Python APIs

Python Example Code

The Python APIs follows closely Python style directives. They rely on numpy and, optionally, on mpi4py, if the underlying ADIOS2 library is compiled with MPI.

For online examples on MyBinder :

Examples in the ADIOS2 repository

Simple file-based examples
- examples/hello/helloWorld/hello-world.py
- examples/hello/bpReader/bpReaderHeatMap2D.py
- examples/hello/bpWriter/bpWriter.py
Staging examples using staging engines SST and DataMan
- examples/hello/sstWriter/sstWriter.py
- examples/hello/sstReader/sstReader.py
- examples/hello/datamanWriter/dataManWriter.py
- examples/hello/datamanReader/dataManReader.py

Python Write example

from mpi4py import MPI
import numpy as np
from adios2 import Stream

comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()

nx = 10
shape = [size * nx]
start = [rank * nx]
count = [nx]

temperature = np.zeros(nx, dtype=np.double)
pressure = np.ones(nx, dtype=np.double)
delta_time = 0.01
physical_time = 0.0
nsteps = 5

with Stream("cfd.bp", "w", comm) as s:
   # NSteps from application
   for _ in s.steps(nsteps):
      if rank == 0 and s.current_step() == 0:
         # write a Python integer
         s.write("nproc", size)

      # write a Python floating point value
      s.write("physical_time", physical_time)
      # temperature and pressure are numpy arrays
      s.write("temperature", temperature, shape, start, count)
      s.write_attribute("temperature/unit", "K")
      s.write("pressure", pressure, shape, start, count)
      s.write_attribute("pressure/unit", "Pa")
      physical_time += delta_time

$ mpirun -n 4 python3 ./adios2-doc-write.py
$ bpls -la cfd.bp
  int64_t  nproc             scalar = 4
  double   physical_time     5*scalar = 0 / 0.04
  double   pressure          5*{40} = 1 / 1
  string   pressure/unit     attr   = "Pa"
  double   temperature       5*{40} = 0 / 0
  string   temperature/unit  attr   = "K"

Python Read “step-by-step” example

import numpy as np
from adios2 import Stream

with Stream("cfd.bp", "r") as s:
    # steps comes from the stream
    for _ in s.steps():

        # track current step
        print(f"Current step is {s.current_step()}")

        # inspect variables in current step
        for name, info in s.available_variables().items():
            print("variable_name: " + name, end=" ")
            for key, value in info.items():
                print("\t" + key + ": " + value, end=" ")
            print()

        if s.current_step() == 0:
            nproc = s.read("nproc")
            print(f"nproc is {nproc} of type {type(nproc)}")

        # read variables return a numpy array with corresponding selection
        physical_time = s.read("physical_time")
        print(f"physical_time is {physical_time} of type {type(physical_time)}")
        temperature = s.read("temperature")
        temp_unit = s.read_attribute("temperature/unit")
        print(f"temperature array size is {temperature.size} of shape {temperature.shape}")
        print(f"temperature unit is {temp_unit} of type {type(temp_unit)}")
        pressure = s.read("pressure")
        press_unit = s.read_attribute("pressure/unit")
        print(f"pressure unit is {press_unit} of type {type(press_unit)}")
        print()

$ python3 adios2-doc-read.py
Current step is 0
variable_name: nproc    AvailableStepsCount: 1  Max: 4  Min: 4  Shape:          SingleValue: true       Type: int64_t
variable_name: physical_time    AvailableStepsCount: 1  Max: 0  Min: 0  Shape:          SingleValue: true       Type: double
variable_name: pressure         AvailableStepsCount: 1  Max: 1  Min: 1  Shape: 40       SingleValue: false      Type: double
variable_name: temperature      AvailableStepsCount: 1  Max: 0  Min: 0  Shape: 40       SingleValue: false      Type: double
nproc is 4 of type <class 'numpy.ndarray'>
physical_time is 0.0 of type <class 'numpy.ndarray'>
temperature array size is 40 of shape (40,)
temperature unit is K of type <class 'str'>
pressure unit is Pa of type <class 'str'>

Current step is 1
variable_name: physical_time    AvailableStepsCount: 1  Max: 0.01       Min: 0.01       Shape:          SingleValue: true   Type: double
variable_name: pressure         AvailableStepsCount: 1  Max: 1  Min: 1  Shape: 40       SingleValue: false      Type: double
variable_name: temperature      AvailableStepsCount: 1  Max: 0  Min: 0  Shape: 40       SingleValue: false      Type: double
physical_time is 0.01 of type <class 'numpy.ndarray'>
temperature array size is 40 of shape (40,)
temperature unit is K of type <class 'str'>
pressure unit is Pa of type <class 'str'>

...

Python Read Random Access example

import numpy as np
from adios2 import FileReader

with FileReader("cfd.bp") as s:
    # inspect variables
    vars = s.available_variables()
    for name, info in vars.items():
        print("variable_name: " + name, end=" ")
        for key, value in info.items():
            print("\t" + key + ": " + value, end=" ")
        print()
    print()

    nproc = s.read("nproc")
    print(f"nproc is {nproc} of type {type(nproc)} with ndim {nproc.ndim}")

    # read variables return a numpy array with corresponding selection
    steps = int(vars['physical_time']['AvailableStepsCount'])
    physical_time = s.read("physical_time", step_selection=[0, steps])
    print(
        f"physical_time is {physical_time} of type {type(physical_time)} with "
        f"ndim {physical_time.ndim} shape = {physical_time.shape}"
    )

    steps = int(vars['temperature']['AvailableStepsCount'])
    temperature = s.read("temperature", step_selection=[0, steps])
    temp_unit = s.read_attribute("temperature/unit")
    print(f"temperature array size is {temperature.size} of shape {temperature.shape}")
    print(f"temperature unit is {temp_unit} of type {type(temp_unit)}")

    steps = int(vars['pressure']['AvailableStepsCount'])
    pressure = s.read("pressure", step_selection=[0, steps])
    press_unit = s.read_attribute("pressure/unit")
    print()

$ python3 adios2-doc-read-filereader.py
variable_name: nproc    AvailableStepsCount: 1  Max: 4  Min: 4  Shape:          SingleValue: true       Type: int64_t
variable_name: physical_time    AvailableStepsCount: 5  Max: 0.04       Min: 0  Shape:          SingleValue: true       Type: double
variable_name: pressure         AvailableStepsCount: 5  Max: 1  Min: 1  Shape: 40       SingleValue: false      Type: double
variable_name: temperature      AvailableStepsCount: 5  Max: 0  Min: 0  Shape: 40       SingleValue: false      Type: double

nproc is 4 of type <class 'numpy.ndarray'> with ndim 0
physical_time is [0.   0.01 0.02 0.03 0.04] of type <class 'numpy.ndarray'> with ndim 1 shape = (5,)
temperature array size is 200 of shape (200,)
temperature unit is K of type <class 'str'>

adios2 classes for Python

Stream is a high-level class that can perform most of the ADIOS functionality. FileReader is just a convenience class and is the same as Stream with “rra” (ReadRandomAccess) mode. FileReaders do not work with for loops as opposed to Streams that work step-by-step, rather one can access any step of any variable at will. The other classes, Adios, IO, Engine, Variable, Attribute and Operator correspond to the C++ classes. One needs to use them to extend the capabilities of the Stream class (e.g. using an external XML file for runtime configuration, changing the engine for the run, setting up a compression operator for an output variable, etc.)

class adios2.Stream(path, mode, comm=None)

High level implementation of the Stream class from the core API

property adios: Adios instance associated to this Stream

all_blocks_info(name)

Extracts all available blocks information for a particular variable. This can be an expensive function, memory scales up with metadata: steps and blocks per step

Args:: name (str): variable name
Returns:: list of dictionaries with information of each step

available_attributes(varname='', separator='/')

Returns a 2-level dictionary with attribute information. Read mode only.

Parameters

variable_name: If varname is set, attributes assigned to that variable are returned. The keys returned are attribute names with the prefix of varname + separator removed.
separator: concatenation string between variable_name and attribute e.g. varname + separator + name (“var/attr”) Not used if varname is empty

Returns

attributes dictionary

key: attribute name
value: attribute information dictionary

available_variables()

Returns a 2-level dictionary with variable information. Read mode only.

Parameters

keys: list of variable information keys to be extracted (case insensitive) keys=[‘AvailableStepsCount’,’Type’,’Max’,’Min’,’SingleValue’,’Shape’] keys=[‘Name’] returns only the variable names as 1st-level keys leave empty to return all possible keys

Returns

variables dictionary

key: variable name
value: variable information dictionary

begin_step(*, timeout=-1.0)

Write mode: declare the starting of an output step. Pass data in stream.write() and stream.write_attribute(). All data will be published in end_step().

Read mode: in streaming mode releases the current step (no effect in file based engines)

close(): Closes stream, thus becoming unreachable. Not required if using open in a with-as statement. Required in all other cases per-open to avoid resource leaks.

current_step()

Inspect current step of the stream. The steps run from 0.

Note that in a real stream, steps from the producer may be missed if the consumer is slow and the producer is told to discard steps when no one is reading them in time. You may see non-consecutive numbers from this function call in this case.

Use loop_index() to get a loop counter in a for … .steps() loop.

Returns: current step

define_variable(name): Define new variable without specifying its type and content. This only works for string output variables

end_step()

Write mode: declaring the end of an output step. All data passed in stream.write() and all attributes passed in stream.write_attribute() will be published for consumers.

Read mode: in streaming mode releases the current step (no effect in file based engines)

property engine: Engine instance associated to this Stream

inquire_attribute(name, variable_name='', separator='/')

Inquire an attribute

Parameters

name: attribute name
variable_name: if attribute is associated with a variable
separator: concatenation string between variable_name and attribute e.g. variable_name + separator + name (“var/attr”) Not used if variable_name is empty

Returns

The attribute if it is defined, otherwise None

inquire_variable(name)

Inquire a variable

Parameters

name: variable name

Returns

The variable if it is defined, otherwise None

property io: IO instance associated to this Stream

loop_index()

Inspect the loop counter when using for-in loops. This function returns consecutive numbers from 0.

Returns: the loop counter

property mode: Selected open mode

num_steps(): READ MODE ONLY. Return the number of steps available. Note that this is the steps of a file/stream. Each variable has its own steps, which needs to inspected with var=stream.inquire_variable() and then with var.steps()

read(variable: Variable, start=[], count=[], block_id=None, step_selection=None)

read(name: str, start=[], count=[], block_id=None, step_selection=None)

Read a variable. Random access read allowed to select steps.

Parameters

variable: adios2.Variable object to be read Use variable.set_selection(), set_block_selection(), set_step_selection() to prepare a read
start: variable offset dimensions
count: variable local dimensions from offset
block_id: (int) Required for reading local variables, local array, and local value.
step_selection: (list): On the form of [start, count].

Returns

array: resulting array from selection

read_attribute(name, variable_name='', separator='/')

Reads a numpy based attribute

Parameters

name: attribute name
variable_name: if attribute is associated with a variable
separator: concatenation string between variable_name and attribute e.g. variable_name + separator + name (var/attr) Not used if variable_name is empty

Returns

array: resulting array attribute data

read_attribute_string(name, variable_name='', separator='/')

Reads a numpy based attribute

Parameters

name: attribute name
variable_name: if attribute is associated with a variable
separator: concatenation string between variable_name and attribute e.g. variable_name + separator + name (var/attr) Not used if variable_name is empty

Returns

array: resulting array attribute data

set_parameters(**kwargs)

Sets parameters using a dictionary. Removes any previous parameter.

Parameters

parameters: input key/value parameters
value: parameter value

step_status(): Inspect the stream status. Return adios2.bindings.StepStatus

steps(num_steps=0, *, timeout=-1.0)

Returns an interator that can be use to itererate throught the steps. In each iteration begin_step() and end_step() will be internally called.

Write Mode: num_steps is a mandatory argument and should specify the number of steps.

Read Mode: if num_steps is not specified there will be as much iterations as provided by the actual engine. If num_steps is given and there is not that many steps in a file/stream, an error will occur.

IMPORTANT NOTE: Do not use with ReadRandomAccess mode.

write(variable: Variable, content)

write(name: str, content, shape=[], start=[], count=[], operations=None)

Writes a variable. Note that the content will be available for consumption only at the end of the for loop or in the end_step() call.

Parameters

variable: adios2.Variable object to be written Use variable.set_selection(), set_shape(), add_operation_string() to prepare a write
content: variable data values

write_attribute(name, content, variable_name='', separator='/')

writes a self-describing single value array (numpy) variable

Parameters

name: attribute name
array: attribute numpy array data
variable_name: if attribute is associated with a variable
separator: concatenation string between variable_name and attribute e.g. variable_name + separator + name (“var/attr”) Not used if variable_name is empty

class adios2.FileReader(path, comm=None): High level implementation of the FileReader class for read Random access mode

class adios2.Adios(config_file=None, comm=None)

High level representation of the ADIOS class in the adios2.bindings

at_io(name)

Inquire IO instance

Args:: name (str): IO instance name
Returns:: IO: IO instance

declare_io(name)

Declare IO instance

Args:: name (str): IO instance name

define_operator(name, kind, parameters={})

Add an operation (operator).

Args:: name (str): name of the operator. kind (str): name type of the operation. params (dict): parameters as a form of a dict for the operation.

flush_all(): Flush all IO instances

property impl: Bindings implementation of the class

inquire_operator(name)

Add an operation (operator).

Args:: name (str): name of the operator.
Return:: Operator: requested operator

remove_all_ios(): Remove all IO instance

remove_io(name)

Remove IO instance

Args:: name (str): IO instance name

class adios2.IO(impl, name, adiosobj)

High level representation of the IO class in the adios2.bindings

add_transport(kind, parameters={})

Adds a transport and its parameters to current IO. Must be supported by current engine type.

Parameters

kind: must be a supported transport type for current engine.
parameters: acceptable parameters for a particular transport CAN’T use the keywords “Transport” or “transport” in key

Returns

transport_index: handler to added transport

adios(): Adios instance associated to this IO

available_attributes(varname='', separator='/')

Returns a 2-level dictionary with attribute information. Read mode only.

Parameters

variable_name: If varname is set, attributes assigned to that variable are returned. The keys returned are attribute names with the prefix of varname + separator removed.
separator: concatenation string between variable_name and attribute e.g. varname + separator + name (“var/attr”) Not used if varname is empty

Returns

attributes dictionary

key: attribute name
value: attribute information dictionary

available_variables()

Returns a 2-level dictionary with variable information. Read mode only.

Parameters

keys: list of variable information keys to be extracted (case insensitive) keys=[‘AvailableStepsCount’,’Type’,’Max’,’Min’,’SingleValue’,’Shape’] keys=[‘Name’] returns only the variable names as 1st-level keys leave empty to return all possible keys

Returns

variables dictionary

key: variable name
value: variable information dictionary

define_attribute(name, content=None, variable_name='', separator='/')

Define an Attribute

Parameters

name: attribute name
content: attribute numpy array data
variable_name: if attribute is associated with a variable
separator: concatenation string between variable_name and attribute e.g. variable_name + separator + name (“var/attr”) Not used if variable_name is empty

define_variable(name, content=None, shape=[], start=[], count=[], is_constant_dims=False)

writes a variable

Parameters

name: variable name
content: variable data values
shape: variable global MPI dimensions.
start: variable offset for current MPI rank.
count: variable dimension for current MPI rank.
isConstantDims: Whether dimensions are constant

engine_type(): Return engine type

flush_all(): Flush all engines attached to this IO instance

property impl: Bindings implementation of the class

inquire_attribute(name, variable_name='', separator='/')

Inquire an Attribute

Parameters

name: attribute name
variable_name: if attribute is associated with a variable
separator: concatenation string between variable_name and attribute e.g. variable_name + separator + name (“var/attr”) Not used if variable_name is empty

inquire_variable(name)

Inquire a variable

Parameters

name: variable name

Returns

The variable if it is defined, otherwise None

open(name, mode, comm=None)

Open an engine

Parameters

name: Engine name
mode: engine mode
comm: MPI communicator, optional

parameters()

Return parameter associated to this io instance

Return:: dict: str->str parameters

remove_all_attributes(): Remove all define attributes

remove_all_variables(): Remove all variables in the IO instance

remove_attribute(name)

Remove an Attribute

Parameters

name: attribute name

remove_variable(name)

Remove a variable

Parameters

name: Variable name

set_engine(name)

Set engine for this IO instance

Args:: name (str): name of engine

set_parameter(key, value)

Set a parameter for this IO instance

Args:: key (str): value (str):

set_parameters(parameters)

Set parameters for this IO instance

Args:: parameters (dict):

class adios2.Engine(implementation)

High level representation of the Engine class in the adios2.bindings

all_blocks_info(name)

Returns a list of BlocksInfo for a all steps

Args:: name (str): variable name
Returns:: list of BlockInfos

begin_step(*args, **kwargs): Start step

between_step_pairs(): End step

blocks_info(name, step)

Returns a BlocksInfo for a given step

Args:: name (str): variable name step (int): step in question
Returns:: list of dicts describing each BlockInfo

close(transport_index=-1)

Close an transports of the engine

Args:: transportIndex (int): if -1 close all transports

current_step(): Returns the current step

end_step(): End step

flush(transport_index=-1): Flush all transports attached to this Engine instance

get(variable, content=None, mode=<Mode.Sync: 6>)

Gets the content of a variable

Parameters

name: variable name
content: output variable data values
mode: when to perform the communication, (Deferred or Asynchronous).

Returns

Content of the variable when the content argument is omitted.

property impl: Bindings implementation of the class

lock_reader_selections(): Locks the data selection for read

lock_writer_definitions(): Locks the data selection for write

perform_data_write(): Perform the transport data writes

perform_gets(): Perform the gets calls

perform_puts(): Perform the puts calls

put(variable, content, mode=<Mode.Deferred: 7>)

Puts content in a variable

Parameters

name: variable name
content: variable data values
mode: when to perform the communication, (Deferred or Asynchronous).

steps(): Returns number of available steps

class adios2.Variable(implementation)

High level representation of the Attribute class in the adios2.bindings

add_operation(operation, params={})

Add an operation (operator).

Args:: name (Operator): name of the operation. params (dict): parameters as a form of a dict for the operation.

add_operation_string(name, params={})

Add an operation (operator) as a string

Args:: name (str): name of the operation. params (dict): parameters as a form of a dict for the operation.

block_id()

BlockID of this variable.

Returns:: int: BlockID of this variable.

count()

Current selected count for this variable.

Returns:: int: Current selected count.

property impl: Bindings implementation of the class

name()

Name of the Variable

Returns:: str: Name of the Variable.

operations()

Current operations (operators) assigned to this Variable.

Returns:: list(Operators): operators assigned.

remove_operations(): Remove operations (operators) assigned to this Variable.

selection_size()

Current selection size selected for this variable.

Returns:: int: Current selection size selected.

set_block_selection(block_id)

Set BlockID for this variable.

Args:: block_id (int): Selected BlockID.

set_selection(selection)

Set selection for this variable.

Args:: selection (list): list of the shape [[start], [count]], note that start and count can contain more than one element.

set_shape(shape)

Set Shape (dimensions) for this variable

Args:: shape (list): desired shape (dimensions).

set_step_selection(step_selection)

Set current step selection (For RRA or ReadRandomAccess)

Args:: step_selection (list): On the form of [start, count].

shape(step=None)

Get the shape assigned to the given step for this variable.

Args:: step (int): Desired step. Only in ReadRandomAccess mode
Returns:: list: shape of the specified step in the form of [start, count].

shape_id()

Get the ShapeID assigned to this variable.

Returns:: int: ShapeID assigned to this variable.

single_value()

Check if this variable is a single value.

Returns:: bool: true if this variable is a single value.

sizeof()

Size in bytes of the contents of the variable.

Returns:: int: size in bytes of the contents.

start()

The current selected start of the variable.

Returns:: int: The current selected start of the variable.

steps()

The number of steps of the variable. This is always 1 in a stream. In ReadRandomAccess mode, this function returns the total number of steps available, which can be used when selecting steps for read.

Returns:: int: The avaialble steps of the variable.

steps_start()

The avaliable start step, this is needed variables can start at any time step. This is for ReadRandomAccess.

Returns:: int: the starting step of for this Variable.

type()

Type of the Variable

Returns:: str: Type of the Variable.

class adios2.Attribute(io, name, *args, **kwargs)

High level representation of the Attribute class in the adios2.bindings

data()

Content of the Attribute

Returns:: Content of the Attribute as a non string.

data_string()

Content of the Attribute

Returns:: Content of the Attribute as a str.

property impl: Bindings implementation of the class

name()

Name of the Attribute

Returns:: Name of the Attribute as a str.

single_value()

True if the attribute is a single value, False if it is an array

Returns:: True or False.

type()

Type of the Attribute

Returns:: Type of the Attribute as a str.

class adios2.Operator(implementation, name)

High level representation of the Attribute class in the adios2.bindings

get_parameters()

Get parameters associated to this Operator

Returns:: dict: parameters

property impl: Bindings implementation of the class

set_parameter(key, value)

Set parameter associated to this Operator

Args:: str: key str: value

Python bindings to C++

Note

The bindings to the C++ functions is the basis of the native Python API described before. It is still accessible to users who used the “Full Python API” pre-2.10. In order to make old scripts working with 2.10 and later versions, change the import line in the python script.

import adios2.bindings as adios2

The full Python APIs follows very closely the full C++11 API interface. All of its functionality is now in the native API as well, so its use is discouraged for future scripts.

Examples using the Python bindings in the ADIOS2 repository

Simple file-based examples
- examples/hello/helloWorld/hello-world-bindings.py
- examples/hello/bpReader/bpReaderHeatMap2D-bindings.py
- examples/hello/bpWriter/bpWriter-bindings.py
Staging examples using staging engines SST and DataMan
- examples/hello/sstWriter/sstWriter-bindings.py
- examples/hello/sstReader/sstReader-bindings.py

ADIOS class

class adios2.bindings.ADIOS

AtIO(self: adios2.bindings.adios2_bindings.ADIOS, arg0: str) → adios2::py11::IO: returns an IO object previously defined IO object with DeclareIO, throws an exception if not found

DeclareIO(self: adios2.bindings.adios2_bindings.ADIOS, arg0: str) → adios2::py11::IO: spawn IO object component returning a IO object with a unique name, throws an exception if IO with the same name is declared twice

DefineOperator(self: adios2.bindings.adios2_bindings.ADIOS, arg0: str, arg1: str, arg2: Dict[str, str]) → adios2::py11::Operator

FlushAll(self: adios2.bindings.adios2_bindings.ADIOS) → None: flushes all engines in all spawned IO objects

InquireOperator(self: adios2.bindings.adios2_bindings.ADIOS, arg0: str) → adios2::py11::Operator

RemoveAllIOs(self: adios2.bindings.adios2_bindings.ADIOS) → None: DANGER ZONE: remove all IOs in current ADIOS object, creates dangling objects to parameters, variable, attributes, engines created with removed IO

RemoveIO(self: adios2.bindings.adios2_bindings.ADIOS, arg0: str) → bool: DANGER ZONE: remove a particular IO by name, creates dangling objects to parameters, variable, attributes, engines created with removed IO

IO class

class adios2.bindings.IO

AddTransport(self: adios2.bindings.adios2_bindings.IO, type: str, parameters: Dict[str, str] = {}) → int

AvailableAttributes(self: adios2.bindings.adios2_bindings.IO, varname: str = '', separator: str = '/') → Dict[str, Dict[str, str]]

AvailableVariables(self: adios2.bindings.adios2_bindings.IO) → Dict[str, Dict[str, str]]

DefineAttribute(*args, **kwargs)

Overloaded function.

DefineAttribute(self: adios2.bindings.adios2_bindings.IO, name: str, array: numpy.ndarray, variable_name: str = ‘’, separator: str = ‘/’) -> adios2::py11::Attribute
DefineAttribute(self: adios2.bindings.adios2_bindings.IO, name: str, stringValue: str, variable_name: str = ‘’, separator: str = ‘/’) -> adios2::py11::Attribute
DefineAttribute(self: adios2.bindings.adios2_bindings.IO, name: str, strings: List[str], variable_name: str = ‘’, separator: str = ‘/’) -> adios2::py11::Attribute
DefineAttribute(self: adios2.bindings.adios2_bindings.IO, name: str, ints: List[int], variable_name: str = ‘’, separator: str = ‘/’) -> adios2::py11::Attribute
DefineAttribute(self: adios2.bindings.adios2_bindings.IO, name: str, doubles: List[float], variable_name: str = ‘’, separator: str = ‘/’) -> adios2::py11::Attribute
DefineAttribute(self: adios2.bindings.adios2_bindings.IO, name: str, complexes: List[complex], variable_name: str = ‘’, separator: str = ‘/’) -> adios2::py11::Attribute
DefineAttribute(self: adios2.bindings.adios2_bindings.IO, name: str, value: object, variable_name: str = ‘’, separator: str = ‘/’) -> adios2::py11::Attribute

DefineVariable(*args, **kwargs)

Overloaded function.

DefineVariable(self: adios2.bindings.adios2_bindings.IO, name: str, array: numpy.ndarray, shape: List[int] = [], start: List[int] = [], count: List[int] = [], isConstantDims: bool = False) -> adios2::py11::Variable
DefineVariable(self: adios2.bindings.adios2_bindings.IO, name: str, value: object, shape: List[int] = [], start: List[int] = [], count: List[int] = [], isConstantDims: bool = False) -> adios2::py11::Variable
DefineVariable(self: adios2.bindings.adios2_bindings.IO, name: str) -> adios2::py11::Variable

EngineType(self: adios2.bindings.adios2_bindings.IO) → str

FlushAll(self: adios2.bindings.adios2_bindings.IO) → None

InquireAttribute(self: adios2.bindings.adios2_bindings.IO, name: str, variable_name: str = '', separator: str = '/') → adios2::py11::Attribute

InquireVariable(self: adios2.bindings.adios2_bindings.IO, arg0: str) → adios2::py11::Variable

Open(self: adios2.bindings.adios2_bindings.IO, arg0: str, arg1: int) → adios2::py11::Engine

Parameters(self: adios2.bindings.adios2_bindings.IO) → Dict[str, str]

RemoveAllAttributes(self: adios2.bindings.adios2_bindings.IO) → None

RemoveAllVariables(self: adios2.bindings.adios2_bindings.IO) → None

RemoveAttribute(self: adios2.bindings.adios2_bindings.IO, arg0: str) → bool

RemoveVariable(self: adios2.bindings.adios2_bindings.IO, arg0: str) → bool

SetEngine(self: adios2.bindings.adios2_bindings.IO, arg0: str) → None

SetParameter(self: adios2.bindings.adios2_bindings.IO, arg0: str, arg1: str) → None

SetParameters(self: adios2.bindings.adios2_bindings.IO, parameters: Dict[str, str] = {}) → None

Variable class

class adios2.bindings.Variable

AddOperation(*args, **kwargs)

Overloaded function.

AddOperation(self: adios2.bindings.adios2_bindings.Variable, arg0: adios2.bindings.adios2_bindings.Operator, arg1: Dict[str, str]) -> int
AddOperation(self: adios2.bindings.adios2_bindings.Variable, arg0: str, arg1: Dict[str, str]) -> int

BlockID(self: adios2.bindings.adios2_bindings.Variable) → int

Count(self: adios2.bindings.adios2_bindings.Variable) → List[int]

Name(self: adios2.bindings.adios2_bindings.Variable) → str

Operations(self: adios2.bindings.adios2_bindings.Variable) → List[adios2.bindings.adios2_bindings.Operator]

RemoveOperations(self: adios2.bindings.adios2_bindings.Variable) → None

SelectionSize(self: adios2.bindings.adios2_bindings.Variable) → int

SetBlockSelection(self: adios2.bindings.adios2_bindings.Variable, arg0: int) → None

SetSelection(self: adios2.bindings.adios2_bindings.Variable, arg0: Tuple[List[int], List[int]]) → None

SetShape(self: adios2.bindings.adios2_bindings.Variable, arg0: List[int]) → None

SetStepSelection(self: adios2.bindings.adios2_bindings.Variable, arg0: Tuple[int, int]) → None

Shape(self: adios2.bindings.adios2_bindings.Variable, step: int = 18446744073709551615) → List[int]

ShapeID(self: adios2.bindings.adios2_bindings.Variable) → adios2.bindings.adios2_bindings.ShapeID

SingleValue(self: adios2.bindings.adios2_bindings.Variable) → int

Sizeof(self: adios2.bindings.adios2_bindings.Variable) → int

Start(self: adios2.bindings.adios2_bindings.Variable) → List[int]

Steps(self: adios2.bindings.adios2_bindings.Variable) → int

StepsStart(self: adios2.bindings.adios2_bindings.Variable) → int

Type(self: adios2.bindings.adios2_bindings.Variable) → str

Attribute class

class adios2.bindings.Attribute

Data(self: adios2.bindings.adios2_bindings.Attribute) → numpy.ndarray

DataString(self: adios2.bindings.adios2_bindings.Attribute) → List[str]

Name(self: adios2.bindings.adios2_bindings.Attribute) → str

SingleValue(self: adios2.bindings.adios2_bindings.Attribute) → bool

Type(self: adios2.bindings.adios2_bindings.Attribute) → str

Engine class

class adios2.bindings.Engine

BeginStep(*args, **kwargs)

Overloaded function.

BeginStep(self: adios2.bindings.adios2_bindings.Engine, mode: adios2.bindings.adios2_bindings.StepMode, timeoutSeconds: float = -1.0) -> adios2.bindings.adios2_bindings.StepStatus
BeginStep(self: adios2.bindings.adios2_bindings.Engine) -> adios2.bindings.adios2_bindings.StepStatus

BetweenStepPairs(self: adios2.bindings.adios2_bindings.Engine) → bool

BlocksInfo(self: adios2.bindings.adios2_bindings.Engine, arg0: str, arg1: int) → List[Dict[str, str]]

Close(self: adios2.bindings.adios2_bindings.Engine, transportIndex: int = -1) → None

CurrentStep(self: adios2.bindings.adios2_bindings.Engine) → int

EndStep(self: adios2.bindings.adios2_bindings.Engine) → None

Flush(self: adios2.bindings.adios2_bindings.Engine, arg0: int) → None

Get(*args, **kwargs)

Overloaded function.

Get(self: adios2.bindings.adios2_bindings.Engine, variable: adios2.bindings.adios2_bindings.Variable, array: numpy.ndarray, launch: adios2.bindings.adios2_bindings.Mode = <Mode.Deferred: 7>) -> None
Get(self: adios2.bindings.adios2_bindings.Engine, variable: adios2.bindings.adios2_bindings.Variable, launch: adios2.bindings.adios2_bindings.Mode = <Mode.Deferred: 7>) -> str

LockReaderSelections(self: adios2.bindings.adios2_bindings.Engine) → None

LockWriterDefinitions(self: adios2.bindings.adios2_bindings.Engine) → None

Name(self: adios2.bindings.adios2_bindings.Engine) → str

PerformDataWrite(self: adios2.bindings.adios2_bindings.Engine) → None

PerformGets(self: adios2.bindings.adios2_bindings.Engine) → None

PerformPuts(self: adios2.bindings.adios2_bindings.Engine) → None

Put(*args, **kwargs)

Overloaded function.

Put(self: adios2.bindings.adios2_bindings.Engine, variable: adios2.bindings.adios2_bindings.Variable, array: numpy.ndarray, launch: adios2.bindings.adios2_bindings.Mode = <Mode.Deferred: 7>) -> None
Put(self: adios2.bindings.adios2_bindings.Engine, arg0: adios2.bindings.adios2_bindings.Variable, arg1: str) -> None
Put(self: adios2.bindings.adios2_bindings.Engine, variable: adios2.bindings.adios2_bindings.Variable, ints: List[int], launch: adios2.bindings.adios2_bindings.Mode = <Mode.Sync: 6>) -> None
Put(self: adios2.bindings.adios2_bindings.Engine, variable: adios2.bindings.adios2_bindings.Variable, floats: List[float], launch: adios2.bindings.adios2_bindings.Mode = <Mode.Sync: 6>) -> None
Put(self: adios2.bindings.adios2_bindings.Engine, variable: adios2.bindings.adios2_bindings.Variable, complexes: List[complex], launch: adios2.bindings.adios2_bindings.Mode = <Mode.Sync: 6>) -> None

Steps(self: adios2.bindings.adios2_bindings.Engine) → int

Type(self: adios2.bindings.adios2_bindings.Engine) → str

Operator class

class adios2.bindings.Operator

Parameters(self: adios2.bindings.adios2_bindings.Operator) → Dict[str, str]

SetParameter(self: adios2.bindings.adios2_bindings.Operator, arg0: str, arg1: str) → None

Type(self: adios2.bindings.adios2_bindings.Operator) → str

Query class

class adios2.bindings.Query

GetBlockIDs(self: adios2.bindings.adios2_bindings.Query) → List[int]

GetResult(self: adios2.bindings.adios2_bindings.Query) → List[Tuple[List[int], List[int]]]

Transition from old API to new API

A python script using the high-level API of 2.9 and earlier needs to be modified to work with 2.10 and later.

adios2.open() is replaced with adios2.Stream(), and does not have 4th and 5th optional arguments for external xml and IO name.
the for in file is replaced with for _ in file.steps() but it works for both writing (by specifying the number of output steps) and reading (for the number of available steps in a stream/file).

# OLD API
import adios2

# NEW API
from adios2 import Adios, Stream

# NEW API: this still works
import adios2


# OLD API
fr = adios2.open(args.instream, "r", mpi.comm_app,"adios2.xml", "SimulationOutput")

# NEW API
adios = Adios("adios2.xml", mpi.comm_app)
io = adios.declare_io("SimulationOutput")
fr = Stream(io, args.instream, "r", mpi.comm_app)


# OLD API
for fr_step in fr:
    fr_step....

# NEW API 1
for _ in fr.steps():
    fr....

# NEW API 2
for fr_step in fr.steps():
    fr_step....