nbodykit.utils

Functions

GatherArray(data, comm[, root]) Gather the input data array from all ranks to the specified root.
ScatterArray(data, comm[, root, counts]) Scatter the input data array across all ranks, assuming data is initially only on root (and None on other ranks).
attrs_to_dict(obj, prefix)
captured_output(comm[, root]) Re-direct stdout and stderr to null for every rank but root
deprecate(name, alternative[, alt_name]) This is a decorator which can be used to mark functions as deprecated.
get_data_bounds(data, comm) Return the global minimum/maximum of a numpy array along the first axis.
split_size_3d(s) Split s into three integers, a, b, c, such
timer(start, end) Utility function to return a string representing the elapsed time,

Classes

JSONDecoder(*args, **kwargs) A subclass of json.JSONDecoder that can also handle numpy arrays, complex values, and astropy.units.Quantity objects.
JSONEncoder(*[, skipkeys, ensure_ascii, …]) A subclass of json.JSONEncoder that can also handle numpy arrays, complex values, and astropy.units.Quantity objects.
nbodykit.utils.GatherArray(data, comm, root=0)[source]

Gather the input data array from all ranks to the specified root.

This uses Gatherv, which avoids mpi4py pickling, and also avoids the 2 GB mpi4py limit for bytes using a custom datatype

Parameters:
  • data (array_like) – the data on each rank to gather
  • comm (MPI communicator) – the MPI communicator
  • root (int) – the rank number to gather the data to
Returns:

recvbuffer – the gathered data on root, and None otherwise
Return type:

array_like, None
class nbodykit.utils.JSONDecoder(*args, **kwargs)[source]

A subclass of json.JSONDecoder that can also handle numpy arrays, complex values, and astropy.units.Quantity objects.

Methods

decode(s[, _w]) Return the Python representation of s (a str instance containing a JSON document).
hook(value)
raw_decode(s[, idx]) Decode a JSON document from s (a str beginning with a JSON document) and return a 2-tuple of the Python representation and the index in s where the document ended.
class nbodykit.utils.JSONEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]

A subclass of json.JSONEncoder that can also handle numpy arrays, complex values, and astropy.units.Quantity objects.

Methods

default(obj)
encode(o) Return a JSON string representation of a Python data structure.
iterencode(o[, _one_shot]) Encode the given object and yield each string representation as available.
nbodykit.utils.ScatterArray(data, comm, root=0, counts=None)[source]

Scatter the input data array across all ranks, assuming data is initially only on root (and None on other ranks).

This uses Scatterv, which avoids mpi4py pickling, and also avoids the 2 GB mpi4py limit for bytes using a custom datatype

Parameters:
  • data (array_like or None) – on root, this gives the data to split and scatter
  • comm (MPI communicator) – the MPI communicator
  • root (int) – the rank number that initially has the data
  • counts (list of int) – list of the lengths of data to send to each rank
Returns:

recvbuffer – the chunk of data that each rank gets
Return type:

array_like
nbodykit.utils.captured_output(comm, root=0)[source]

Re-direct stdout and stderr to null for every rank but root

nbodykit.utils.deprecate(name, alternative, alt_name=None)[source]

This is a decorator which can be used to mark functions as deprecated. It will result in a warning being emmitted when the function is used.

nbodykit.utils.get_data_bounds(data, comm)[source]

Return the global minimum/maximum of a numpy array along the first axis.

Parameters:
  • data (numpy.ndarray) – the data to find the bounds of
  • comm – the MPI communicator
Returns:

the min/max of data
Return type:

min, max
nbodykit.utils.split_size_3d(s)[source]

Split s into three integers, a, b, c, such that a * b * c == s and a <= b <= c

Parameters:s (int) – integer to split
Returns:a, b, c – integers such that a * b * c == s and a <= b <= c
Return type:int
nbodykit.utils.timer(start, end)[source]

Utility function to return a string representing the elapsed time, as computed from the input start and end times

Parameters:
  • start (int) – the start time in seconds
  • end (int) – the end time in seconds
Returns:

the elapsed time as a string, using the format hours:minutes:seconds
Return type:

str