adios2

Descriptions of the contents of the adios2 module.

class pysemtools.io.adios2.stream.DataStreamer(comm, from_nek=True)

Class used to communicate data between codes using adios2.

Use this to send and recieve data.

The data is always transported as a 1d array, so it is necessary to reshape.

Parameters:

commComm: MPI communicator.
from_nekbool: Define if the data that is being stream comes from a nek-like code. (Default value = True).

Attributes:

glb_nelvint: Total number of elements in the global domain.
lxyzint: Number of points per element.
gdimint: Problem dimension.
nelvint: Number of elements that this rank has.

Methods

`finalize`()	Finalize the execution of the module.
`recieve`([fld, variable])	Recieve data from another code using adios2.
`stream`(fld)	Send data to another code using adios2.

Examples

This type must be paired with another streaming in the other executable/code. The codes will not start if the streams are not paired.

A full of example of recieving data is shown below. It is possible to pair with other classes to, for example, write data to disk.

>>> ds = data_streamer_c(comm)
>>> x = get_fld_from_ndarray(ds.recieve(), ds.lx, ds.ly, ds.lz, ds.nelv) # Recieve and reshape x
>>> y = get_fld_from_ndarray(ds.recieve(), ds.lx, ds.ly, ds.lz, ds.nelv) # Recieve and reshape y
>>> z = get_fld_from_ndarray(ds.recieve(), ds.lx, ds.ly, ds.lz, ds.nelv) # Recieve and reshape z
>>> ds.finalize()
>>> msh = msh_c(comm, x = x, y = y, z = z)
>>> write_fld_file_from_list("field0.f00001", comm, msh, [x, y, z])

To send data to the other code, use the stream method.

>>> ds.stream(x.reshape(x.size))

finalize()

Finalize the execution of the module.

Used to close reader and writer. The stream will end and the code will not be coupled.

recieve(fld=None, variable='f2py_field')

Recieve data from another code using adios2.

The data is always transported as a 1d array, so it is necessary to reshape to deinred shape.

Parameters:

fldndarray: Buffer to contain the data. If None, it will be created. (Default value = None).
variablestr: Name of the adios2 variable to be read. Neko used default name. Change as needed. This name can remain the same during the execution even if different quantities are being transported. (Default value = “f2py_field”).

Returns:

ndarray: Returns the field that was recieved.

stream(fld)

Send data to another code using adios2.

Couple 2 code or executables.

Parameters:

fldndarray: Field to be sent. Must be a 1d array.

class pysemtools.io.adios2.compress.DataCompressor(comm, mesh_info=None, wrd_size=4)

Class used to write compressed data to disk.

This Assumes that the input data has a msh object available.

Parameters:

commComm: MPI communicator.
mesh_infodict: Dictionary with mesh information.
wrd_sizeint: Word size to write data. (Default value = 4). Single precsiion is 4, double is 8.

Methods

`read`(comm[, fname, variable_names])	Read data from disk using adios2.
`write`(comm[, fname, variable_names, data])	Write data to disk using adios2.

Returns:

Examples

This class is used to write data to disk. The data is compressed using bzip2.

>>> mesh_info = {"glb_nelv": msh.glb_nelv, "lxyz": msh.lxyz, "gdim": msh.gdim}
>>> dc = DataCompressor(comm, mesh_info = mesh_info, wrd_size = 4)

read(comm, fname='compress.bp', variable_names=None)

Read data from disk using adios2.

Read compressed data and internally decompress it.

Parameters:

commComm: MPI communicator.
fnamestr: File name to read. (Default value = “compress.bp”).
variable_nameslist: List of string with the names of the variables to read. These names NEED to match the names adios2 used to write the data.

Returns:

list: List of numpy arrays with the data read. the ndarrays in the list are 1d.

Examples

This function is used to read data from disk. The data is compressed using bzip2.

>>> variable_names = ["x", "y", "z"]
>>> data = dc.read(comm, fname = "compress.bp", variable_names = variable_names)

write(comm, fname='compress.bp', variable_names=None, data=None)

Write data to disk using adios2.

Lossless compression with bzip2.

Parameters:

commComm: MPI communicator.
fnamestr: File name to write. (Default value = “compress.bp”).
variable_nameslist: List of string with the names of the variables to write. This is very important, as adios2 will use these names to process the data.
datalist: List of numpy arrays with the data to write. Corresponding in index to variable_names. The arrays must be 1d.

Examples

This function is used to write data to disk. The data is compressed using bzip2.

>>> variable_names = ["x", "y", "z"]
>>> data = [msh.x, msh.y, msh.z]
>>> dc.write(comm, fname = "compress.bp", variable_names = variable_names, data = data)

pysemtools.io.adios2.compress.write_field(comm, msh=None, fld=None, fname='compressed_field0.f00001', wrd_size=4, write_mesh=True)

Wrapper to data compressor writer.

Writes nek like data compressed.

Parameters:

commComm: MPI communicator.
mshMesh: Mesh object to write. (Default value = None).
fldField: Field object to write. (Default value = None).
fnamestr: File name to write. (Default value = “compressed_field0.f00001”).
wrd_sizeint: Word size to write data. (Default value = 4). Single precsiion is 4, double is 8.
write_meshbool: Flag to write the mesh. (Default value = True).

Examples

This function is used to write data to disk. The data is compressed using bzip2.

>>> write_field(comm, msh = msh, fld = fld, fname = "compressed_field0.f00001", wrd_size = 4, write_mesh = True)

pysemtools.io.adios2.compress.read_field(comm, fname='compressed_field0.f00001')

Wrapper to data compressor reader.

Reads nek like data compressed.

Parameters:

commComm: MPI communicator.
fnamestr: File name to read. (Default value = “compressed_field0.f00001”).

Returns:

msh: Mesh: Mesh object read.
fldField: Field object read.

Examples

This function is used to read data from disk. The data is compressed using bzip2.

>>> msh, fld = read_field(comm, fname = "compressed_field0.f00001")