", help="Quiet mode (reports when fail)", action="store_true")
args = parser.parse_args()

if args.q: verbose = False
verbose = False if args.q else True

filename = args.dir

if verbose and rank == 0:
print("{}: example of getting MPI-IO hints".format(os.path.basename(__file__)))

try:
pnetcdf_io(filename)
except BaseException as err:
Expand Down
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