in reply to Re^6: Storing large data structures on disk
in thread Storing large data structures on disk

when the ds becomes too large to store it all in memory, is tying with MLDBM the preferred paradigm? What are the alternatives?

It really depends upon what is in the data structure and how you are using it. Some of the questions that might influence the best choice are:

The best solution may depend upon the answers to some or all of these questions, and more that arise from those answers. A clear description of the data set and how it is used would be the quickest way of eliciting good answers.

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.
RIP an inspiration; A true Folk's Guy
  • Comment on Re^7: Storing large data structures on disk

Replies are listed 'Best First'.
Re^8: Storing large data structures on disk
by roibrodo (Sexton) on Jun 01, 2010 at 06:54 UTC

    Here is a shot description of my application and its intended use

    .

    The data structure holds results of some biological experiments. The main array of the AoA represent a genome, each subarray holds the results for a specific location in the genome ("nucleotide"), hence the size of the main array might be very large (up to ~10^10 "nucleotides").

    Each such subarray holds a list of measurements referring to this nucleotide. The results themselves are stored in a separate array @res (as some objects) and what I keep in the each subarray of my AoA are the indices to those result in other array @res. This is because many nucleotides may point to the same results (they are highly depended). This way, when I want to get the results for some nucleotide, I go to its location in the AoA and follow the list of indices specified there to pull the objects out of @res.

    This is not supposed to work as a web app. The normal usage will be to focus on some specific region (a range of nucleotides) than pull out there results and do something with it (this "something" can be many things). So, yes, the data will usually be taken out of the large AoA in arbitrary chunks. The size of the chunks may vary but will usually be less than 5% of the entire dataset. The dataset is written once and can then become read-only.

[reply]

      How big is @res?

[reply]

        @res is in the order of 10^5-10^6. Each result "object" is just a small hash with just a few fields in it.

        Now that I think about it again, I might want to add an extra level to my AoA - each nucleotide could have multiple (10^3) different list of experiments, not only one set. The reason is we also simulate "random experimental results" so we will actually have multiple @res arrays.

[reply]
      The data structure holds results of some biological experiments.

      Might Perl and Bioinformatics be of interest to you?

      HTH,

      planetscape
[reply]

        Is the planetscape userid a bot? Cos matching on "bio" isn't useful.

[reply]

In Section Seekers of Perl Wisdom