Module autopartition

A module to provide multiset partition, combination and processor topology decomposition.

Functions

[hide private]

_next_multiset_comb(m, state)

_multicomb(m, k)
@type m: list of integer @param m: multiset.

_list2array(m, n)

_array2list(m)

all_multicomb(m)
Return all combinations for multiset m

get_next_partition(factors)
A partition generator

next_prime(n)
A prmie number generator that generates prime number less than or equal to n

get_prime_factors(n)
A function to generate all factorizations of a given integer n.

auto_partition(dims, nproc)
A function to calculate best cpu partition based on dimension and number of processor.

Variables

[hide private]

__package__ = 'schrodinger.application.desmond'

Function Details

[hide private]

_next_multiset_comb(m, state)

To Do: convert it to a generator.

_multicomb(m, k)


@type m: list of integer 
@param m: multiset.

@type k: int
@param k: the total number of element that will show up in the combination.

@return the combination in an integer number array. 


for i in _multicomb([0, 0, 0, 1, 1, 2, 2, 2, 2, 2], 7):
    print i 
Above statement will generate below combinations:

[0, 0, 0, 1, 1, 2, 2]
[0, 0, 0, 1, 2, 2, 2]
[0, 0, 0, 2, 2, 2, 2]
[0, 0, 1, 1, 2, 2, 2]
[0, 0, 1, 2, 2, 2, 2]
[0, 0, 2, 2, 2, 2, 2]
[0, 1, 1, 2, 2, 2, 2]
[0, 1, 2, 2, 2, 2, 2]
[1, 1, 2, 2, 2, 2, 2]

@todo: provide a mapping function

all_multicomb(m)

Return all combinations for multiset m

Parameters:

m (list of integer) - the array contains the maximum number of individual unique element in the multiset.

get_next_partition(factors)

A partition generator

Parameters:

factors (list of integer) - a list of prime numbers @return a three element tuple that represent the partition

To Do: this algorithm is still not very efficient due to the generation of duplicate combination. A vector partition function with restricted growth order will be a better option.

next_prime(n)

A prmie number generator that generates prime number less than or equal to n

Parameters:

n (int) - @return prime number

get_prime_factors(n)

A function to generate all factorizations of a given integer n.

Parameters:

n (int) - an integer to be factorized
@return a list of prime factors.

auto_partition(dims, nproc)

A function to calculate best cpu partition based on dimension and number of processor. The object function to optimize:

Parameters:

dims (list of integer) - simulation box
nproc (int) - number of cores
@return an three element integer array that represents the best partition.