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Given a nucleotide sequence, I'm writing some Julia code to generate a sparse vector of (masked) kmer counts, and I would like it to run as fast as possible.
Here is my current implementation,
using Distributions
using SparseArrays
function kmer_profile(seq, k, mask)
basis = [4^i for i in (k - 1):-1:0]
d = Dict('A'=>0, 'C'=>1, 'G'=>2, 'T'=>3)
kmer_dict = Dict{Int, Int32}(4^k=>0)
for n in 1:(length(seq) - length(mask) + 1)
kmer_hash = 1
j = 1
for i in 1:length(mask)
if mask[i]
kmer_hash += d[seq[n+i-1]] * basis[j]
j += 1
end
end
haskey(kmer_dict, kmer_hash) ? kmer_dict[kmer_hash] += 1 : kmer_dict[kmer_hash] = 1
end
return sparsevec(kmer_dict)
end
seq = join(sample(['A','C','G','T'], 1000000))
mask_str = "111111011111001111111111111110"
mask = BitArray([parse(Bool, string(m)) for m in split(mask_str, "")])
k = sum(mask)
#time kmer_profile(seq, k, mask)
This code runs in about 0.3 seconds on my M1 MacBook Pro, is there any way to make it run significantly faster?
The function kmer_profile uses a sliding window of size length(mask) to count the number of times each masked kmer appears in the nucleotide sequence. A mask is a binary sequence, and a masked kmer is a kmer with nucleotides dropped at positions at which the mask is zero. E.g. the kmer ACGT and mask 1001 will produce the masked kmer AT.
To produce the kmer hash, the function treats each kmer as a base 4 number and then converts it to a (base 10) 64-bit integer, for indexing into the kmer vector.
The size of k is equal to the number of ones in the mask string, and is implicitly limited to 31 so that kmer hashes can fit into a 64-bit integer type.
There are several possible optimizations to make this code faster.
First of all, one can convert the Dict to an array since array-based indexing is faster than dictionary-based indexing one and this is possible here since the key is an ASCII character.
Moreover, the extraction of the sequence codes can be done once instead of length(mask) times by pre-computing code and putting the result in a temporary array.
Additionally, the mask-based conditional and the loop carried dependency make things slow. Indeed, the condition cannot be (easily) predicted by the processor causing it to stall for several cycles. The loop carried dependency make things even worse since the processor can hardly execute other instructions during this stall. This problem can be solved by pre-computing the factors based on both mask and basis. The result is a faster branch-less loop.
Once the above optimizations are done, the biggest bottleneck is sparsevec. In fact, it was also taking nearly half the time of the initial implementation! Optimizing this step is difficult but not impossible. It is slow because of random accesses in the Julia implementation. One can speed this up by sorting the keys-values pairs in the first place. It is faster due to a more cache-friendly execution and it can also help the prediction unit of the processor. This is a complex topic. For more details about how this works, please read Why is processing a sorted array faster than processing an unsorted array?.
Here is the final optimized code:
function kmer_profile_opt(seq, k, mask)
basis = [4^i for i in (k - 1):-1:0]
d = zeros(Int8, 128)
d[Int64('A')] = 0
d[Int64('C')] = 1
d[Int64('G')] = 2
d[Int64('T')] = 3
seq_codes = [d[Int8(e)] for e in seq]
j = 1
premult = zeros(Int64, length(mask))
for i in 1:length(mask)
if mask[i]
premult[i] = basis[j]
j += 1
end
end
kmer_dict = Dict{Int, Int32}(4^k=>0)
for n in 1:(length(seq) - length(mask) + 1)
kmer_hash = 1
j = 1
for i in 1:length(mask)
kmer_hash += seq_codes[n+i-1] * premult[i]
end
haskey(kmer_dict, kmer_hash) ? kmer_dict[kmer_hash] += 1 : kmer_dict[kmer_hash] = 1
end
sorted_kmer_pairs = sort(collect(kmer_dict))
sorted_kmer_keys = [e[1] for e in sorted_kmer_pairs]
sorted_kmer_values = [e[2] for e in sorted_kmer_pairs]
return sparsevec(sorted_kmer_keys, sorted_kmer_values)
end
This code is a bit more than twice faster than the initial implementation on my machine. A significant fraction of the time is still spent in the sorting algorithm.
The code can still be optimized further. One way is to use a parallel sort algorithm. Another way is to replace the premult[i] multiplication by a shift which is faster assuming premult[i] is modified so to contain exponents. I expect the code to be about 4 times faster than the original code. The main bottleneck should be the big dictionary creation. Improving further the performance of this is very hard (though it is still possible).
Inspired by Jérôme's answer, and squeezing some more by avoiding Dicts altogether:
function kmer_profile_opt3a(seq, k, mask)
d = zeros(Int8, 128)
d[Int64('A')] = 0
d[Int64('C')] = 1
d[Int64('G')] = 2
d[Int64('T')] = 3
seq_codes = [d[Int8(e)] for e in seq]
basis = [4^i for i in (k-1):-1:0]
j = 1
premult = zeros(Int64, length(mask))
for i in 1:length(mask)
if mask[i]
premult[i] = basis[j]
j += 1
end
end
kmer_vec = Vector{Int}(undef, length(seq)-length(mask)+1)
#inbounds for n in 1:(length(seq) - length(mask) + 1)
kmer_hash = 1
for i in 1:length(mask)
kmer_hash += seq_codes[n+i-1] * premult[i]
end
kmer_vec[n] = kmer_hash
end
sort!(kmer_vec)
return sparsevec(kmer_vec, ones(length(kmer_vec)), 4^k, +)
end
This achieved another 2x over Jérôme's answer on my machine.
The auto-combining feature of sparsevec makes the code a bit more compact.
Trying to slim the code further, and avoid unnecessary allocations in sparse vector creation, the following can be used:
using SparseArrays, LinearAlgebra
function specialsparsevec(nzs, n)
vals = Vector{Int}(undef, length(nzs))
j, k, count, last = (1, 1, 0, nzs[1])
while k <= length(nzs)
if nzs[k] == last
count += 1
else
vals[j], nzs[j] = (count, last)
count, last = (1, nzs[k])
j += 1
end
k += 1
end
vals[j], nzs[j] = (count, last)
resize!(nzs, j)
resize!(vals, j)
return SparseVector(n, nzs, vals)
end
function kmer_profile_opt3(seq, k, mask)
d = zeros(Int8, 128)
foreach(((i,c),) -> d[Int(c)]=i-1, enumerate(collect("ACGT")))
seq_codes = getindex.(Ref(d), Int8.(collect(seq)))
premult = foldr(
(i,(p,j))->(mask[i] && (p[i]=j ; j<<=2) ; (p,j)),
1:length(mask); init=(zeros(Int64,length(mask)),1)) |> first
kmer_vec = sort(
[ dot(#view(seq_codes[n:n+length(mask)-1]),premult) + 1 for
n in 1:(length(seq)-length(mask)+1)
])
return specialsparsevec(kmer_vec, 4^k)
end
This last version gets another 10% speedup (but is a little cryptic):
julia> #btime kmer_profile_opt($seq, $k, $mask);
367.584 ms (81 allocations: 134.71 MiB) # other answer
julia> #btime kmer_profile_opt3a($seq, $k, $mask);
140.882 ms (22 allocations: 54.36 MiB) # 1st this answer
julia> #btime kmer_profile_opt3($seq, $k, $mask);
127.016 ms (14 allocations: 27.66 MiB) # 2nd this answer
I'm solving some Project Euler problems using Ruby, and specifically here I'm talking about problem 25 (What is the index of the first term in the Fibonacci sequence to contain 1000 digits?).
At first, I was using Ruby 2.2.3 and I coded the problem as such:
number = 3
a = 1
b = 2
while b.to_s.length < 1000
a, b = b, a + b
number += 1
end
puts number
But then I found out that version 2.4.2 has a method called digits which is exactly what I needed. I transformed to code to:
while b.digits.length < 1000
And when I compared the two methods, digits was much slower.
Time
./025/problem025.rb 0.13s user 0.02s system 80% cpu 0.190 total
./025/problem025.rb 2.19s user 0.03s system 97% cpu 2.275 total
Does anyone have an idea why?
Ruby's digits
... is implemented in rb_int_digits.
Which for non-tiny numbers (i.e., most of your numbers) uses rb_int_digits_bigbase.
Which extracts digit after digit naively with division/modulo by base.
So it should take quadratic time (at least with a small base such as 10).
Ruby's to_s
... is implemented in int_to_s.
Which uses rb_int2str.
Which for non-tiny numbers uses rb_big2str.
Which uses rb_big2str1.
Which might use big2str_gmp if available (which sounds/looks like it uses the fast GMP library) or ...
... uses big2str_generic.
Which uses big2str_karatsuba (sweet, I recognize that name!).
Which looks like it has something to do with ...
... Karatsuba's algorithm, which is a fast multiplication algorithm. If you multiply two n-digit numbers the naive way you learned in school, you take n2 single-digit products. Karatsuba on the other hand only needs about n1.585, which is quite a lot better. And I didn't read into this further, but I suspect what Ruby does here is also this efficient. Eric Lippert's answer with a base conversion algorithm uses Karatsuba multiplication and says "this [base conversion] algorithm is utterly dominated by the cost of the multiplication".
Comparing quadratic to n1.585 over the number lengths from 1 digit to 1000 digits gives factor 15:
(1..1000).sum { |i| i**2 } / (1..1000).sum { |i| i**1.585 }
=> 15.150583254950678
Which is roughly the factor you observed as well. Of course that's a rather naive comparison, but, well, why not.
GMP by the way apparently uses/used a "near O(n * log(n)) FFT-based multiplication algorithm".
Thanks to #Drenmi's answer for motivating me to dig into the source after all. I hope I did this right, no guarantees, I'm a Ruby beginner. But that's why I left all the links there for you to check for yourself :-P
Integer#digits doesn't just "split" the number. From the documentation:
Returns the array including the digits extracted by place-value
notation with radix base of int.
This extraction is done even if a base argument is omitted. The relevant source:
# ruby/numeric.c:4809
while (!FIXNUM_P(num) || FIX2LONG(num) > 0) {
VALUE qr = rb_int_divmod(num, base);
rb_ary_push(digits, RARRAY_AREF(qr, 1));
num = RARRAY_AREF(qr, 0);
}
As you can see, this process includes repeated modulo arithmetics, which likely accounts for the additional runtime.
Many ruby methods create objects (strins, arrays, etc.)
In ruby, object creation in ruby is "expensive".
For instance to_s creates a string and digits creates an array every time the while condition is evaluated.
If you want to optimize your example, you can do the following:
# create the smallest possible 1000 digits number
max = 10**999
number = 3
a = 1
b = 2
# do not create objects in while condition
while b < max
a, b = b, a + b
number += 1
end
puts number
I have not answered your question, but wish to suggest an improved algorithm for the problem you have addressed. For a given number of decimal digits, n, I have implemented the following algorithm.
estimate the number f of Fibonacci numbers ("FNs") that have n or fewer decimal digits.
compute the fth and (f-1)st FNs, and the number of digits m in the fth FN.
if m >= n back down from down from the (f-1)st FN until the (f-1)st FN has fewer than n decimal digits, at which time the fth FN is the smallest FN to have n decimal digits.
if m < n increase the fth FN until the it has n decimal digits, at which time it is the smallest FN to have n decimal digits.
The key is to compute a close estimate f in the first step.
Code
AVG_FNs_PER_DIGIT = 4.784971966781667
def first_fibonacci_with_n_digits(n)
return [1, 1] if n == 1
idx = (n * AVG_FNs_PER_DIGIT).round
fn, prev_fn = fib(idx)
fn.to_s.size >= n ? fib_down(n, fn, prev_fn, idx) : fib_up(n, fn, prev_fn, idx)
end
def fib(idx)
a = 1
b = 2
(idx - 2).times {a, b = b, a + b }
[b, a]
end
def fib_up(n, b, a, idx)
loop do
a, b = b, a + b
idx += 1
break [idx, b] if b.to_s.size == n
end
end
def fib_down(n, b, a, idx)
loop do
a, b = b - a, a
break [idx, b] if a.to_s.size == n - 1
idx -= 1
end
end
Benchmarks
In computing each Fibonacci number two operations are typically performed:
compute the number of digits in the last-computed Fibonacci number and if that number is equal to the target number of digits, terminate (for reasons made clear in the Explanation section below, it cannot be larger than the target number); else
compute the next number in the Fibonacci sequence.
By contrast, the method I have proposed performs the first step a relatively small number of times.
How important is the first step relative to the second and how does the use of n.digits.size compare with that of n.to_s.size in the first step? Let's run some benchmarks to find out.
def use_to_s(ndigits)
case ndigits
when 1
[1, 1]
else
a = 1
b = 2
idx = 3
loop do
break [idx, b] if b.to_s.length == ndigits
a, b = b, a + b
idx += 1
end
end
end
def use_digits(ndigits)
case ndigits
when 1
[1, 1]
else
a = 1
b = 2
idx = 3
loop do
break [idx, b] if b.digits.size == ndigits
a, b = b, a + b
idx += 1
end
end
end
require 'fruity'
def test(ndigits)
nfibs, last_fib = use_to_s(ndigits)
puts "\nndigits = #{ndigits}, nfibs=#{nfibs}, last_fib=#{last_fib}"
compare do
try_use_to_s { use_to_s(ndigits) }
try_use_digits { use_digits(ndigits) }
try_estimate { first_fibonacci_with_n_digits(ndigits) }
end
end
test 20
ndigits = 20, nfibs=93, last_fib=12200160415121876738
Running each test 128 times. Test will take about 1 second.
try_estimate is faster than try_use_to_s by 2x ± 0.1
try_use_to_s is faster than try_use_digits by 80.0% ± 10.0%
test 100
ndigits = 100, nfibs=476, last_fib=13447...37757 (90 digits omitted)
Running each test 16 times. Test will take about 4 seconds.
try_estimate is faster than try_use_to_s by 5x ± 0.1
try_use_to_s is faster than try_use_digits by 10x ± 1.0
test 500
ndigits = 500, nfibs=2390, last_fib=13519...63145 (490 digits omitted)
Running each test 2 times. Test will take about 27 seconds.
try_estimate is faster than try_use_to_s by 9x ± 0.1
try_use_to_s is faster than try_use_digits by 60x ± 1.0
test 1000
ndigits = 1000, nfibs=4782, last_fib=10700...27816 (990 digits omitted)
Running each test once. Test will take about 1 minute.
try_estimate is faster than try_use_to_s by 12x ± 10.0
try_use_to_s is faster than try_use_digits by 120x ± 100.0
There are two main take-aways from these results:
"try_estimate" is the fastest because it performs the first step relatively few times; and
the use of to_s is much faster than that of digits.
Further to the first of these observations note that the initial estimates of the index of the first FN having a given number of digits, compared to the actual index, are as follows:
for 20 digits: 96 est. vs 93 actual
for 100 digits: 479 est. vs 476 actual
for 500 digits: 2392 est. vs 2390 actual
for 1000 digits: 4785 est. vs 4782 actual
The deviation was at most 3, meaning numbers of digits had to be calculated for at most 3 FNs to obtain the desired result.
Explanation
The only explanation of the methods given in the section Code above is the derivation of the constant AVG_FNs_PER_DIGIT, which is used to calculate an estimate of the index of the first FN having the specified number of digits.
The derivation of this constant derives from the question and selected answer given here. (The Wiki for Fibonacci numbers provides a good overview of the mathematical properties of FNs.)
It is known that the first 7 FNs (including zero) have one digit; thereafter the FNs gain an additional digit every 4 or 5 FNs (i.e., sometimes 4, else 5). Therefore, as a very crude calculation, we see that to calculate the first FN with n digits, n >= 2, it will not be less than the 4*nth FN. For n = 1000, that would be 4,000. (In fact, the 4,782nd is the smallest to have 1,000 digits.) In other words, we don't need to calculate the number of digits in the first 4,000 FNs. We can improve on this estimate, however.
As n approaches infinity, the ratio of ranges 10**n...10**(n+1) (n-digit intervals) that contain 5 FNs to those that contain 4 FNs can be computed as follows.
LOG_10 = Math.log(10)
#=> 2.302585092994046
GR = (1 + Math.sqrt(5))/2
#=> 1.618033988749895
LOG_GR = Math.log(GR)
#=> 0.48121182505960347
RATIO_5to4 = (LOG_10 - 4*LOG_GR)/(5*LOG_GR - LOG_10)
#=> 3.6505564183095474
where GR is the Golden Ratio.
Over a large number of n-digit intervals let n4 be the number of those intervals containing 4 FNs and n5 be the number containing 5 FNs. The average number of FNs per interval is therefore (n4*4 + n5*5)/(n4 + n5). Since n5/n4 converges to RATIO_5to4, n5 approaches RATIO_5to4 * n4 in the limit (discarding roundoff error). If we substitute out n5, and let
b = 1/(1 + RATIO_5to4)
#=> 0.21502803321833364
we find the average number of FNs per n-digit interval converges to
avg = b * 4 + (1-b) *5
#=> 4.784971966781667
If fn is the first FN to have n decimal digits, the number of FNs in the sequence up to an including fn can therefore be approximated to be
n * avg
If, for example, the estimate of the index of the first FN to have 1000 decimal digits would be 1000 * 4.784971966781667).round #=> 4785.
Problem:-
input = n
output :-
1 2 3.......n [first row]
2n+1 2n+2 2n+3....3n [second row]
3n+1 3n+2 3n+3...4n [second last row]
n+1 n+2 n+3....2n [last row]
In the problem we have to print a square such that we have 'n' numbers of rows in our square and in every row we have 'n' numbers. We prepare rows from numbers from 1 to square(n) in such way we fill numbers for first row, then last row, second row, second last row and so on.....
for e.g. if n = 4
We start from 1 print upto 4 then print a newline, so our first row is:-
1 2 3 4
Then our last row comes in continuation
5 6 7 8
then our second row will be
9 10 11 12
few examples:
input = 1
output = 1
input = 2
output = 1 2
3 4
input = 3
output = 1 2 3
7 8 9
4 5 6
My Code:
n = int(input().strip())
lines = [i for i in range (1, n + 1)]
line_order1 = []
line_order2 = []
#Reordering lines so we know the staring element of our method
for i in lines:
if(i % 2 == 1):
line_order1.append(i)
else:
line_order2.append(i)
print(line_order1)
print(line_order2)
// Getting the desired order of lines
line_order2.reverse()
line_order1.extend(line_order2)
print(line_order1)
// Now printing the desired square
for l in line_order1:
for i in range (1, n+1):
k = n * (l - 1)
print(k + i, end = " ")
print("\n")
Is there a better way to do this in terms of execution time?
While I see a few minor places you can improve your code, the performance is unlikely to be much better (my suggestions below might not make any performance difference at all). Your code will take O(n**2) time, which is the best you can do, since you need to print out that many numbers to form your square. Even if you combine some of your longer, more verbose steps into more compact versions, they'll can only possibly be better by a constant factor.
My first suggestion is to number the lines from 0 to n-1 instead of from 1 to n. This will save you some effort when you have to calculate how what multiple of n to include in the values for the row. Currently you've got an awkward l - 1 in your calculation that you could skip if you just used zero-indexed numbers for the rows. (Also l is a terrible variable name, since it looks like the digit 1 (one) in some fonts.)
My next suggestion is to simplify your code that builds the order. You don't need three lists, you can do the whole thing with one list that you feed two range objects, each counting up or down by two.
line_order = list(range(0, n, 2)) # count up by twos
line_order.extend(range(n - 1 - n%2, 0, -2)) # count down starting at either n-1 or n-2
Or, if you're willing to use a standard library module, you could import itertools and then use:
line_order = itertools.chain(range(0, n, 2), range(n - 1 - n%2, 0, -2))
The itertools.chain function returns an iterator that yields values from each of its iterable arguments as if they were concatenated together, without making any copies of the data or using significant extra memory. The difference is not likely to be a much here (since the maximum n you can usefully print out is fairly small), but if you were doing something different with the result of this algorithm and n was in the billions it would be very nice to avoid filling a list with that many values.
My last suggestion is to use a range again to generate all the numbers in each row directly, rather than explicitly looping from 1 to n and adding k each time.
for row_num in line_order:
print(*range(n * row_num + 1, n * (rownum + 1) + 1))
You can compute the start and end points with the multiples of n already included, rather than needing to do that in a separate step for each one. You certainly didn't need to be recomputing k as often as you were before. You can pass all the values from the range to print in one go using iterable unpacking syntax (*args).
Note though that unpacking the range that way is sort of the reverse of the previous suggestion regarding itertools.chain. If n is large, using a loop over the range would be more memory efficient, since you won't need all n values to exist in memory at a the same time. Here's what that would look like:
for line_num in line_order:
for value in range(n * row_num + 1, n * (rownum + 1) + 1):
print(value, end=" ")
print()
I have a variable, between 0 and 1, which should dictate the likelyhood that a second variable, a random number between 0 and 1, is greater than 0.5. In other words, if I were to generate the second variable 1000 times, the average should be approximately equal to the first variable's value. How do I make this code?
Oh, and the second variable should always be capable of producing either 0 or 1 in any condition, just more or less likely depending on the value of the first variable. Here is a link to a graph which models approximately how I would like the program to behave. Each equation represents a separate value for the first variable.
You have a variable p and you are looking for a mapping function f(x) that maps random rolls between x in [0, 1] to the same interval [0, 1] such that the expected value, i.e. the average of all rolls, is p.
You have chosen the function prototype
f(x) = pow(x, c)
where c must be chosen appropriately. If x is uniformly distributed in [0, 1], the average value is:
int(f(x) dx, [0, 1]) == p
With the integral:
int(pow(x, c) dx) == pow(x, c + 1) / (c + 1) + K
one gets:
c = 1/p - 1
A different approach is to make p the median value of the distribution, such that half of the rolls fall below p, the other half above p. This yields a different distribution. (I am aware that you didn't ask for that.) Now, we have to satisfy the condition:
f(0.5) == pow(0.5, c) == p
which yields:
c = log(p) / log(0.5)
With the current function prototype, you cannot satisfy both requirements. Your function is also asymmetric (f(x, p) != f(1-x, 1-p)).
Python functions below:
def medianrand(p):
"""Random number between 0 and 1 whose median is p"""
c = math.log(p) / math.log(0.5)
return math.pow(random.random(), c)
def averagerand(p):
"""Random number between 0 and 1 whose expected value is p"""
c = 1/p - 1
return math.pow(random.random(), c)
You can do this by using a dummy. First set the first variable to a value between 0 and 1. Then create a random number in the dummy between 0 and 1. If this dummy is bigger than the first variable, you generate a random number between 0 and 0.5, and otherwise you generate a number between 0.5 and 1.
In pseudocode:
real a = 0.7
real total = 0.0
for i between 0 and 1000 begin
real dummy = rand(0,1)
real b
if dummy > a then
b = rand(0,0.5)
else
b = rand(0.5,1)
end if
total = total + b
end for
real avg = total / 1000
Please note that this algorithm will generate average values between 0.25 and 0.75. For a = 1 it will only generate random values between 0.5 and 1, which should average to 0.75. For a=0 it will generate only random numbers between 0 and 0.5, which should average to 0.25.
I've made a sort of pseudo-solution to this problem, which I think is acceptable.
Here is the algorithm I made;
a = 0.2 # variable one
b = 0 # variable two
b = random.random()
b = b^(1/(2^(4*a-1)))
It doesn't actually produce the average results that I wanted, but it's close enough for my purposes.
Edit: Here's a graph I made that consists of a large amount of datapoints I generated with a python script using this algorithm;
import random
mod = 6
div = 100
for z in xrange(div):
s = 0
for i in xrange (100000):
a = (z+1)/float(div) # variable one
b = random.random() # variable two
c = b**(1/(2**((mod*a*2)-mod)))
s += c
print str((z+1)/float(div)) + "\t" + str(round(s/100000.0, 3))
Each point in the table is the result of 100000 randomly generated points from the algorithm; their x positions being the a value given, and their y positions being their average. Ideally they would fit to a straight line of y = x, but as you can see they fit closer to an arctan equation. I'm trying to mess around with the algorithm so that the averages fit the line, but I haven't had much luck as of yet.
Regular numbers are numbers that evenly divide powers of 60. As an example, 602 = 3600 = 48 × 75, so both 48 and 75 are divisors of a power of 60. Thus, they are also regular numbers.
This is an extension of rounding up to the next power of two.
I have an integer value N which may contain large prime factors and I want to round it up to a number composed of only small prime factors (2, 3 and 5)
Examples:
f(18) == 18 == 21 * 32
f(19) == 20 == 22 * 51
f(257) == 270 == 21 * 33 * 51
What would be an efficient way to find the smallest number satisfying this requirement?
The values involved may be large, so I would like to avoid enumerating all regular numbers starting from 1 or maintaining an array of all possible values.
One can produce arbitrarily thin a slice of the Hamming sequence around the n-th member in time ~ n^(2/3) by direct enumeration of triples (i,j,k) such that N = 2^i * 3^j * 5^k.
The algorithm works from log2(N) = i+j*log2(3)+k*log2(5); enumerates all possible ks and for each, all possible js, finds the top i and thus the triple (k,j,i) and keeps it in a "band" if inside the given "width" below the given high logarithmic top value (when width < 1 there can be at most one such i) then sorts them by their logarithms.
WP says that n ~ (log N)^3, i.e. run time ~ (log N)^2. Here we don't care for the exact position of the found triple in the sequence, so all the count calculations from the original code can be thrown away:
slice hi w = sortBy (compare `on` fst) b where -- hi>log2(N) is a top value
lb5=logBase 2 5 ; lb3=logBase 2 3 -- w<1 (NB!) is log2(width)
b = concat -- the slice
[ [ (r,(i,j,k)) | frac < w ] -- store it, if inside width
| k <- [ 0 .. floor ( hi /lb5) ], let p = fromIntegral k*lb5,
j <- [ 0 .. floor ((hi-p)/lb3) ], let q = fromIntegral j*lb3 + p,
let (i,frac)=properFraction(hi-q) ; r = hi - frac ] -- r = i + q
-- properFraction 12.7 == (12, 0.7)
-- update: in pseudocode:
def slice(hi, w):
lb5, lb3 = logBase(2, 5), logBase(2, 3) -- logs base 2 of 5 and 3
for k from 0 step 1 to floor(hi/lb5) inclusive:
p = k*lb5
for j from 0 step 1 to floor((hi-p)/lb3) inclusive:
q = j*lb3 + p
i = floor(hi-q)
frac = hi-q-i -- frac < 1 , always
r = hi - frac -- r == i + q
if frac < w:
place (r,(i,j,k)) into the output array
sort the output array's entries by their "r" component
in ascending order, and return thus sorted array
Having enumerated the triples in the slice, it is a simple matter of sorting and searching, taking practically O(1) time (for arbitrarily thin a slice) to find the first triple above N. Well, actually, for constant width (logarithmic), the amount of numbers in the slice (members of the "upper crust" in the (i,j,k)-space below the log(N) plane) is again m ~ n^2/3 ~ (log N)^2 and sorting takes m log m time (so that searching, even linear, takes ~ m run time then). But the width can be made smaller for bigger Ns, following some empirical observations; and constant factors for the enumeration of triples are much higher than for the subsequent sorting anyway.
Even with constant width (logarthmic) it runs very fast, calculating the 1,000,000-th value in the Hamming sequence instantly and the billionth in 0.05s.
The original idea of "top band of triples" is due to Louis Klauder, as cited in my post on a DDJ blogs discussion back in 2008.
update: as noted by GordonBGood in the comments, there's no need for the whole band but rather just about one or two values above and below the target. The algorithm is easily amended to that effect. The input should also be tested for being a Hamming number itself before proceeding with the algorithm, to avoid round-off issues with double precision. There are no round-off issues comparing the logarithms of the Hamming numbers known in advance to be different (though going up to a trillionth entry in the sequence uses about 14 significant digits in logarithm values, leaving only 1-2 digits to spare, so the situation may in fact be turning iffy there; but for 1-billionth we only need 11 significant digits).
update2: turns out the Double precision for logarithms limits this to numbers below about 20,000 to 40,000 decimal digits (i.e. 10 trillionth to 100 trillionth Hamming number). If there's a real need for this for such big numbers, the algorithm can be switched back to working with the Integer values themselves instead of their logarithms, which will be slower.
Okay, hopefully third time's a charm here. A recursive, branching algorithm for an initial input of p, where N is the number being 'built' within each thread. NB 3a-c here are launched as separate threads or otherwise done (quasi-)asynchronously.
Calculate the next-largest power of 2 after p, call this R. N = p.
Is N > R? Quit this thread. Is p composed of only small prime factors? You're done. Otherwise, go to step 3.
After any of 3a-c, go to step 4.
a) Round p up to the nearest multiple of 2. This number can be expressed as m * 2.
b) Round p up to the nearest multiple of 3. This number can be expressed as m * 3.
c) Round p up to the nearest multiple of 5. This number can be expressed as m * 5.
Go to step 2, with p = m.
I've omitted the bookkeeping to do regarding keeping track of N but that's fairly straightforward I take it.
Edit: Forgot 6, thanks ypercube.
Edit 2: Had this up to 30, (5, 6, 10, 15, 30) realized that was unnecessary, took that out.
Edit 3: (The last one I promise!) Added the power-of-30 check, which helps prevent this algorithm from eating up all your RAM.
Edit 4: Changed power-of-30 to power-of-2, per finnw's observation.
Here's a solution in Python, based on Will Ness answer but taking some shortcuts and using pure integer math to avoid running into log space numerical accuracy errors:
import math
def next_regular(target):
"""
Find the next regular number greater than or equal to target.
"""
# Check if it's already a power of 2 (or a non-integer)
try:
if not (target & (target-1)):
return target
except TypeError:
# Convert floats/decimals for further processing
target = int(math.ceil(target))
if target <= 6:
return target
match = float('inf') # Anything found will be smaller
p5 = 1
while p5 < target:
p35 = p5
while p35 < target:
# Ceiling integer division, avoiding conversion to float
# (quotient = ceil(target / p35))
# From https://stackoverflow.com/a/17511341/125507
quotient = -(-target // p35)
# Quickly find next power of 2 >= quotient
# See https://stackoverflow.com/a/19164783/125507
try:
p2 = 2**((quotient - 1).bit_length())
except AttributeError:
# Fallback for Python <2.7
p2 = 2**(len(bin(quotient - 1)) - 2)
N = p2 * p35
if N == target:
return N
elif N < match:
match = N
p35 *= 3
if p35 == target:
return p35
if p35 < match:
match = p35
p5 *= 5
if p5 == target:
return p5
if p5 < match:
match = p5
return match
In English: iterate through every combination of 5s and 3s, quickly finding the next power of 2 >= target for each pair and keeping the smallest result. (It's a waste of time to iterate through every possible multiple of 2 if only one of them can be correct). It also returns early if it ever finds that the target is already a regular number, though this is not strictly necessary.
I've tested it pretty thoroughly, testing every integer from 0 to 51200000 and comparing to the list on OEIS http://oeis.org/A051037, as well as many large numbers that are ±1 from regular numbers, etc. It's now available in SciPy as fftpack.helper.next_fast_len, to find optimal sizes for FFTs (source code).
I'm not sure if the log method is faster because I couldn't get it to work reliably enough to test it. I think it has a similar number of operations, though? I'm not sure, but this is reasonably fast. Takes <3 seconds (or 0.7 second with gmpy) to calculate that 2142 × 380 × 5444 is the next regular number above 22 × 3454 × 5249+1 (the 100,000,000th regular number, which has 392 digits)
You want to find the smallest number m that is m >= N and m = 2^i * 3^j * 5^k where all i,j,k >= 0.
Taking logarithms the equations can be rewritten as:
log m >= log N
log m = i*log2 + j*log3 + k*log5
You can calculate log2, log3, log5 and logN to (enough high, depending on the size of N) accuracy. Then this problem looks like a Integer Linear programming problem and you could try to solve it using one of the known algorithms for this NP-hard problem.
EDITED/CORRECTED: Corrected the codes to pass the scipy tests:
Here's an answer based on endolith's answer, but almost eliminating long multi-precision integer calculations by using float64 logarithm representations to do a base comparison to find triple values that pass the criteria, only resorting to full precision comparisons when there is a chance that the logarithm value may not be accurate enough, which only occurs when the target is very close to either the previous or the next regular number:
import math
def next_regulary(target):
"""
Find the next regular number greater than or equal to target.
"""
if target < 2: return ( 0, 0, 0 )
log2hi = 0
mant = 0
# Check if it's already a power of 2 (or a non-integer)
try:
mant = target & (target - 1)
target = int(target) # take care of case where not int/float/decimal
except TypeError:
# Convert floats/decimals for further processing
target = int(math.ceil(target))
mant = target & (target - 1)
# Quickly find next power of 2 >= target
# See https://stackoverflow.com/a/19164783/125507
try:
log2hi = target.bit_length()
except AttributeError:
# Fallback for Python <2.7
log2hi = len(bin(target)) - 2
# exit if this is a power of two already...
if not mant: return ( log2hi - 1, 0, 0 )
# take care of trivial cases...
if target < 9:
if target < 4: return ( 0, 1, 0 )
elif target < 6: return ( 0, 0, 1 )
elif target < 7: return ( 1, 1, 0 )
else: return ( 3, 0, 0 )
# find log of target, which may exceed the float64 limit...
if log2hi < 53: mant = target << (53 - log2hi)
else: mant = target >> (log2hi - 53)
log2target = log2hi + math.log2(float(mant) / (1 << 53))
# log2 constants
log2of2 = 1.0; log2of3 = math.log2(3); log2of5 = math.log2(5)
# calculate range of log2 values close to target;
# desired number has a logarithm of log2target <= x <= top...
fctr = 6 * log2of3 * log2of5
top = (log2target**3 + 2 * fctr)**(1/3) # for up to 2 numbers higher
btm = 2 * log2target - top # or up to 2 numbers lower
match = log2hi # Anything found will be smaller
result = ( log2hi, 0, 0 ) # placeholder for eventual matches
count = 0 # only used for debugging counting band
fives = 0; fiveslmt = int(math.ceil(top / log2of5))
while fives < fiveslmt:
log2p = top - fives * log2of5
threes = 0; threeslmt = int(math.ceil(log2p / log2of3))
while threes < threeslmt:
log2q = log2p - threes * log2of3
twos = int(math.floor(log2q)); log2this = top - log2q + twos
if log2this >= btm: count += 1 # only used for counting band
if log2this >= btm and log2this < match:
# logarithm precision may not be enough to differential between
# the next lower regular number and the target, so do
# a full resolution comparison to eliminate this case...
if (2**twos * 3**threes * 5**fives) >= target:
match = log2this; result = ( twos, threes, fives )
threes += 1
fives += 1
return result
print(next_regular(2**2 * 3**454 * 5**249 + 1)) # prints (142, 80, 444)
Since most long multi-precision calculations have been eliminated, gmpy isn't needed, and on IDEOne the above code takes 0.11 seconds instead of 0.48 seconds for endolith's solution to find the next regular number greater than the 100 millionth one as shown; it takes 0.49 seconds instead of 5.48 seconds to find the next regular number past the billionth (next one is (761,572,489) past (1334,335,404) + 1), and the difference will get even larger as the range goes up as the multi-precision calculations get increasingly longer for the endolith version compared to almost none here. Thus, this version could calculate the next regular number from the trillionth in the sequence in about 50 seconds on IDEOne, where it would likely take over an hour with the endolith version.
The English description of the algorithm is almost the same as for the endolith version, differing as follows:
1) calculates the float log estimation of the argument target value (we can't use the built-in log function directly as the range may be much too large for representation as a 64-bit float),
2) compares the log representation values in determining qualifying values inside an estimated range above and below the target value of only about two or three numbers (depending on round-off),
3) compare multi-precision values only if within the above defined narrow band,
4) outputs the triple indices rather than the full long multi-precision integer (would be about 840 decimal digits for the one past the billionth, ten times that for the trillionth), which can then easily be converted to the long multi-precision value if required.
This algorithm uses almost no memory other than for the potentially very large multi-precision integer target value, the intermediate evaluation comparison values of about the same size, and the output expansion of the triples if required. This algorithm is an improvement over the endolith version in that it successfully uses the logarithm values for most comparisons in spite of their lack of precision, and that it narrows the band of compared numbers to just a few.
This algorithm will work for argument ranges somewhat above ten trillion (a few minute's calculation time at IDEOne rates) when it will no longer be correct due to lack of precision in the log representation values as per #WillNess's discussion; in order to fix this, we can change the log representation to a "roll-your-own" logarithm representation consisting of a fixed-length integer (124 bits for about double the exponent range, good for targets of over a hundred thousand digits if one is willing to wait); this will be a little slower due to the smallish multi-precision integer operations being slower than float64 operations, but not that much slower since the size is limited (maybe a factor of three or so slower).
Now none of these Python implementations (without using C or Cython or PyPy or something) are particularly fast, as they are about a hundred times slower than as implemented in a compiled language. For reference sake, here is a Haskell version:
{-# OPTIONS_GHC -O3 #-}
import Data.Word
import Data.Bits
nextRegular :: Integer -> ( Word32, Word32, Word32 )
nextRegular target
| target < 2 = ( 0, 0, 0 )
| target .&. (target - 1) == 0 = ( fromIntegral lg2hi - 1, 0, 0 )
| target < 9 = case target of
3 -> ( 0, 1, 0 )
5 -> ( 0, 0, 1 )
6 -> ( 1, 1, 0 )
_ -> ( 3, 0, 0 )
| otherwise = match
where
lg3 = logBase 2 3 :: Double; lg5 = logBase 2 5 :: Double
lg2hi = let cntplcs v cnt =
let nv = v `shiftR` 31 in
if nv <= 0 then
let cntbts x c =
if x <= 0 then c else
case c + 1 of
nc -> nc `seq` cntbts (x `shiftR` 1) nc in
cntbts (fromIntegral v :: Word32) cnt
else case cnt + 31 of ncnt -> ncnt `seq` cntplcs nv ncnt
in cntplcs target 0
lg2tgt = let mant = if lg2hi <= 53 then target `shiftL` (53 - lg2hi)
else target `shiftR` (lg2hi - 53)
in fromIntegral lg2hi +
logBase 2 (fromIntegral mant / 2^53 :: Double)
lg2top = (lg2tgt^3 + 2 * 6 * lg3 * lg5)**(1/3) -- for 2 numbers or so higher
lg2btm = 2* lg2tgt - lg2top -- or two numbers or so lower
match =
let klmt = floor (lg2top / lg5)
loopk k mtchlgk mtchtplk =
if k > klmt then mtchtplk else
let p = lg2top - fromIntegral k * lg5
jlmt = fromIntegral $ floor (p / lg3)
loopj j mtchlgj mtchtplj =
if j > jlmt then loopk (k + 1) mtchlgj mtchtplj else
let q = p - fromIntegral j * lg3
( i, frac ) = properFraction q; r = lg2top - frac
( nmtchlg, nmtchtpl ) =
if r < lg2btm || r >= mtchlgj then
( mtchlgj, mtchtplj ) else
if 2^i * 3^j * 5^k >= target then
( r, ( i, j, k ) ) else ( mtchlgj, mtchtplj )
in nmtchlg `seq` nmtchtpl `seq` loopj (j + 1) nmtchlg nmtchtpl
in loopj 0 mtchlgk mtchtplk
in loopk 0 (fromIntegral lg2hi) ( fromIntegral lg2hi, 0, 0 )
trival :: ( Word32, Word32, Word32 ) -> Integer
trival (i,j,k) = 2^i * 3^j * 5^k
main = putStrLn $ show $ nextRegular $ (trival (1334,335,404)) + 1 -- (1126,16930,40)
This code calculates the next regular number following the billionth in too small a time to be measured and following the trillionth in 0.69 seconds on IDEOne (and potentially could run even faster except that IDEOne doesn't support LLVM). Even Julia will run at something like this Haskell speed after the "warm-up" for JIT compilation.
EDIT_ADD: The Julia code is as per the following:
function nextregular(target :: BigInt) :: Tuple{ UInt32, UInt32, UInt32 }
# trivial case of first value or anything less...
target < 2 && return ( 0, 0, 0 )
# Check if it's already a power of 2 (or a non-integer)
mant = target & (target - 1)
# Quickly find next power of 2 >= target
log2hi :: UInt32 = 0
test = target
while true
next = test & 0x7FFFFFFF
test >>>= 31; log2hi += 31
test <= 0 && (log2hi -= leading_zeros(UInt32(next)) - 1; break)
end
# exit if this is a power of two already...
mant == 0 && return ( log2hi - 1, 0, 0 )
# take care of trivial cases...
if target < 9
target < 4 && return ( 0, 1, 0 )
target < 6 && return ( 0, 0, 1 )
target < 7 && return ( 1, 1, 0 )
return ( 3, 0, 0 )
end
# find log of target, which may exceed the Float64 limit...
if log2hi < 53 mant = target << (53 - log2hi)
else mant = target >>> (log2hi - 53) end
log2target = log2hi + log(2, Float64(mant) / (1 << 53))
# log2 constants
log2of2 = 1.0; log2of3 = log(2, 3); log2of5 = log(2, 5)
# calculate range of log2 values close to target;
# desired number has a logarithm of log2target <= x <= top...
fctr = 6 * log2of3 * log2of5
top = (log2target^3 + 2 * fctr)^(1/3) # for 2 numbers or so higher
btm = 2 * log2target - top # or 2 numbers or so lower
# scan for values in the given narrow range that satisfy the criteria...
match = log2hi # Anything found will be smaller
result :: Tuple{UInt32,UInt32,UInt32} = ( log2hi, 0, 0 ) # placeholder for eventual matches
fives :: UInt32 = 0; fiveslmt = UInt32(ceil(top / log2of5))
while fives < fiveslmt
log2p = top - fives * log2of5
threes :: UInt32 = 0; threeslmt = UInt32(ceil(log2p / log2of3))
while threes < threeslmt
log2q = log2p - threes * log2of3
twos = UInt32(floor(log2q)); log2this = top - log2q + twos
if log2this >= btm && log2this < match
# logarithm precision may not be enough to differential between
# the next lower regular number and the target, so do
# a full resolution comparison to eliminate this case...
if (big(2)^twos * big(3)^threes * big(5)^fives) >= target
match = log2this; result = ( twos, threes, fives )
end
end
threes += 1
end
fives += 1
end
result
end
Here's another possibility I just thought of:
If N is X bits long, then the smallest regular number R ≥ N will be in the range
[2X-1, 2X]
e.g. if N = 257 (binary 100000001) then we know R is 1xxxxxxxx unless R is exactly equal to the next power of 2 (512)
To generate all the regular numbers in this range, we can generate the odd regular numbers (i.e. multiples of powers of 3 and 5) first, then take each value and multiply by 2 (by bit-shifting) as many times as necessary to bring it into this range.
In Python:
from itertools import ifilter, takewhile
from Queue import PriorityQueue
def nextPowerOf2(n):
p = max(1, n)
while p != (p & -p):
p += p & -p
return p
# Generate multiples of powers of 3, 5
def oddRegulars():
q = PriorityQueue()
q.put(1)
prev = None
while not q.empty():
n = q.get()
if n != prev:
prev = n
yield n
if n % 3 == 0:
q.put(n // 3 * 5)
q.put(n * 3)
# Generate regular numbers with the same number of bits as n
def regularsCloseTo(n):
p = nextPowerOf2(n)
numBits = len(bin(n))
for i in takewhile(lambda x: x <= p, oddRegulars()):
yield i << max(0, numBits - len(bin(i)))
def nextRegular(n):
bigEnough = ifilter(lambda x: x >= n, regularsCloseTo(n))
return min(bigEnough)
You know what? I'll put money on the proposition that actually, the 'dumb' algorithm is fastest. This is based on the observation that the next regular number does not, in general, seem to be much larger than the given input. So simply start counting up, and after each increment, refactor and see if you've found a regular number. But create one processing thread for each available core you have, and for N cores have each thread examine every Nth number. When each thread has found a number or crossed the power-of-2 threshold, compare the results (keep a running best number) and there you are.
I wrote a small c# program to solve this problem. It's not very optimised but it's a start.
This solution is pretty fast for numbers as big as 11 digits.
private long GetRegularNumber(long n)
{
long result = n - 1;
long quotient = result;
while (quotient > 1)
{
result++;
quotient = result;
quotient = RemoveFactor(quotient, 2);
quotient = RemoveFactor(quotient, 3);
quotient = RemoveFactor(quotient, 5);
}
return result;
}
private static long RemoveFactor(long dividend, long divisor)
{
long remainder = 0;
long quotient = dividend;
while (remainder == 0)
{
dividend = quotient;
quotient = Math.DivRem(dividend, divisor, out remainder);
}
return dividend;
}