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*******************
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 :
- `Python-MPI Notebooks <https://mybinder.org/v2/gh/ornladios/ADIOS2-Jupyter.git/python-mpi>`_
- `Python-noMPI Notebooks <https://mybinder.org/v2/gh/ornladios/ADIOS2-Jupyter.git/python-nompi>`_
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
--------------------
.. code-block:: python
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
.. code-block:: bash
$ 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
----------------------------------
.. code-block:: python
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()
.. code-block:: bash
$ 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
----------------------------------
.. code-block:: python
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()
.. code-block:: bash
$ 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'>
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