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 test_writer_default_group(self):
self.temp = TempFile()
fw = ad.writer(self.temp.path, method="POSIX1")
fw.close()
f = ad.file(self.temp.path)
f.close()
def test_simple1(self):
self.temp = TempFile()
NX = 10
size = 2
t = np.array(list(range(NX * size)), dtype=np.float64)
tt = t.reshape((size, NX))
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()
f = ad.file(self.temp.path)
t = f["temperature"]
# here t could have a member dictionary attr(s) again
# which looks up all attributes starting with t.name
# now match: f.attrs["/temperature/description"]
self.assertEqual(t.attrs["description"],
f.attrs["/temperature/description"])
# the same should be possible for groups
g = f["/someSubGroup/anOtherGroup"]
# now match: f.attrs["/someSubGroup/anOtherGroup/anOtherAttribute"]
self.assertEqual(
g.attrs["anOtherAttribute"],
f.attrs["/someSubGroup/anOtherGroup/anOtherAttribute"])
# now match: f["/someSubGroup/anOtherGroup/anOtherVariable"]
self.assertEqual(g["anOtherVariable"],
f["/someSubGroup/anOtherGroup/anOtherVariable"])
# Missing '/'
g = f["someSubGroup/anOtherGroup"]
# now match: f.attrs["/someSubGroup/anOtherGroup/anOtherAttribute"]
self.assertEqual(
g.attrs["anOtherAttribute"],
f.attrs["/someSubGroup/anOtherGroup/anOtherAttribute"])
# now match: f["/someSubGroup/anOtherGroup/anOtherVariable"]
self.assertEqual(g["anOtherVariable"],
f["/someSubGroup/anOtherGroup/anOtherVariable"])
## Testing name acess
self.assertEqual(g["anOtherVariable"][...], g.anOtherVariable[...])
self.assertEqual(g["anOtherAttribute"].value, g.anOtherAttribute.value)
def test_simple2(self):
self.temp = TempFile()
NX = 10
size = 2
t = np.array(list(range(NX*size)), dtype=np.float64)
tt = t.reshape((size, NX))
fw = ad.writer(self.temp.path)
fw.declare_group('mygroup', method='POSIX1')
fw['/data/0/fields/FieldE/x'] = tt
fw['/data/0/fields/FieldE/y'] = tt*2
fw['/data/0/particles/i/globalCellIdx/x'] = t
fw['/data/0/particles/i/globalCellIdx/y'] = t*2
fw.attrs['/data/0/fields/FieldE/x/sim_unit'] = 77
fw.attrs['/data/0/fields/FieldE/y/sim_unit'] = 99
fw.attrs['/data/0/fields/e_chargeDensity/sim_unit'] = 88
fw.attrs['/data/0/iteration'] = 33
fw.attrs['/data/0/sim_slides'] = 55
fw.close()
f = ad.file(self.temp.path)
g = f["data/0"]
self.assertTrue((g['fields/FieldE/x'][...] == tt).all())
self.assertEqual(g['fields/FieldE/y/sim_unit'][...], 99)
self.assertEqual(g['iteration'][...], 33)
g1 = f["/data/0"]
self.assertTrue((g1['fields/FieldE/x'][...] == tt).all())
self.assertEqual(g1['fields/FieldE/y/sim_unit'][...], 99)
self.assertEqual(g1['iteration'][...], 33)
g = f["data"]
g = f["/data"]
g = f["/data/"]
g = f["data/0/"]
g = f["/data/0"]
g2 = g["fields"]
self.assertTrue((g2['FieldE/x'][...] == tt).all())
self.assertTrue((g2['FieldE/y'][...] == tt*2).all())
self.assertEqual(g2['FieldE/x/sim_unit'][...], 77)
self.assertEqual(g2['FieldE/y/sim_unit'][...], 99)
## Check dirs()
self.assertEqual(sorted(g.dirs()), sorted(['particles', 'fields']))
self.assertEqual(sorted(g['fields'].dirs()), sorted(['e_chargeDensity', 'FieldE']))
self.assertEqual(f.dirs(), ['data'])
def test_softdict2(self):
self.temp = TempFile()
fw = ad.writer(self.temp.path)
fw.vars['a1'] = 12
fw.vars['/a2'] = 42
fw.close()
f = ad.file(self.temp.path)
self.assertEqual(f.vars['/a1'][...], f['/a1'][...])
self.assertEqual(f.vars['a1'][...], f['a1'][...])
self.assertEqual(f.vars['/a2'][...], f['/a2'][...])
self.assertEqual(f.vars['a2'][...], f['a2'][...])
def test_writer_varname(self):
self.temp = TempFile()
fw = ad.writer(self.temp.path, method="POSIX1")
NVARS = 99
fw.vars['nvars'] = NVARS
fw.vars['/nvars'] = NVARS
fw.vars['_nvars'] = NVARS
fw.close()
f = ad.file(self.temp.path)
self.assertEqual(f.nvars, 3)
self.assertEqual(f._nvars[...], NVARS)
def test_writer_attr(self):
self.temp = TempFile()
NX = 10
val1 = np.array(list(range(NX)), dtype=np.int32)
val2 = np.array(list(range(5)), dtype='f8')
single_string = "ABCD"
three_string = ("AA", "BBB", "CCCC")
single_int = 10
five_int = np.array(list(range(5)), dtype=np.int32)
single_double = 1.1
five_double = np.array(list(range(5)), dtype='double') * 1.1
unicode_string = u"unicode"
bytes_string = u"bytes"
fw = ad.writer(self.temp.path)
fw.declare_group("group", method="POSIX1")
fw.define_attr("single_string")
fw.define_attr("three_string")
fw.define_attr("single_int")
fw.define_attr("five_int")
fw.define_attr("single_double")
fw.define_attr("five_double")
fw.define_attr("unicode_string")
fw.define_attr("bytes_string")
fw['single_string'] = single_string
fw['three_string'] = three_string
fw['single_int'] = single_int
fw['five_int'] = five_int
fw['single_double'] = single_double
fw['five_double'] = five_double
fw['unicode_string'] = unicode_string
fw['bytes_string'] = bytes_string
fw.close()
f = ad.file(self.temp.path)
self.assertEqual(f['single_string'].value, single_string.encode())
##self.assertTrue((f['three_string'].value == three_string).all())
self.assertTrue(f['three_string'].value[0], three_string[0].encode())
self.assertTrue(f['three_string'].value[1], three_string[1].encode())
self.assertTrue(f['three_string'].value[2], three_string[2].encode())
self.assertEqual(f['single_int'].value, single_int)
self.assertTrue((f['five_int'].value == five_int).all())
self.assertEqual(f['single_double'].value, single_double)
self.assertTrue((f['five_double'].value == five_double).all())
self.assertTrue(f['unicode_string'].value, unicode_string.encode())
self.assertTrue(f['bytes_string'].value, bytes_string)
def test_writer_undefined_var(self):
self.temp = TempFile()
NX = 10
val1 = np.array(list(range(NX)), dtype=np.int32)
val2 = np.array(list(range(5)), dtype='f8')
fw = ad.writer(self.temp.path, method="POSIX1")
fw['NX'] = NX
fw['val1'] = val1
fw['val2'] = val2
fw.close()
f = ad.file(self.temp.path)
self.assertEqual(f['NX'][...], NX)
self.assertTrue((f['val1'][:] == val1).all())
self.assertTrue((f['val2'][:] == val2).all())
def test_writer_undefined_var(self):
self.temp = TempFile()
NX = 10
val1 = np.array(range(NX), dtype=np.int32)
val2 = np.array(range(5), dtype="f8")
fw = ad.writer(self.temp.path)
fw.declare_group("group", method="POSIX1")
fw["NX"] = NX
fw["val1"] = val1
fw["val2"] = val2
fw.close()
f = ad.file(self.temp.path)
self.assertEqual(f["NX"][:], NX)
self.assertTrue((f["val1"][:] == val1).all())
self.assertTrue((f["val2"][:] == val2).all())
def test_writer_transform(self):
self.temp = TempFile()
NX = 10
val1 = np.array(list(range(NX)), dtype=np.int32)
val2 = np.array(list(range(5)), dtype='f8')
fw = ad.writer(self.temp.path)
fw.declare_group("group", method="POSIX1")
fw['NX'] = NX
fw['val1'] = val1
fw['val2'] = val2
fw['val1'].transform = 'identity'
fw.close()
f = ad.file(self.temp.path)
self.assertEqual(f['NX'][...], NX)
self.assertTrue((f['val1'][:] == val1).all())
self.assertTrue((f['val2'][:] == val2).all())
def test_writer_timeaggregation(self):
self.temp = TempFile()
NX = 10
val1 = np.array(list(range(NX)), dtype=np.int32)
val2 = np.array(list(range(5)), dtype='f8')
fw = ad.writer(self.temp.path)
fw.declare_group("group", method="POSIX1")
fw.set_time_aggregation(3200)
fw['NX'] = NX
fw['val1'] = val1
fw['val2'] = val2
fw.close()
ad.finalize()
f = ad.file(self.temp.path)
self.assertEqual(f['NX'][...], NX)
self.assertTrue((f['val1'][:] == val1).all())
self.assertTrue((f['val2'][:] == val2).all())
def test_writer_attr(self):
self.temp = TempFile()
NX = 10
val1 = np.array(range(NX), dtype=np.int32)
val2 = np.array(range(5), dtype='f8')
single_string = "ABCD"
three_string = ("AA", "BBB", "CCCC")
single_int = 10
five_int = np.array(range(5), dtype=np.int32)
single_double = 1.1
five_double = np.array(range(5), dtype='double') * 1.1
fw = ad.writer(self.temp.path)
fw.declare_group("group", method="POSIX1")
fw.define_attr("single_string")
fw.define_attr("three_string")
fw.define_attr("single_int")
fw.define_attr("five_int")
fw.define_attr("single_double")
fw.define_attr("five_double")
fw['single_string'] = single_string
fw['three_string'] = three_string
fw['single_int'] = single_int
fw['five_int'] = five_int
fw['single_double'] = single_double
fw['five_double'] = five_double
fw.close()
f = ad.file(self.temp.path)
self.assertEqual(f['single_string'].value, single_string)
self.assertTrue((f['three_string'].value == three_string).all())
self.assertEqual(f['single_int'].value, single_int)
self.assertTrue((f['five_int'].value == five_int).all())
self.assertEqual(f['single_double'].value, single_double)
self.assertTrue((f['five_double'].value == five_double).all())
def test_writer_attr(self):
self.temp = TempFile()
NX = 10
val1 = np.array(range(NX), dtype=np.int32)
val2 = np.array(range(5), dtype="f8")
single_string = "ABCD"
three_string = ("AA", "BBB", "CCCC")
single_int = 10
five_int = np.array(range(5), dtype=np.int32)
single_double = 1.1
five_double = np.array(range(5), dtype="double") * 1.1
fw = ad.writer(self.temp.path)
fw.declare_group("group", method="POSIX1")
fw.define_attr("single_string")
fw.define_attr("three_string")
fw.define_attr("single_int")
fw.define_attr("five_int")
fw.define_attr("single_double")
fw.define_attr("five_double")
fw["single_string"] = single_string
fw["three_string"] = three_string
fw["single_int"] = single_int
fw["five_int"] = five_int
fw["single_double"] = single_double
fw["five_double"] = five_double
fw.close()
f = ad.file(self.temp.path)
self.assertEqual(f["single_string"].value, single_string)
self.assertTrue((f["three_string"].value == three_string).all())
self.assertEqual(f["single_int"].value, single_int)
self.assertTrue((f["five_int"].value == five_int).all())
self.assertEqual(f["single_double"].value, single_double)
self.assertTrue((f["five_double"].value == five_double).all())
def test_writer_var(self):
self.temp = TempFile()
NX = 10
val1 = np.array(range(NX), dtype=np.int32)
val2 = np.array(range(5), dtype='f8')
fw = ad.writer(self.temp.path)
fw.declare_group("group", method="POSIX1")
fw.define_var("NX")
fw.define_var("val1", "NX")
fw.define_var("val2", val2.shape)
fw['NX'] = NX
fw['val1'] = val1
fw['val2'] = val2
fw.close()
f = ad.file(self.temp.path)
self.assertEqual(f['NX'][...], NX)
self.assertTrue((f['val1'][:] == val1).all())
self.assertTrue((f['val2'][:] == val2).all())
def test_writer_var(self):
self.temp = TempFile()
NX = 10
val1 = np.array(range(NX), dtype=np.int32)
val2 = np.array(range(5), dtype='f8')
fw = ad.writer(self.temp.path)
fw.declare_group("group", method="POSIX1")
fw.define_var("NX")
fw.define_var("val1", "NX")
fw.define_var("val2", val2.shape)
fw['NX'] = NX
fw['val1'] = val1
fw['val2'] = val2
fw.close()
f = ad.file(self.temp.path)
self.assertEqual(f['NX'][:], NX)
self.assertTrue((f['val1'][:] == val1).all())
self.assertTrue((f['val2'][:] == val2).all())
""" Import ADIOS Python/Numpy wrapper """
import adios as ad
import numpy as np
print("\n>>> Prepare ...\n")
fname = 'adios_test_writer.bp'
NX = 10
size = 2
tt = np.arange(NX*size, dtype=np.float64).reshape((size, NX))
""" Writing """
print("\n>>> Writing ...\n")
ad.init_noxml()
ad.set_max_buffer_size (10)
fw = ad.writer(fname, method='POSIX1')
fw['NX'] = NX
fw['size'] = size
fw['temperature'] = tt
fw['temperature'].transform = "zfp:accuracy=0.001"
fw.attrs['/temperature/description'] = "Global array written from 'size' processes"
fw.close()
""" Reading """
print("\n>>> Reading ...\n")
f = ad.file(fname)
for key, val in f.vars.items():
print(key, '=', val.read())
import adios as ad
import numpy as np
print "\n>>> Prepare ...\n"
fname = 'adios_test_writer.bp'
NX = 10
size = 2
t = np.array(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)
for key, val in f.vars.iteritems():
print key, '=', val.read()
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)
for key, val in f.vars.items():
print(key, '=', val.read())