Non-associative RDOM parallellization in Halide - parallel-processing

I am trying to write a decoder for GPU. My encoding scheme has data dependencies between lines. So when decoding columns of data each column depends on the previous. I want to parallellize the internal computation of each column, but execute each column one-by-one and sequentially, but I am having trouble getting this correctly.
Below I have modeled a toy example to show the problem:
Func f;
Var x,y;
RDom r(1,3,1,3); // goes from (1,1) to (4,4)
f(x,y) = 0;
f(0,y) = y;
Expr p_1 = f(r.x-1,r.y);
Expr p_2 = f(r.x-1,r.y-1);
f(r.x,r.y) = p_1 + p_2;
Buffer<int32_t> output_2D = f.realize({4,4});
A visualization of this program can be seen here: Serial Computation Visualisation
This reduction should give the following array():
int expected_output[4][4] = {{0,0,0,0},
{1,1,1,1},
{2,3,4,5},
{3,5,8,12}};
And checking using Catch2 I can see that it actually calculates it correctly
for(int j = 0; j < output_2D.height(); j++){
for(int i = 0; i < output_2D.width(); i++){
CAPTURE(i,j);
REQUIRE(expected_output[j][i]==output_2D(i,j));
}
}
My task is to speed this computation up. Since column one depends on column zero I have to calculate each column in series. I can however, calculate all the values in the column in parallel. Please see Computation Steps Parallel and Desired Pipeline to see how I want Halide to compute the pipeline.
I tried doing this in halide using the f.update(1).allow_race_conditions().parallel(r.y); and this does almost what I want.
f(r.x,r.y) = p_1 + p_2;
f.update(1).allow_race_conditions().parallel(r.y);
f.trace_stores();
Buffer<int32_t> output_2D = f.realize({4,4});
For some reason however, it seems that parallel(y) executes the columns in seemingly random order.
It yields the following store_trace:
Init Image:
Store f29.0(0, 0) = 0
Store f29.0(1, 0) = 0
....
Store f29.0(3, 3) = 0
Init first row:
Store f29.0(0, 0) = 0
Store f29.0(1, 0) = 1
Store f29.0(2, 0) = 2
Store f29.0(3, 0) = 3
Start Parallel Computation:
Store f29.0(1, 1) = 1 // First parallel column
Store f29.0(2, 1) = 1
Store f29.0(3, 1) = 1
Store f29.0(1, 3) = 5 // Second parallel column: THIS IS MY PROBLEM
Store f29.0(2, 3) = 5 // This should be column 2 not column 3.
Store f29.0(3, 3) = 5
Store f29.0(1, 2) = 3
Store f29.0(2, 2) = 4
Store f29.0(3, 2) = 5
A visualization of this pattern can be seen here in this figure: Current Pipeline.
I know that I explicitly enabling the race_conditions so I must be doing something wrong, but I dont know what is the right way to do this and this is the closest I got. I could vectorize() with respect to y and that gives the correct evaluation, but I want to use the parallel() block to gain greater speedup for larger matrixes/images. RFactor might be a solution as my problem should be associative in the y direction, but it might not work as it is non-associative in the x-direction(each column depends on the previous) Does anyone know how to be serial in x and parallel in y when using RDoms?

Related

Image Processing: Algorithm taking too long in MATLAB

I am working in MATLAB to process two 512x512 images, the domain image and the range image. What I am trying to accomplish is the following:
Divide both domain and range images into 8x8 pixel blocks
For each 8x8 block in the domain image, I have to apply a linear transformations to it and compare each of the 4096 transformed blocks with each of the 4096 range blocks.
Compute error in each case between the transformed block and the range image block and find the minimum error.
Finally I'll have for each 8x8 range block, the id of the 8x8 domain block for which the error was minimum (error between the range block and the transformed domain block)
To achieve this, I have written the following code:
RangeImagecolor = imread('input.png'); %input is 512x512
DomainImagecolor = imread('input.png'); %Range and Domain images are identical
RangeImagetemp = rgb2gray(RangeImagecolor);
DomainImagetemp = rgb2gray(DomainImagecolor);
RangeImage = im2double(RangeImagetemp);
DomainImage = im2double(DomainImagetemp);
%For the (k,l)th 8x8 range image block
for k = 1:64
for l = 1:64
minerror = 9999;
min_i = 0;
min_j = 0;
for i = 1:64
for j = 1:64
%here I compute for the (i,j)th domain block, the transformed domain block stored in D_trans
error = 0;
D_trans = zeros(8,8);
R = zeros(8,8); %Contains the pixel values of the (k,l)th range block
for m = 1:8
for n = 1:8
R(m,n) = RangeImage(8*k-8+m,8*l-8+n);
%ApplyTransformation can depend on (k,l) so I can't compute the transformation outside the k,l loop.
[m_dash,n_dash] = ApplyTransformation(8*i-8+m,8*j-8+n);
D_trans(m,n) = DomainImage(m_dash,n_dash);
error = error + (R(m,n)-D_trans(m,n))^2;
end
end
if(error < minerror)
minerror = error;
min_i = i;
min_j = j;
end
end
end
end
end
As an example ApplyTransformation, one can use the identity transformation:
function [x_dash,y_dash] = Iden(x,y)
x_dash = x;
y_dash = y;
end
Now the problem I am facing is the high computation time. The order of computation in the above code is 64^5, which is of the order 10^9. This computation should take at the worst minutes or an hour. It takes about 40 minutes to compute just 50 iterations. I don't know why the code is running so slow.
Thanks for reading my question.
You can use im2col* to convert the image to column format so each block forms a column of a [64 * 4096] matrix. Then apply transformation to each column and use bsxfun to vectorize computation of error.
DomainImage=rand(512);
RangeImage=rand(512);
DomainImage_col = im2col(DomainImage,[8 8],'distinct');
R = im2col(RangeImage,[8 8],'distinct');
[x y]=ndgrid(1:8);
function [x_dash, y_dash] = ApplyTransformation(x,y)
x_dash = x;
y_dash = y;
end
[x_dash, y_dash] = ApplyTransformation(x,y);
idx = sub2ind([8 8],x_dash, y_dash);
D_trans = DomainImage_col(idx,:); %transformation is reduced to matrix indexing
Error = 0;
for mn = 1:64
Error = Error + bsxfun(#minus,R(mn,:),D_trans(mn,:).').^2;
end
[minerror ,min_ij]= min(Error,[],2); % linear index of minimum of each block;
[min_i min_j]=ind2sub([64 64],min_ij); % convert linear index to subscript
Explanation:
Our goal is to reduce number of loops as much as possible. For it we should avoid matrix indexing and instead we should use vectorization. Nested loops should be converted to one loop. As the first step we can create a more optimized loop as here:
min_ij = zeros(4096,1);
for kl = 1:4096 %%% => 1:size(D_trans,2)
minerror = 9999;
min_ij(kl) = 0;
for ij = 1:4096 %%% => 1:size(R,2)
Error = 0;
for mn = 1:64
Error = Error + (R(mn,kl) - D_trans(mn,ij)).^2;
end
if(Error < minerror)
minerror = Error;
min_ij(kl) = ij;
end
end
end
We can re-arrange the loops and we can make the most inner loop as the outer loop and separate computation of the minimum from the computation of the error.
% Computation of the error
Error = zeros(4096,4096);
for mn = 1:64
for kl = 1:4096
for ij = 1:4096
Error(kl,ij) = Error(kl,ij) + (R(mn,kl) - D_trans(mn,ij)).^2;
end
end
end
% Computation of the min
min_ij = zeros(4096,1);
for kl = 1:4096
minerror = 9999;
min_ij(kl) = 0;
for ij = 1:4096
if(Error(kl,ij) < minerror)
minerror = Error(kl,ij);
min_ij(kl) = ij;
end
end
end
Now the code is arranged in a way that can best be vectorized:
Error = 0;
for mn = 1:64
Error = Error + bsxfun(#minus,R(mn,:),D_trans(mn,:).').^2;
end
[minerror ,min_ij] = min(Error, [], 2);
[min_i ,min_j] = ind2sub([64 64], min_ij);
*If you don't have the Image Processing Toolbox a more efficient implementation of im2col can be found here.
*The whole computation takes less than a minute.
First things first - your code doesn't do anything. But you likely do something with this minimum error stuff and only forgot to paste this here, or still need to code that bit. Never mind for now.
One big issue with your code is that you calculate transformation for 64x64 blocks of resulting image AND source image. 64^5 iterations of a complex operation are bound to be slow. Rather, you should calculate all transformations at once and save them.
allTransMats = cell(64);
for i = 1 : 64
for j = 1 : 64
allTransMats{i,j} = getTransformation(DomainImage, i, j)
end
end
function D_trans = getTransformation(DomainImage, i,j)
D_trans = zeros(8);
for m = 1 : 8
for n = 1 : 8
[m_dash,n_dash] = ApplyTransformation(8*i-8+m,8*j-8+n);
D_trans(m,n) = DomainImage(m_dash,n_dash);
end
end
end
This serves to get allTransMat and is OUTSIDE the k, l loop. Preferably as a simple function.
Now, you make your big k, l, i, j loop, where you compare all the elements as needed. Comparison could be also done block-wise instead of filling a small 8x8 matrix, yet doing it per element for some reason.
m = 1 : 8;
n = m;
for ...
R = RangeImage(...); % This will give 8x8 output as n and m are vectors.
D = allTransMats{i,j};
difference = sum(sum((R-D).^2));
if (difference < minDifference) ...
end
Even though this is a simple no transformations case, this speeds up code a lot.
Finally, are you sure you need to compare each block of transformed output with each block in the source? Typically you compare block1(a,b) with block2(a,b) - blocks (or pixels) on the same position.
EDIT: allTransMats requires k and l too. Ouch. There is NO WAY to make this fast for a single iteration, as you require 64^5 calls to ApplyTransformation (or a vectorization of that function, but even then it might not be fast - we would have to see the function to help here).
Therefore, I will re-iterate my advice to generate all transformations and then perform lookup: this upper part of the answer with allTransMats generation should be changed to have all 4 loops and generate allTransMats{i,j,k,l};. It WILL be slow, there is no way around that as I mentioned in the upper part of edit. But, it is a cost you pay once, as after saving the allTransMats, all further image analyses will be able to simply load it instead of generating it again.
But ... what do you even do? Transformation that depends on source and destination block indices plus pixel indices (= 6 values total) sounds like a mistake somewhere, or a prime candidate to optimize instead of all the rest.

Algorithm for equiprobable random square binary matrices with two non-adjacent non-zeros in each row and column

It would be great if someone could point me towards an algorithm that would allow me to :
create a random square matrix, with entries 0 and 1, such that
every row and every column contain exactly two non-zero entries,
two non-zero entries cannot be adjacent,
all possible matrices are equiprobable.
Right now I manage to achieve points 1 and 2 doing the following : such a matrix can be transformed, using suitable permutations of rows and columns, into a diagonal block matrix with blocks of the form
1 1 0 0 ... 0
0 1 1 0 ... 0
0 0 1 1 ... 0
.............
1 0 0 0 ... 1
So I start from such a matrix using a partition of [0, ..., n-1] and scramble it by permuting rows and columns randomly. Unfortunately, I can't find a way to integrate the adjacency condition, and I am quite sure that my algorithm won't treat all the matrices equally.
Update
I have managed to achieve point 3. The answer was actually straight under my nose : the block matrix I am creating contains all the information needed to take into account the adjacency condition. First some properties and definitions:
a suitable matrix defines permutations of [1, ..., n] that can be build like so: select a 1 in row 1. The column containing this entry contains exactly one other entry equal to 1 on a row a different from 1. Again, row a contains another entry 1 in a column which contains a second entry 1 on a row b, and so on. This starts a permutation 1 -> a -> b ....
For instance, with the following matrix, starting with the marked entry
v
1 0 1 0 0 0 | 1
0 1 0 0 0 1 | 2
1 0 0 1 0 0 | 3
0 0 1 0 1 0 | 4
0 0 0 1 0 1 | 5
0 1 0 0 1 0 | 6
------------+--
1 2 3 4 5 6 |
we get permutation 1 -> 3 -> 5 -> 2 -> 6 -> 4 -> 1.
the cycles of such a permutation lead to the block matrix I mentioned earlier. I also mentioned scrambling the block matrix using arbitrary permutations on the rows and columns to rebuild a matrix compatible with the requirements.
But I was using any permutation, which led to some adjacent non-zero entries. To avoid that, I have to choose permutations that separate rows (and columns) that are adjacent in the block matrix. Actually, to be more precise, if two rows belong to a same block and are cyclically consecutive (the first and last rows of a block are considered consecutive too), then the permutation I want to apply has to move these rows into non-consecutive rows of the final matrix (I will call two rows incompatible in that case).
So the question becomes : How to build all such permutations ?
The simplest idea is to build a permutation progressively by randomly adding rows that are compatible with the previous one. As an example, consider the case n = 6 using partition 6 = 3 + 3 and the corresponding block matrix
1 1 0 0 0 0 | 1
0 1 1 0 0 0 | 2
1 0 1 0 0 0 | 3
0 0 0 1 1 0 | 4
0 0 0 0 1 1 | 5
0 0 0 1 0 1 | 6
------------+--
1 2 3 4 5 6 |
Here rows 1, 2 and 3 are mutually incompatible, as are 4, 5 and 6. Choose a random row, say 3.
We will write a permutation as an array: [2, 5, 6, 4, 3, 1] meaning 1 -> 2, 2 -> 5, 3 -> 6, ... This means that row 2 of the block matrix will become the first row of the final matrix, row 5 will become the second row, and so on.
Now let's build a suitable permutation by choosing randomly a row, say 3:
p = [3, ...]
The next row will then be chosen randomly among the remaining rows that are compatible with 3 : 4, 5and 6. Say we choose 4:
p = [3, 4, ...]
Next choice has to be made among 1 and 2, for instance 1:
p = [3, 4, 1, ...]
And so on: p = [3, 4, 1, 5, 2, 6].
Applying this permutation to the block matrix, we get:
1 0 1 0 0 0 | 3
0 0 0 1 1 0 | 4
1 1 0 0 0 0 | 1
0 0 0 0 1 1 | 5
0 1 1 0 0 0 | 2
0 0 0 1 0 1 | 6
------------+--
1 2 3 4 5 6 |
Doing so, we manage to vertically isolate all non-zero entries. Same has to be done with the columns, for instance by using permutation p' = [6, 3, 5, 1, 4, 2] to finally get
0 1 0 1 0 0 | 3
0 0 1 0 1 0 | 4
0 0 0 1 0 1 | 1
1 0 1 0 0 0 | 5
0 1 0 0 0 1 | 2
1 0 0 0 1 0 | 6
------------+--
6 3 5 1 4 2 |
So this seems to work quite efficiently, but building these permutations needs to be done with caution, because one can easily be stuck: for instance, with n=6 and partition 6 = 2 + 2 + 2, following the construction rules set up earlier can lead to p = [1, 3, 2, 4, ...]. Unfortunately, 5 and 6 are incompatible, so choosing one or the other makes the last choice impossible. I think I've found all situations that lead to a dead end. I will denote by r the set of remaining choices:
p = [..., x, ?], r = {y} with x and y incompatible
p = [..., x, ?, ?], r = {y, z} with y and z being both incompatible with x (no choice can be made)
p = [..., ?, ?], r = {x, y} with x and y incompatible (any choice would lead to situation 1)
p = [..., ?, ?, ?], r = {x, y, z} with x, y and z being cyclically consecutive (choosing x or z would lead to situation 2, choosing y to situation 3)
p = [..., w, ?, ?, ?], r = {x, y, z} with xwy being a 3-cycle (neither x nor y can be chosen, choosing z would lead to situation 3)
p = [..., ?, ?, ?, ?], r = {w, x, y, z} with wxyz being a 4-cycle (any choice would lead to situation 4)
p = [..., ?, ?, ?, ?], r = {w, x, y, z} with xyz being a 3-cycle (choosing w would lead to situation 4, choosing any other would lead to situation 4)
Now it seems that the following algorithm gives all suitable permutations:
As long as there are strictly more than 5 numbers to choose, choose randomly among the compatible ones.
If there are 5 numbers left to choose: if the remaining numbers contain a 3-cycle or a 4-cycle, break that cycle (i.e. choose a number belonging to that cycle).
If there are 4 numbers left to choose: if the remaining numbers contain three cyclically consecutive numbers, choose one of them.
If there are 3 numbers left to choose: if the remaining numbers contain two cyclically consecutive numbers, choose one of them.
I am quite sure that this allows me to generate all suitable permutations and, hence, all suitable matrices.
Unfortunately, every matrix will be obtained several times, depending on the partition that was chosen.
Intro
Here is some prototype-approach, trying to solve the more general task of
uniform combinatorial sampling, which for our approach here means: we can use this approach for everything which we can formulate as SAT-problem.
It's not exploiting your problem directly and takes a heavy detour. This detour to the SAT-problem can help in regards to theory (more powerful general theoretical results) and efficiency (SAT-solvers).
That being said, it's not an approach if you want to sample within seconds or less (in my experiments), at least while being concerned about uniformity.
Theory
The approach, based on results from complexity-theory, follows this work:
GOMES, Carla P.; SABHARWAL, Ashish; SELMAN, Bart. Near-uniform sampling of combinatorial spaces using XOR constraints. In: Advances In Neural Information Processing Systems. 2007. S. 481-488.
The basic idea:
formulate the problem as SAT-problem
add randomly generated xors to the problem (acting on the decision-variables only! that's important in practice)
this will reduce the number of solutions (some solutions will get impossible)
do that in a loop (with tuned parameters) until only one solution is left!
search for some solution is being done by SAT-solvers or #SAT-solvers (=model-counting)
if there is more than one solution: no xors will be added but a complete restart will be done: add random-xors to the start-problem!
The guarantees:
when tuning the parameters right, this approach achieves near-uniform sampling
this tuning can be costly, as it's based on approximating the number of possible solutions
empirically this can also be costly!
Ante's answer, mentioning the number sequence A001499 actually gives a nice upper bound on the solution-space (as it's just ignoring adjacency-constraints!)
The drawbacks:
inefficient for large problems (in general; not necessarily compared to the alternatives like MCMC and co.)
need to change / reduce parameters to produce samples
those reduced parameters lose the theoretical guarantees
but empirically: good results are still possible!
Parameters:
In practice, the parameters are:
N: number of xors added
L: minimum number of variables part of one xor-constraint
U: maximum number of variables part of one xor-constraint
N is important to reduce the number of possible solutions. Given N constant, the other variables of course also have some effect on that.
Theory says (if i interpret correctly), that we should use L = R = 0.5 * #dec-vars.
This is impossible in practice here, as xor-constraints hurt SAT-solvers a lot!
Here some more scientific slides about the impact of L and U.
They call xors of size 8-20 short-XORS, while we will need to use even shorter ones later!
Implementation
Final version
Here is a pretty hacky implementation in python, using the XorSample scripts from here.
The underlying SAT-solver in use is Cryptominisat.
The code basically boils down to:
Transform the problem to conjunctive normal-form
as DIMACS-CNF
Implement the sampling-approach:
Calls XorSample (pipe-based + file-based)
Call SAT-solver (file-based)
Add samples to some file for later analysis
Code: (i hope i did warn you already about the code-quality)
from itertools import count
from time import time
import subprocess
import numpy as np
import os
import shelve
import uuid
import pickle
from random import SystemRandom
cryptogen = SystemRandom()
""" Helper functions """
# K-ARY CONSTRAINT GENERATION
# ###########################
# SINZ, Carsten. Towards an optimal CNF encoding of boolean cardinality constraints.
# CP, 2005, 3709. Jg., S. 827-831.
def next_var_index(start):
next_var = start
while(True):
yield next_var
next_var += 1
class s_index():
def __init__(self, start_index):
self.firstEnvVar = start_index
def next(self,i,j,k):
return self.firstEnvVar + i*k +j
def gen_seq_circuit(k, input_indices, next_var_index_gen):
cnf_string = ''
s_index_gen = s_index(next_var_index_gen.next())
# write clauses of first partial sum (i.e. i=0)
cnf_string += (str(-input_indices[0]) + ' ' + str(s_index_gen.next(0,0,k)) + ' 0\n')
for i in range(1, k):
cnf_string += (str(-s_index_gen.next(0, i, k)) + ' 0\n')
# write clauses for general case (i.e. 0 < i < n-1)
for i in range(1, len(input_indices)-1):
cnf_string += (str(-input_indices[i]) + ' ' + str(s_index_gen.next(i, 0, k)) + ' 0\n')
cnf_string += (str(-s_index_gen.next(i-1, 0, k)) + ' ' + str(s_index_gen.next(i, 0, k)) + ' 0\n')
for u in range(1, k):
cnf_string += (str(-input_indices[i]) + ' ' + str(-s_index_gen.next(i-1, u-1, k)) + ' ' + str(s_index_gen.next(i, u, k)) + ' 0\n')
cnf_string += (str(-s_index_gen.next(i-1, u, k)) + ' ' + str(s_index_gen.next(i, u, k)) + ' 0\n')
cnf_string += (str(-input_indices[i]) + ' ' + str(-s_index_gen.next(i-1, k-1, k)) + ' 0\n')
# last clause for last variable
cnf_string += (str(-input_indices[-1]) + ' ' + str(-s_index_gen.next(len(input_indices)-2, k-1, k)) + ' 0\n')
return (cnf_string, (len(input_indices)-1)*k, 2*len(input_indices)*k + len(input_indices) - 3*k - 1)
# K=2 clause GENERATION
# #####################
def gen_at_most_2_constraints(vars, start_var):
constraint_string = ''
used_clauses = 0
used_vars = 0
index_gen = next_var_index(start_var)
circuit = gen_seq_circuit(2, vars, index_gen)
constraint_string += circuit[0]
used_clauses += circuit[2]
used_vars += circuit[1]
start_var += circuit[1]
return [constraint_string, used_clauses, used_vars, start_var]
def gen_at_least_2_constraints(vars, start_var):
k = len(vars) - 2
vars = [-var for var in vars]
constraint_string = ''
used_clauses = 0
used_vars = 0
index_gen = next_var_index(start_var)
circuit = gen_seq_circuit(k, vars, index_gen)
constraint_string += circuit[0]
used_clauses += circuit[2]
used_vars += circuit[1]
start_var += circuit[1]
return [constraint_string, used_clauses, used_vars, start_var]
# Adjacency conflicts
# ###################
def get_all_adjacency_conflicts_4_neighborhood(N, X):
conflicts = set()
for x in range(N):
for y in range(N):
if x < (N-1):
conflicts.add(((x,y),(x+1,y)))
if y < (N-1):
conflicts.add(((x,y),(x,y+1)))
cnf = '' # slow string appends
for (var_a, var_b) in conflicts:
var_a_ = X[var_a]
var_b_ = X[var_b]
cnf += '-' + var_a_ + ' ' + '-' + var_b_ + ' 0 \n'
return cnf, len(conflicts)
# Build SAT-CNF
#############
def build_cnf(N, verbose=False):
var_counter = count(1)
N_CLAUSES = 0
X = np.zeros((N, N), dtype=object)
for a in range(N):
for b in range(N):
X[a,b] = str(next(var_counter))
# Adjacency constraints
CNF, N_CLAUSES = get_all_adjacency_conflicts_4_neighborhood(N, X)
# k=2 constraints
NEXT_VAR = N*N+1
for row in range(N):
constraint_string, used_clauses, used_vars, NEXT_VAR = gen_at_most_2_constraints(X[row, :].astype(int).tolist(), NEXT_VAR)
N_CLAUSES += used_clauses
CNF += constraint_string
constraint_string, used_clauses, used_vars, NEXT_VAR = gen_at_least_2_constraints(X[row, :].astype(int).tolist(), NEXT_VAR)
N_CLAUSES += used_clauses
CNF += constraint_string
for col in range(N):
constraint_string, used_clauses, used_vars, NEXT_VAR = gen_at_most_2_constraints(X[:, col].astype(int).tolist(), NEXT_VAR)
N_CLAUSES += used_clauses
CNF += constraint_string
constraint_string, used_clauses, used_vars, NEXT_VAR = gen_at_least_2_constraints(X[:, col].astype(int).tolist(), NEXT_VAR)
N_CLAUSES += used_clauses
CNF += constraint_string
# build final cnf
CNF = 'p cnf ' + str(NEXT_VAR-1) + ' ' + str(N_CLAUSES) + '\n' + CNF
return X, CNF, NEXT_VAR-1
# External tools
# ##############
def get_random_xor_problem(CNF_IN_fp, N_DEC_VARS, N_ALL_VARS, s, min_l, max_l):
# .cnf not part of arg!
p = subprocess.Popen(['./gen-wff', CNF_IN_fp,
str(N_DEC_VARS), str(N_ALL_VARS),
str(s), str(min_l), str(max_l), 'xored'],
stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
result = p.communicate()
os.remove(CNF_IN_fp + '-str-xored.xor') # file not needed
return CNF_IN_fp + '-str-xored.cnf'
def solve(CNF_IN_fp, N_DEC_VARS):
seed = cryptogen.randint(0, 2147483647) # actually no reason to do it; but can't hurt either
p = subprocess.Popen(["./cryptominisat5", '-t', '4', '-r', str(seed), CNF_IN_fp], stdin=subprocess.PIPE, stdout=subprocess.PIPE)
result = p.communicate()[0]
sat_line = result.find('s SATISFIABLE')
if sat_line != -1:
# solution found!
vars = parse_solution(result)[:N_DEC_VARS]
# forbid solution (DeMorgan)
negated_vars = list(map(lambda x: x*(-1), vars))
with open(CNF_IN_fp, 'a') as f:
f.write( (str(negated_vars)[1:-1] + ' 0\n').replace(',', ''))
# assume solve is treating last constraint despite not changing header!
# solve again
seed = cryptogen.randint(0, 2147483647)
p = subprocess.Popen(["./cryptominisat5", '-t', '4', '-r', str(seed), CNF_IN_fp], stdin=subprocess.PIPE, stdout=subprocess.PIPE)
result = p.communicate()[0]
sat_line = result.find('s SATISFIABLE')
if sat_line != -1:
os.remove(CNF_IN_fp) # not needed anymore
return True, False, None
else:
return True, True, vars
else:
return False, False, None
def parse_solution(output):
# assumes there is one
vars = []
for line in output.split("\n"):
if line:
if line[0] == 'v':
line_vars = list(map(lambda x: int(x), line.split()[1:]))
vars.extend(line_vars)
return vars
# Core-algorithm
# ##############
def xorsample(X, CNF_IN_fp, N_DEC_VARS, N_VARS, s, min_l, max_l):
start_time = time()
while True:
# add s random XOR constraints to F
xored_cnf_fp = get_random_xor_problem(CNF_IN_fp, N_DEC_VARS, N_VARS, s, min_l, max_l)
state_lvl1, state_lvl2, var_sol = solve(xored_cnf_fp, N_DEC_VARS)
print('------------')
if state_lvl1 and state_lvl2:
print('FOUND')
d = shelve.open('N_15_70_4_6_TO_PLOT')
d[str(uuid.uuid4())] = (pickle.dumps(var_sol), time() - start_time)
d.close()
return True
else:
if state_lvl1:
print('sol not unique')
else:
print('no sol found')
print('------------')
""" Run """
N = 15
N_DEC_VARS = N*N
X, CNF, N_VARS = build_cnf(N)
with open('my_problem.cnf', 'w') as f:
f.write(CNF)
counter = 0
while True:
print('sample: ', counter)
xorsample(X, 'my_problem', N_DEC_VARS, N_VARS, 70, 4, 6)
counter += 1
Output will look like (removed some warnings):
------------
no sol found
------------
------------
no sol found
------------
------------
no sol found
------------
------------
sol not unique
------------
------------
FOUND
Core: CNF-formulation
We introduce one variable for every cell of the matrix. N=20 means 400 binary-variables.
Adjancency:
Precalculate all symmetry-reduced conflicts and add conflict-clauses.
Basic theory:
a -> !b
<->
!a v !b (propositional logic)
Row/Col-wise Cardinality:
This is tough to express in CNF and naive approaches need an exponential number
of constraints.
We use some adder-circuit based encoding (SINZ, Carsten. Towards an optimal CNF encoding of boolean cardinality constraints) which introduces new auxiliary-variables.
Remark:
sum(var_set) <= k
<->
sum(negated(var_set)) >= len(var_set) - k
These SAT-encodings can be put into exact model-counters (for small N; e.g. < 9). The number of solutions equals Ante's results, which is a strong indication for a correct transformation!
There are also interesting approximate model-counters (also heavily based on xor-constraints) like approxMC which shows one more thing we can do with the SAT-formulation. But in practice i have not been able to use these (approxMC = autoconf; no comment).
Other experiments
I did also build a version using pblib, to use more powerful cardinality-formulations
for the SAT-CNF formulation. I did not try to use the C++-based API, but only the reduced pbencoder, which automatically selects some best encoding, which was way worse than my encoding used above (which is best is still a research-problem; often even redundant-constraints can help).
Empirical analysis
For the sake of obtaining some sample-size (given my patience), i only computed samples for N=15. In this case we used:
N=70 xors
L,U = 4,6
I also computed some samples for N=20 with (100,3,6), but this takes a few mins and we reduced the lower bound!
Visualization
Here some animation (strengthening my love-hate relationship with matplotlib):
Edit: And a (reduced) comparison to brute-force uniform-sampling with N=5 (NXOR,L,U = 4, 10, 30):
(I have not yet decided on the addition of the plotting-code. It's as ugly as the above one and people might look too much into my statistical shambles; normalizations and co.)
Theory
Statistical analysis is probably hard to do as the underlying problem is of such combinatoric nature. It's even not entirely obvious how that final cell-PDF should look like. In the case of N=odd, it's probably non-uniform and looks like a chess-board (i did brute-force check N=5 to observe this).
One thing we can be sure about (imho): symmetry!
Given a cell-PDF matrix, we should expect, that the matrix is symmetric (A = A.T).
This is checked in the visualization and the euclidean-norm of differences over time is plotted.
We can do the same on some other observation: observed pairings.
For N=3, we can observe the following pairs:
0,1
0,2
1,2
Now we can do this per-row and per-column and should expect symmetry too!
Sadly, it's probably not easy to say something about the variance and therefore the needed samples to speak about confidence!
Observation
According to my simplified perception, current-samples and the cell-PDF look good, although convergence is not achieved yet (or we are far away from uniformity).
The more important aspect are probably the two norms, nicely decreasing towards 0.
(yes; one could tune some algorithm for that by transposing with prob=0.5; but this is not done here as it would defeat it's purpose).
Potential next steps
Tune parameters
Check out the approach using #SAT-solvers / Model-counters instead of SAT-solvers
Try different CNF-formulations, especially in regards to cardinality-encodings and xor-encodings
XorSample is by default using tseitin-like encoding to get around exponentially grow
for smaller xors (as used) it might be a good idea to use naive encoding (which propagates faster)
XorSample supports that in theory; but the script's work differently in practice
Cryptominisat is known for dedicated XOR-handling (as it was build for analyzing cryptography including many xors) and might gain something by naive encoding (as inferring xors from blown-up CNFs is much harder)
More statistical-analysis
Get rid of XorSample scripts (shell + perl...)
Summary
The approach is very general
This code produces feasible samples
It should be not hard to prove, that every feasible solution can be sampled
Others have proven theoretical guarantees for uniformity for some params
does not hold for our params
Others have empirically / theoretically analyzed smaller parameters (in use here)
(Updated test results, example run-through and code snippets below.)
You can use dynamic programming to calculate the number of solutions resulting from every state (in a much more efficient way than a brute-force algorithm), and use those (pre-calculated) values to create equiprobable random solutions.
Consider the example of a 7x7 matrix; at the start, the state is:
0,0,0,0,0,0,0
meaning that there are seven adjacent unused columns. After adding two ones to the first row, the state could be e.g.:
0,1,0,0,1,0,0
with two columns that now have a one in them. After adding ones to the second row, the state could be e.g.:
0,1,1,0,1,0,1
After three rows are filled, there is a possibility that a column will have its maximum of two ones; this effectively splits the matrix into two independent zones:
1,1,1,0,2,0,1 -> 1,1,1,0 + 0,1
These zones are independent in the sense that the no-adjacent-ones rule has no effect when adding ones to different zones, and the order of the zones has no effect on the number of solutions.
In order to use these states as signatures for types of solutions, we have to transform them into a canonical notation. First, we have to take into account the fact that columns with only 1 one in them may be unusable in the next row, because they contain a one in the current row. So instead of a binary notation, we have to use a ternary notation, e.g.:
2,1,1,0 + 0,1
where the 2 means that this column was used in the current row (and not that there are 2 ones in the column). At the next step, we should then convert the twos back into ones.
Additionally, we can also mirror the seperate groups to put them into their lexicographically smallest notation:
2,1,1,0 + 0,1 -> 0,1,1,2 + 0,1
Lastly, we sort the seperate groups from small to large, and then lexicographically, so that a state in a larger matrix may be e.g.:
0,0 + 0,1 + 0,0,2 + 0,1,0 + 0,1,0,1
Then, when calculating the number of solutions resulting from each state, we can use memoization using the canonical notation of each state as a key.
Creating a dictionary of the states and the number of solutions for each of them only needs to be done once, and a table for larger matrices can probably be used for smaller matrices too.
Practically, you'd generate a random number between 0 and the total number of solutions, and then for every row, you'd look at the different states you could create from the current state, look at the number of unique solutions each one would generate, and see which option leads to the solution that corresponds with your randomly generated number.
Note that every state and the corresponding key can only occur in a particular row, so you can store the keys in seperate dictionaries per row.
TEST RESULTS
A first test using unoptimized JavaScript gave very promising results. With dynamic programming, calculating the number of solutions for a 10x10 matrix now takes a second, where a brute-force algorithm took several hours (and this is the part of the algorithm that only needs to be done once). The size of the dictionary with the signatures and numbers of solutions grows with a diminishing factor approaching 2.5 for each step in size; the time to generate it grows with a factor of around 3.
These are the number of solutions, states, signatures (total size of the dictionaries), and maximum number of signatures per row (largest dictionary per row) that are created:
size unique solutions states signatures max/row
4x4 2 9 6 2
5x5 16 73 26 8
6x6 722 514 107 40
7x7 33,988 2,870 411 152
8x8 2,215,764 13,485 1,411 596
9x9 179,431,924 56,375 4,510 1,983
10x10 17,849,077,140 218,038 13,453 5,672
11x11 2,138,979,146,276 801,266 38,314 14,491
12x12 304,243,884,374,412 2,847,885 104,764 35,803
13x13 50,702,643,217,809,908 9,901,431 278,561 96,414
14x14 9,789,567,606,147,948,364 33,911,578 723,306 238,359
15x15 2,168,538,331,223,656,364,084 114,897,838 1,845,861 548,409
16x16 546,386,962,452,256,865,969,596 ... 4,952,501 1,444,487
17x17 155,420,047,516,794,379,573,558,433 12,837,870 3,754,040
18x18 48,614,566,676,379,251,956,711,945,475 31,452,747 8,992,972
19x19 17,139,174,923,928,277,182,879,888,254,495 74,818,773 20,929,008
20x20 6,688,262,914,418,168,812,086,412,204,858,650 175,678,000 50,094,203
(Additional results obtained with C++, using a simple 128-bit integer implementation. To count the states, the code had to be run using each state as a seperate signature, which I was unable to do for the largest sizes. )
EXAMPLE
The dictionary for a 5x5 matrix looks like this:
row 0: 00000 -> 16 row 3: 101 -> 0
1112 -> 1
row 1: 20002 -> 2 1121 -> 1
00202 -> 4 1+01 -> 0
02002 -> 2 11+12 -> 2
02020 -> 2 1+121 -> 1
0+1+1 -> 0
row 2: 10212 -> 1 1+112 -> 1
12012 -> 1
12021 -> 2 row 4: 0 -> 0
12102 -> 1 11 -> 0
21012 -> 0 12 -> 0
02121 -> 3 1+1 -> 1
01212 -> 1 1+2 -> 0
The total number of solutions is 16; if we randomly pick a number from 0 to 15, e.g. 13, we can find the corresponding (i.e. the 14th) solution like this:
state: 00000
options: 10100 10010 10001 01010 01001 00101
signature: 00202 02002 20002 02020 02002 00202
solutions: 4 2 2 2 2 4
This tells us that the 14th solution is the 2nd solution of option 00101. The next step is:
state: 00101
options: 10010 01010
signature: 12102 02121
solutions: 1 3
This tells us that the 2nd solution is the 1st solution of option 01010. The next step is:
state: 01111
options: 10100 10001 00101
signature: 11+12 1112 1+01
solutions: 2 1 0
This tells us that the 1st solution is the 1st solution of option 10100. The next step is:
state: 11211
options: 01010 01001
signature: 1+1 1+1
solutions: 1 1
This tells us that the 1st solutions is the 1st solution of option 01010. The last step is:
state: 12221
options: 10001
And the 5x5 matrix corresponding to randomly chosen number 13 is:
0 0 1 0 1
0 1 0 1 0
1 0 1 0 0
0 1 0 1 0
1 0 0 0 1
And here's a quick'n'dirty code example; run the snippet to generate the signature and solution count dictionary, and generate a random 10x10 matrix (it takes a second to generate the dictionary; once that is done, it generates random solutions in half a millisecond):
function signature(state, prev) {
var zones = [], zone = [];
for (var i = 0; i < state.length; i++) {
if (state[i] == 2) {
if (zone.length) zones.push(mirror(zone));
zone = [];
}
else if (prev[i]) zone.push(3);
else zone.push(state[i]);
}
if (zone.length) zones.push(mirror(zone));
zones.sort(function(a,b) {return a.length - b.length || a - b;});
return zones.length ? zones.join("2") : "2";
function mirror(zone) {
var ltr = zone.join('');
zone.reverse();
var rtl = zone.join('');
return (ltr < rtl) ? ltr : rtl;
}
}
function memoize(n) {
var memo = [], empty = [];
for (var i = 0; i <= n; i++) memo[i] = [];
for (var i = 0; i < n; i++) empty[i] = 0;
memo[0][signature(empty, empty)] = next_row(empty, empty, 1);
return memo;
function next_row(state, prev, row) {
if (row > n) return 1;
var solutions = 0;
for (var i = 0; i < n - 2; i++) {
if (state[i] == 2 || prev[i] == 1) continue;
for (var j = i + 2; j < n; j++) {
if (state[j] == 2 || prev[j] == 1) continue;
var s = state.slice(), p = empty.slice();
++s[i]; ++s[j]; ++p[i]; ++p[j];
var sig = signature(s, p);
var sol = memo[row][sig];
if (sol == undefined)
memo[row][sig] = sol = next_row(s, p, row + 1);
solutions += sol;
}
}
return solutions;
}
}
function random_matrix(n, memo) {
var matrix = [], empty = [], state = [], prev = [];
for (var i = 0; i < n; i++) empty[i] = state[i] = prev[i] = 0;
var total = memo[0][signature(empty, empty)];
var pick = Math.floor(Math.random() * total);
document.write("solution " + pick.toLocaleString('en-US') +
" from a total of " + total.toLocaleString('en-US') + "<br>");
for (var row = 1; row <= n; row++) {
var options = find_options(state, prev);
for (var i in options) {
var state_copy = state.slice();
for (var j in state_copy) state_copy[j] += options[i][j];
var sig = signature(state_copy, options[i]);
var solutions = memo[row][sig];
if (pick < solutions) {
matrix.push(options[i].slice());
prev = options[i].slice();
state = state_copy.slice();
break;
}
else pick -= solutions;
}
}
return matrix;
function find_options(state, prev) {
var options = [];
for (var i = 0; i < n - 2; i++) {
if (state[i] == 2 || prev[i] == 1) continue;
for (var j = i + 2; j < n; j++) {
if (state[j] == 2 || prev[j] == 1) continue;
var option = empty.slice();
++option[i]; ++option[j];
options.push(option);
}
}
return options;
}
}
var size = 10;
var memo = memoize(size);
var matrix = random_matrix(size, memo);
for (var row in matrix) document.write(matrix[row] + "<br>");
The code snippet below shows the dictionary of signatures and solution counts for a matrix of size 10x10. I've used a slightly different signature format from the explanation above: the zones are delimited by a '2' instead of a plus sign, and a column which has a one in the previous row is marked with a '3' instead of a '2'. This shows how the keys could be stored in a file as integers with 2×N bits (padded with 2's).
function signature(state, prev) {
var zones = [], zone = [];
for (var i = 0; i < state.length; i++) {
if (state[i] == 2) {
if (zone.length) zones.push(mirror(zone));
zone = [];
}
else if (prev[i]) zone.push(3);
else zone.push(state[i]);
}
if (zone.length) zones.push(mirror(zone));
zones.sort(function(a,b) {return a.length - b.length || a - b;});
return zones.length ? zones.join("2") : "2";
function mirror(zone) {
var ltr = zone.join('');
zone.reverse();
var rtl = zone.join('');
return (ltr < rtl) ? ltr : rtl;
}
}
function memoize(n) {
var memo = [], empty = [];
for (var i = 0; i <= n; i++) memo[i] = [];
for (var i = 0; i < n; i++) empty[i] = 0;
memo[0][signature(empty, empty)] = next_row(empty, empty, 1);
return memo;
function next_row(state, prev, row) {
if (row > n) return 1;
var solutions = 0;
for (var i = 0; i < n - 2; i++) {
if (state[i] == 2 || prev[i] == 1) continue;
for (var j = i + 2; j < n; j++) {
if (state[j] == 2 || prev[j] == 1) continue;
var s = state.slice(), p = empty.slice();
++s[i]; ++s[j]; ++p[i]; ++p[j];
var sig = signature(s, p);
var sol = memo[row][sig];
if (sol == undefined)
memo[row][sig] = sol = next_row(s, p, row + 1);
solutions += sol;
}
}
return solutions;
}
}
var memo = memoize(10);
for (var i in memo) {
document.write("row " + i + ":<br>");
for (var j in memo[i]) {
document.write(""" + j + "": " + memo[i][j] + "<br>");
}
}
Just few thoughts. Number of matrices satisfying conditions for n <= 10:
3 0
4 2
5 16
6 722
7 33988
8 2215764
9 179431924
10 17849077140
Unfortunatelly there is no sequence with these numbers in OEIS.
There is one similar (A001499), without condition for neighbouring one's. Number of nxn matrices in this case is 'of order' as A001499's number of (n-1)x(n-1) matrices. That is to be expected since number
of ways to fill one row in this case, position 2 one's in n places with at least one zero between them is ((n-1) choose 2). Same as to position 2 one's in (n-1) places without the restriction.
I don't think there is an easy connection between these matrix of order n and A001499 matrix of order n-1, meaning that if we have A001499 matrix than we can construct some of these matrices.
With this, for n=20, number of matrices is >10^30. Quite a lot :-/
This solution use recursion in order to set the cell of the matrix one by one. If the random walk finish with an impossible solution then we rollback one step in the tree and we continue the random walk.
The algorithm is efficient and i think that the generated data are highly equiprobable.
package rndsqmatrix;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.stream.IntStream;
public class RndSqMatrix {
/**
* Generate a random matrix
* #param size the size of the matrix
* #return the matrix encoded in 1d array i=(x+y*size)
*/
public static int[] generate(final int size) {
return generate(size, new int[size * size], new int[size],
new int[size]);
}
/**
* Build a matrix recursivly with a random walk
* #param size the size of the matrix
* #param matrix the matrix encoded in 1d array i=(x+y*size)
* #param rowSum
* #param colSum
* #return
*/
private static int[] generate(final int size, final int[] matrix,
final int[] rowSum, final int[] colSum) {
// generate list of valid positions
final List<Integer> positions = new ArrayList();
for (int y = 0; y < size; y++) {
if (rowSum[y] < 2) {
for (int x = 0; x < size; x++) {
if (colSum[x] < 2) {
final int p = x + y * size;
if (matrix[p] == 0
&& (x == 0 || matrix[p - 1] == 0)
&& (x == size - 1 || matrix[p + 1] == 0)
&& (y == 0 || matrix[p - size] == 0)
&& (y == size - 1 || matrix[p + size] == 0)) {
positions.add(p);
}
}
}
}
}
// no valid positions ?
if (positions.isEmpty()) {
// if the matrix is incomplete => return null
for (int i = 0; i < size; i++) {
if (rowSum[i] != 2 || colSum[i] != 2) {
return null;
}
}
// the matrix is complete => return it
return matrix;
}
// random walk
Collections.shuffle(positions);
for (int p : positions) {
// set '1' and continue recursivly the exploration
matrix[p] = 1;
rowSum[p / size]++;
colSum[p % size]++;
final int[] solMatrix = generate(size, matrix, rowSum, colSum);
if (solMatrix != null) {
return solMatrix;
}
// rollback
matrix[p] = 0;
rowSum[p / size]--;
colSum[p % size]--;
}
// we can't find a valid matrix from here => return null
return null;
}
public static void printMatrix(final int size, final int[] matrix) {
for (int y = 0; y < size; y++) {
for (int x = 0; x < size; x++) {
System.out.print(matrix[x + y * size]);
System.out.print(" ");
}
System.out.println();
}
}
public static void printStatistics(final int size, final int count) {
final int sumMatrix[] = new int[size * size];
for (int i = 0; i < count; i++) {
final int[] matrix = generate(size);
for (int j = 0; j < sumMatrix.length; j++) {
sumMatrix[j] += matrix[j];
}
}
printMatrix(size, sumMatrix);
}
public static void checkAlgorithm() {
final int size = 8;
final int count = 2215764;
final int divisor = 122;
final int sumMatrix[] = new int[size * size];
for (int i = 0; i < count/divisor ; i++) {
final int[] matrix = generate(size);
for (int j = 0; j < sumMatrix.length; j++) {
sumMatrix[j] += matrix[j];
}
}
int total = 0;
for(int i=0; i < sumMatrix.length; i++) {
total += sumMatrix[i];
}
final double factor = (double)total / (count/divisor);
System.out.println("Factor=" + factor + " (theory=16.0)");
}
public static void benchmark(final int size, final int count,
final boolean parallel) {
final long begin = System.currentTimeMillis();
if (!parallel) {
for (int i = 0; i < count; i++) {
generate(size);
}
} else {
IntStream.range(0, count).parallel().forEach(i -> generate(size));
}
final long end = System.currentTimeMillis();
System.out.println("rate="
+ (double) (end - begin) / count + "ms/matrix");
}
public static void main(String[] args) {
checkAlgorithm();
benchmark(8, 10000, true);
//printStatistics(8, 2215764/36);
printStatistics(8, 2215764);
}
}
The output is:
Factor=16.0 (theory=16.0)
rate=0.2835ms/matrix
552969 554643 552895 554632 555680 552753 554567 553389
554071 554847 553441 553315 553425 553883 554485 554061
554272 552633 555130 553699 553604 554298 553864 554028
554118 554299 553565 552986 553786 554473 553530 554771
554474 553604 554473 554231 553617 553556 553581 553992
554960 554572 552861 552732 553782 554039 553921 554661
553578 553253 555721 554235 554107 553676 553776 553182
553086 553677 553442 555698 553527 554850 553804 553444
Here is a very fast approach of generating the matrix row by row, written in Java:
public static void main(String[] args) throws Exception {
int n = 100;
Random rnd = new Random();
byte[] mat = new byte[n*n];
byte[] colCount = new byte[n];
//generate row by row
for (int x = 0; x < n; x++) {
//generate a random first bit
int b1 = rnd.nextInt(n);
while ( (x > 0 && mat[(x-1)*n + b1] == 1) || //not adjacent to the one above
(colCount[b1] == 2) //not in a column which has 2
) b1 = rnd.nextInt(n);
//generate a second bit, not equal to the first one
int b2 = rnd.nextInt(n);
while ( (b2 == b1) || //not the same as bit 1
(x > 0 && mat[(x-1)*n + b2] == 1) || //not adjacent to the one above
(colCount[b2] == 2) || //not in a column which has 2
(b2 == b1 - 1) || //not adjacent to b1
(b2 == b1 + 1)
) b2 = rnd.nextInt(n);
//fill the matrix values and increment column counts
mat[x*n + b1] = 1;
mat[x*n + b2] = 1;
colCount[b1]++;
colCount[b2]++;
}
String arr = Arrays.toString(mat).substring(1, n*n*3 - 1);
System.out.println(arr.replaceAll("(.{" + n*3 + "})", "$1\n"));
}
It essentially generates each a random row at a time. If the row will violate any of the conditions, it is generated again (again randomly). I believe this will satisfy condition 4 as well.
Adding a quick note that it will spin forever for N-s where there is no solutions (like N=3).

Efficient way to generate a seemingly random permutation from a very large set without repeating?

I have a very large set (billions or more, it's expected to grow exponentially to some level), and I want to generate seemingly random elements from it without repeating. I know I can pick a random number and repeat and record the elements I have generated, but that takes more and more memory as numbers are generated, and wouldn't be practical after couple millions elements out.
I mean, I could say 1, 2, 3 up to billions and each would be constant time without remembering all the previous, or I can say 1,3,5,7,9 and on then 2,4,6,8,10, but is there a more sophisticated way to do that and eventually get a seemingly random permutation of that set?
Update
1, The set does not change size in the generation process. I meant when the user's input increases linearly, the size of the set increases exponentially.
2, In short, the set is like the set of every integer from 1 to 10 billions or more.
3, In long, it goes up to 10 billion because each element carries the information of many independent choices, for example. Imagine an RPG character that have 10 attributes, each can go from 1 to 100 (for my problem different choices can have different ranges), thus there's 10^20 possible characters, number "10873456879326587345" would correspond to a character that have "11, 88, 35...", and I would like an algorithm to generate them one by one without repeating, but makes it looks random.
Thanks for the interesting question. You can create a "pseudorandom"* (cyclic) permutation with a few bytes using modular exponentiation. Say we have n elements. Search for a prime p that's bigger than n+1. Then find a primitive root g modulo p. Basically by definition of primitive root, the action x --> (g * x) % p is a cyclic permutation of {1, ..., p-1}. And so x --> ((g * (x+1))%p) - 1 is a cyclic permutation of {0, ..., p-2}. We can get a cyclic permutation of {0, ..., n-1} by repeating the previous permutation if it gives a value bigger (or equal) n.
I implemented this idea as a Go package. https://github.com/bwesterb/powercycle
package main
import (
"fmt"
"github.com/bwesterb/powercycle"
)
func main() {
var x uint64
cycle := powercycle.New(10)
for i := 0; i < 10; i++ {
fmt.Println(x)
x = cycle.Apply(x)
}
}
This outputs something like
0
6
4
1
2
9
3
5
8
7
but that might vary off course depending on the generator chosen.
It's fast, but not super-fast: on my five year old i7 it takes less than 210ns to compute one application of a cycle on 1000000000000000 elements. More details:
BenchmarkNew10-8 1000000 1328 ns/op
BenchmarkNew1000-8 500000 2566 ns/op
BenchmarkNew1000000-8 50000 25893 ns/op
BenchmarkNew1000000000-8 200000 7589 ns/op
BenchmarkNew1000000000000-8 2000 648785 ns/op
BenchmarkApply10-8 10000000 170 ns/op
BenchmarkApply1000-8 10000000 173 ns/op
BenchmarkApply1000000-8 10000000 172 ns/op
BenchmarkApply1000000000-8 10000000 169 ns/op
BenchmarkApply1000000000000-8 10000000 201 ns/op
BenchmarkApply1000000000000000-8 10000000 204 ns/op
Why did I say "pseudorandom"? Well, we are always creating a very specific kind of cycle: namely one that uses modular exponentiation. It looks pretty pseudorandom though.
I would use a random number and swap it with an element at the beginning of the set.
Here's some pseudo code
set = [1, 2, 3, 4, 5, 6]
picked = 0
Function PickNext(set, picked)
If picked > Len(set) - 1 Then
Return Nothing
End If
// random number between picked (inclusive) and length (exclusive)
r = RandomInt(picked, Len(set))
// swap the picked element to the beginning of the set
result = set[r]
set[r] = set[picked]
set[picked] = result
// update picked
picked++
// return your next random element
Return temp
End Function
Every time you pick an element there is one swap and the only extra memory being used is the picked variable. The swap can happen if the elements are in a database or in memory.
EDIT Here's a jsfiddle of a working implementation http://jsfiddle.net/sun8rw4d/
JavaScript
var set = [];
set.picked = 0;
function pickNext(set) {
if(set.picked > set.length - 1) { return null; }
var r = set.picked + Math.floor(Math.random() * (set.length - set.picked));
var result = set[r];
set[r] = set[set.picked];
set[set.picked] = result;
set.picked++;
return result;
}
// testing
for(var i=0; i<100; i++) {
set.push(i);
}
while(pickNext(set) !== null) { }
document.body.innerHTML += set.toString();
EDIT 2 Finally, a random binary walk of the set. This can be accomplished with O(Log2(N)) stack space (memory) which for 10billion is only 33. There's no shuffling or swapping involved. Using trinary instead of binary might yield even better pseudo random results.
// on the fly set generator
var count = 0;
var maxValue = 64;
function nextElement() {
// restart the generation
if(count == maxValue) {
count = 0;
}
return count++;
}
// code to pseudo randomly select elements
var current = 0;
var stack = [0, maxValue - 1];
function randomBinaryWalk() {
if(stack.length == 0) { return null; }
var high = stack.pop();
var low = stack.pop();
var mid = ((high + low) / 2) | 0;
// pseudo randomly choose the next path
if(Math.random() > 0.5) {
if(low <= mid - 1) {
stack.push(low);
stack.push(mid - 1);
}
if(mid + 1 <= high) {
stack.push(mid + 1);
stack.push(high);
}
} else {
if(mid + 1 <= high) {
stack.push(mid + 1);
stack.push(high);
}
if(low <= mid - 1) {
stack.push(low);
stack.push(mid - 1);
}
}
// how many elements to skip
var toMid = (current < mid ? mid - current : (maxValue - current) + mid);
// skip elements
for(var i = 0; i < toMid - 1; i++) {
nextElement();
}
current = mid;
// get result
return nextElement();
}
// test
var result;
var list = [];
do {
result = randomBinaryWalk();
list.push(result);
} while(result !== null);
document.body.innerHTML += '<br/>' + list.toString();
Here's the results from a couple of runs with a small set of 64 elements. JSFiddle http://jsfiddle.net/yooLjtgu/
30,46,38,34,36,35,37,32,33,31,42,40,41,39,44,45,43,54,50,52,53,51,48,47,49,58,60,59,61,62,56,57,55,14,22,18,20,19,21,16,15,17,26,28,29,27,24,25,23,6,2,4,5,3,0,1,63,10,8,7,9,12,11,13
30,14,22,18,16,15,17,20,19,21,26,28,29,27,24,23,25,6,10,8,7,9,12,13,11,2,0,63,1,4,5,3,46,38,42,44,45,43,40,41,39,34,36,35,37,32,31,33,54,58,56,55,57,60,59,61,62,50,48,49,47,52,51,53
As I mentioned in my comment, unless you have an efficient way to skip to a specific point in your "on the fly" generation of the set this will not be very efficient.
if it is enumerable then use a pseudo-random integer generator adjusted to the period 0 .. 2^n - 1 where the upper bound is just greater than the size of your set and generate pseudo-random integers discarding those more than the size of your set. Use those integers to index items from your set.
Pre- compute yourself a series of indices (e.g. in a file), which has the properties you need and then randomly choose a start index for your enumeration and use the series in a round-robin manner.
The length of your pre-computed series should be > the maximum size of the set.
If you combine this (depending on your programming language etc.) with file mappings, your final nextIndex(INOUT state) function is (nearly) as simple as return mappedIndices[state++ % PERIOD];, if you have a fixed size of each entry (e.g. 8 bytes -> uint64_t).
Of course, the returned value could be > your current set size. Simply draw indices until you get one which is <= your sets current size.
Update (In response to question-update):
There is another option to achieve your goal if it is about creating 10Billion unique characters in your RPG: Generate a GUID and write yourself a function which computes your number from the GUID. man uuid if you are are on a unix system. Else google it. Some parts of the uuid are not random but contain meta-info, some parts are either systematic (such as your network cards MAC address) or random, depending on generator algorithm. But they are very very most likely unique. So, whenever you need a new unique number, generate a uuid and transform it to your number by means of some algorithm which basically maps the uuid bytes to your number in a non-trivial way (e.g. use hash functions).

Faster concatenation of cell arrays of different sizes

I have a cell array of size m x 1 and each cell is again s x t cell array (size varies). I would like to concatenate vertically. The code is as follows:
function(cell_out) = vert_cat(cell_in)
[row,col] = cellfun(#size,cell_in,'Uni',0);
fcn_vert = #(x)([x,repmat({''},size(x,1),max(cell2mat(col))-size(x,2))]);
cell_out = cellfun(fcn_vert,cell_in,'Uni',0); % Taking up lot of time
cell_out = vertcat(cell_out{:});
end
Step 3 takes a lot of time. Is it the right way to do or is there any another faster way to achieve this?
cellfun has been found to be slower than loops (kind of old, but agrees with what I have seen).
In addition, repmat has also been a performance hit in the past (though that may be different now).
Try this two-loop code that aims to accomplish your task:
function cellOut = vert_cat(c)
nElem = length(c);
colPad = zeros(nElem,1);
nRow = zeros(nElem,1);
for k = 1:nElem
[nRow(k),colPad(k)] = size(c{k});
end
colMax = max(colPad);
colPad = colMax - colPad;
cellOut = cell(sum(nRow),colMax);
bottom = cumsum(nRow) - nRow + 1;
top = bottom + nRow - 1;
for k = 1:nElem
cellOut(bottom(k):top(k),:) = [c{k},cell(nRow(k),colPad(k))];
end
end
My test for this code was
A = rand(20,20);
A = mat2cell(A,ones(20,1),ones(20,1));
C = arrayfun(#(c) A(1:c,1:c),randi([1,15],1,5),'UniformOutput',false);
ccat = vert_cat(c);
I used this pice of code to generate data:
%generating some dummy data
m=1000;
s=100;
t=100;
cell_in=cell(m,1);
for idx=1:m
cell_in{idx}=cell(randi(s),randi(t));
end
Applying some minor modifications, I was able to speed up the code by a factor of 5
%Minor modifications of the original code
%use arrays instead of cells for row and col
[row,col] = cellfun(#size,cell_in);
%claculate max(col) once
tcol=max(col);
%use cell instead of repmat to generate an empty cell
fcn_vert = #(x)([x,cell(size(x,1),tcol-size(x,2))]);
cell_out = cellfun(fcn_vert,cell_in,'Uni',0); % Taking up lot of time
cell_out = vertcat(cell_out{:});
Using simply a for loop is even faster, because the data is only moved once
%new approac. Basic idea: move every data only once
[row,col] = cellfun(#size,cell_in);
trow=sum(row);
tcol=max(col);
r=1;
cell_out2 = cell(trow,tcol);
for idx=1:numel(cell_in)
cell_out2(r:r+row(idx)-1,1:col(idx))=cell_in{idx};
r=r+row(idx);
end

RX LINQ partition the input stream

I have a input stream where the input element consist of Date, Depth and Area.
I want to plot the Area against the Depth and want therefor to take out a window of Depth e.g. between 1.0-100.0m.
The problem is that I want to down sample the input stream since there can be many inputs with close Depth values.
I want to partition the input into x bins, e.g. 2 bins means all depth values between 1-50 is averaged in the first bin and 51-100 in the second bin.
I was thinking something like this:
var q = from e in input
where (e.Depth > 1) && (e.Depth <= 100)
// here I need some way of partition the sequence into bins
// and averaging the elements.
Split a collection into `n` parts with LINQ? wants to do something similar without rx.
Modified answer as per your comment. steps = number of buckets.
var min = 1, max = 100;
var steps = 10;
var f = (max - min + 1) / steps; // The extra 1 is really an epsilon. #hack
var q = from e in input
where e.Depth > 1 && e.depth <= 100
let x = e.Depth - min
group e by x < max ? (x - (x % f)) : ;
This is the function we're grouping by for the given e.Depth.
This probably won't work so great with floating point values (due to precision), unless you floor/ceil the selection, but then you might run out of integers, so you may need to scale a bit... something like group e by Math.Floor((x - (x % f)) * scaleFactor).
This should do what you want
static int GetBucket(double value, double min, double max, int bucketCount)
{
return (int)((value - min) / (max - min) * bucketCount + 0.5);
}
var grouped = input.GroupBy(e => GetBucket(e.Depth, 1, 100, 50));

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