def setUp(self):
self.temp = TempFile()
ad.init_noxml()
ad.allocate_buffer(ad.BUFFER_ALLOC_WHEN.NOW, 10)
g = ad.declare_group("temperature", "", ad.FLAG.YES)
ad.define_var(g, "NX", "", ad.DATATYPE.integer, "", "", "")
ad.define_var(g, "size", "", ad.DATATYPE.integer, "", "", "")
ad.define_var(g, "temperature", "", ad.DATATYPE.double, "size,NX",
"size,NX", "0,0")
self.msg = "this is a test"
ad.define_attribute(g, "desc", "", ad.DATATYPE.string, self.msg, "")
ad.select_method(g, "POSIX1", "verbose=3", "")
for i in range(5):
mode = "a"
if i == 0: mode = "w"
fd = ad.open("temperature", self.temp.path, mode)
self.NX = 10
self.size = 2
groupsize = 4 + 4 + 8 * self.size * self.NX
t = np.array(range(self.NX * self.size),
dtype=np.float64) + 100 * i
self.tt = t.reshape((self.size, self.NX))
ad.set_group_size(fd, groupsize)
ad.write_int(fd, "NX", self.NX)
ad.write_int(fd, "size", self.size)
ad.write(fd, "temperature", self.tt)
ad.close(fd)
ad.finalize()
self.f = ad.file(self.temp.path)
def setUp(self):
NX = 10
size = 2
t = np.array(range(NX*size), dtype=np.float64)
tt = t.reshape((size, NX))
self.temp = TempFile()
ad.init_noxml()
ad.allocate_buffer (ad.BUFFER_ALLOC_WHEN.NOW, 10);
fw = ad.writer(self.temp.path)
fw.declare_group('group', method='POSIX1')
fw['NX'] = NX
fw['size'] = size
fw['temperature'] = tt
fw.attrs['/temperature/description'] = "Global array written from 'size' processes"
fw.attrs["/someSubGroup/anOtherGroup/anOtherAttribute"] = 99
fw["/someSubGroup/anOtherGroup/anOtherVariable"] = 77
fw.close()
ad.finalize()
self.f = ad.file(self.temp.path)
def setUp(self):
self.temp = TempFile()
ad.init_noxml()
ad.allocate_buffer(ad.BUFFER_ALLOC_WHEN.NOW, 10)
g = ad.declare_group("temperature", "", ad.FLAG.YES)
ad.define_var(g, "NX", "", ad.DATATYPE.integer, "", "", "")
ad.define_var(g, "size", "", ad.DATATYPE.integer, "", "", "")
ad.define_var(g, "temperature", "", ad.DATATYPE.double, "size,NX",
"size,NX", "0,0")
self.msg = "this is a test"
self.unit = "C"
## attr must be <varpath> + / + something without / (line 857, common_read.c)
ad.define_attribute(g, "temperature/desc", "", ad.DATATYPE.string,
self.msg, "")
ad.define_attribute(g, "temperature/unit", "", ad.DATATYPE.string,
self.unit, "")
ad.select_method(g, "POSIX1", "verbose=3", "")
fd = ad.open("temperature", self.temp.path, "w")
self.NX = 10
self.size = 2
groupsize = 4 + 4 + 8 * self.size * self.NX
t = np.array(range(self.NX * self.size), dtype=np.float64)
self.tt = t.reshape((self.size, self.NX))
ad.set_group_size(fd, groupsize)
ad.write_int(fd, "NX", self.NX)
ad.write_int(fd, "size", self.size)
ad.write(fd, "temperature", self.tt)
ad.close(fd)
ad.finalize()
self.f = ad.file(self.temp.path)
def setUp(self):
self.temp = TempFile()
ad.init_noxml()
ad.allocate_buffer (ad.BUFFER_ALLOC_WHEN.NOW, 10);
g = ad.declare_group("temperature", "", ad.FLAG.YES)
ad.define_var(g, "NX", "", ad.DATATYPE.integer, "", "", "")
ad.define_var(g, "size", "", ad.DATATYPE.integer, "", "", "")
ad.define_var(g, "temperature", "", ad.DATATYPE.double, "size,NX", "size,NX", "0,0")
ad.define_var(g, "temperature", "", ad.DATATYPE.double, "size,NX", "size,NX", "0,0")
self.msg = "this is a test"
ad.define_attribute(g, "desc", "", ad.DATATYPE.string, self.msg, "")
ad.define_attribute(g, "temperature/unit", "", ad.DATATYPE.string, "C", "")
ad.define_attribute(g, "temperature/desc", "", ad.DATATYPE.string, "description", "")
ad.define_attribute(g, "/subgroup/subsubgroup/otherattr", "", ad.DATATYPE.string, "another", "")
ad.define_var(g, "/subgroup/subsubgroup/othervar", "", ad.DATATYPE.integer, "", "", "")
ad.select_method(g, "POSIX1", "verbose=3", "")
fd = ad.open("temperature", self.temp.path, "w")
self.NX = 10
self.size = 2
groupsize = 4 + 4 + 8 * self.size * self.NX + 4
t = np.array(range(self.NX * self.size), dtype=np.float64)
self.tt = t.reshape((self.size, self.NX))
ad.set_group_size(fd, groupsize)
ad.write_int(fd, "NX", self.NX)
ad.write_int(fd, "size", self.size)
ad.write(fd, "temperature", self.tt)
ad.write_int(fd, "/subgroup/subsubgroup/othervar", 99)
ad.close(fd)
ad.finalize()
self.f = ad.file(self.temp.path)
def setUp(self):
self.temp = TempFile()
ad.init_noxml()
ad.allocate_buffer (ad.BUFFER_ALLOC_WHEN.NOW, 10);
g = ad.declare_group("temperature", "", ad.FLAG.YES)
ad.define_var(g, "NX", "", ad.DATATYPE.integer, "", "", "")
ad.define_var(g, "size", "", ad.DATATYPE.integer, "", "", "")
ad.define_var(g, "temperature", "", ad.DATATYPE.double, "size,NX", "size,NX", "0,0")
self.msg = "this is a test"
self.unit = "C"
## attr must be <varpath> + / + something without / (line 857, common_read.c)
ad.define_attribute(g, "temperature/desc", "", ad.DATATYPE.string, self.msg, "")
ad.define_attribute(g, "temperature/unit", "", ad.DATATYPE.string, self.unit, "")
ad.select_method(g, "POSIX1", "verbose=3", "")
fd = ad.open("temperature", self.temp.path, "w")
self.NX = 10
self.size = 2
groupsize = 4 + 4 + 8 * self.size * self.NX
t = np.array(range(self.NX * self.size), dtype=np.float64)
self.tt = t.reshape((self.size, self.NX))
ad.set_group_size(fd, groupsize)
ad.write_int(fd, "NX", self.NX)
ad.write_int(fd, "size", self.size)
ad.write(fd, "temperature", self.tt)
ad.close(fd)
ad.finalize()
self.f = ad.file(self.temp.path)
def write(self, msg):
doid = msg['doid']
column = msg['column']
rows = msg['rows']
shape = msg['shape']
rowid = msg['row']
datatype = msg['datatype']
data = msg['data']
filename = self.filepath + '/' + doid
dimension = [rows] + copy.copy(shape)
global_dimension = copy.copy(dimension)
global_dimension[0] = self.maxrows
offset = [0] * len(dimension)
offset[0] = rowid
ad.init_noxml()
ad.allocate_buffer(ad.BUFFER_ALLOC_WHEN.NOW, self.buffersize)
adios_group = ad.declare_group("shore", "", ad.FLAG.YES)
local_dimension = str(dimension)[1:-1]
global_dimension = str(global_dimension)[1:-1]
offset = str(offset)[1:-1]
ad.select_method(adios_group, "POSIX", "", "")
ad.define_var(adios_group, column, "",
self.dtype_numpy2adios[datatype], local_dimension,
global_dimension, offset)
adios_file = ad.open("shore", filename, 'u')
group_size = 1000000
if data.nbytes > group_size:
group_size = data.nbytes
ad.set_group_size(adios_file, group_size)
ad.write(adios_file, column, data, datatype)
ad.close(adios_file)
ad.finalize()
return True
def write_scalar(self, adtype, val, varname='val'):
ad.init_noxml()
ad.allocate_buffer(ad.BUFFER_ALLOC_WHEN.NOW, 10)
g = ad.declare_group("group", "", ad.FLAG.YES)
ad.define_var(g, varname, "", adtype, "", "", "")
ad.select_method(g, "POSIX1", "", "")
if adtype == ad.DATATYPE.string:
dtype = ad.adios2npdtype(adtype, len(str(val)))
npval = np.array(val, dtype=dtype)
else:
dtype = ad.adios2npdtype(adtype)
npval = np.array(val, dtype=dtype)
fd = ad.open("group", self.temp.path, "w")
ad.set_group_size(fd, npval.nbytes)
ad.write(fd, varname, val, dtype)
ad.close(fd)
ad.finalize()
f = ad.file(self.temp.path)
v = f.vars['val']
self.assertEqual(v.read(), npval)
def write_scalar(self, adtype, val, varname='val'):
ad.init_noxml()
ad.allocate_buffer (ad.BUFFER_ALLOC_WHEN.NOW, 10);
g = ad.declare_group("group", "", ad.FLAG.YES)
ad.define_var(g, varname, "", adtype, "", "", "")
ad.select_method(g, "POSIX1", "", "")
if adtype == ad.DATATYPE.string:
dtype = ad.adios2npdtype(adtype, len(str(val)))
npval = np.array(val, dtype=dtype)
else:
dtype = ad.adios2npdtype(adtype)
npval = np.array(val, dtype=dtype)
fd = ad.open("group", self.temp.path, "w")
ad.set_group_size(fd, npval.nbytes)
ad.write(fd, varname, val, dtype)
ad.close(fd)
ad.finalize()
f = ad.file(self.temp.path)
v = f.vars['val']
self.assertEqual(v.read(), npval)
import numpy as np
import getopt, sys
import os
method = "POSIX"
init = "verbose=3;"
if len(sys.argv) > 1:
method = sys.argv[1]
if len(sys.argv) > 2:
init = sys.argv[2]
## Init
ad.init_noxml()
ad.allocate_buffer (ad.BUFFER_ALLOC_WHEN.NOW, 10);
g = ad.declare_group("temperature", "", 1)
ad.define_var(g, "NX", "", ad.DATATYPE.integer, "", "", "")
ad.define_var(g, "size", "", ad.DATATYPE.integer, "", "", "")
ad.define_var(g, "temperature", "", ad.DATATYPE.double, "size,NX", "size,NX", "0,0")
ad.select_method(g, method, init, "")
print ">>> Method:", method
## Writing
for i in range(5):
fd = ad.open("temperature", "temp.bp", "a")
NX = 10
size = 2
groupsize = 4 + 4 + 8 * size * NX
t = np.array(range(NX*size), dtype=np.float64) + 100*i
$ python ./test_adios_write.py
"""
import adios as ad
import numpy as np
print("\n>>> Prepare ...\n")
fname = 'adios_test_writer.bp'
NX = 10
size = 2
t = np.array(list(range(NX * size)), dtype=np.float64)
tt = t.reshape((size, NX))
print("\n>>> Writing ...\n")
ad.init_noxml()
ad.allocate_buffer(ad.BUFFER_ALLOC_WHEN.NOW, 10)
fw = ad.writer(fname)
fw.declare_group('group', method='POSIX1')
fw['NX'] = NX
fw['size'] = size
fw['temperature'] = tt
fw.attrs[
'/temperature/description'] = "Global array written from 'size' processes"
fw.close()
## Reading
print("\n>>> Reading ...\n")
f = ad.file(fname)
def setUp(self):
ad.init_noxml()
ad.allocate_buffer(ad.BUFFER_ALLOC_WHEN.NOW, 10)
def setUp(self):
ad.init_noxml()
ad.allocate_buffer(ad.BUFFER_ALLOC_WHEN.NOW, 10)