[Beowulf] Generation of strings MPI fashion..
tjrc at sanger.ac.uk
Sun Oct 9 21:56:21 PDT 2016
Sent from my iPhone
> On 9 Oct 2016, at 11:05 pm, John Hearns <John.Hearns at xma.co.uk> wrote:
> This sounds interesting.
> I would question this step though, as it seems intrinically a bottlneck:
>> Removes duplicate lines:
>> $ sort filename.txt | uniq
> First off - do you need a sorted list? If not do not perform the sort...
> Secondly - how efficient is the Unix 'uniq' utility?
The command could be collapsed to
Gnu sort is quite efficient I think.
> How about, every time you generate a string, check if it has already been generated. I guess this then starts to depend on the efficiency of searching through a file.
Assuming you're using a binary tree to store those, you're effectively sorting the list anyway. Probably with O(N log N) execution time.
> Thinking about this problem, would it be better to allocate each MPI rank a unique set of string to generate?
> Say there are N characters in the set A-Z a-z 0-9 plus symbols . This is likely to be 255 as I'm assuming you are talking the ASCII character set.
> So then if you have 256 MPI ranks then allocate rank 1 to generate all strings commencing with 'A' then rank 2 'B' etc.
> If you are lucky enough to have 256x256 cores to allocate then it goes 'AA' 'AB' 'AC' etc. etc.
That's no longer random though is it? You're absolutely fixing the frequency of the first letter. The more you do that, the less random your strings will become.
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