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cmuratori's profile
Casey Muratori
Casey Muratori
Casey Muratori
@cmuratori

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Casey Muratori

@cmuratori

I'm worried that the baby thinks people can't change.

Seattle
caseymuratori.com
Joined March 2009

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    1. Tássio‏ @umtassio Oct 27

      I would love to learn to read very large files at a decent speed (ex: genomic files, in the tens of gbs, where I'm looking for "close" matches to some gene sequence). What things like memory alignment, threads, parallelism, mmap, SIMD, or other things be used to help? @cmuratori

      3 replies 0 retweets 0 likes
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    2. Casey Muratori‏ @cmuratori Oct 27
      Replying to @umtassio

      Threads, overlapped IO, and SIMD would all help. mmap, probably not, since you would not be randomly accessing the data, although you could try it. I would start with io_uring, queue block reads of 256k or something like that, fast check each block with 32-wide AVX2 compares.

      1 reply 0 retweets 11 likes
      Casey Muratori‏ @cmuratori Oct 27
      Replying to @cmuratori @umtassio

      Since you know the size of the file ahead of time, you should be able to partition the file into n chunks where n is the number of cores in the machine, so each core can process a completely independent section of the file, so you have no cross-thread communication.

      2:16 PM - 27 Oct 2021
      • 6 Likes
      • Vivitsu Maharaja Paolo Meroni Dzhaid Nizam José Eduardo Ramírez sagt mir wie ich heißen soll Tássio
      2 replies 0 retweets 6 likes
        1. Tássio‏ @umtassio Oct 27
          Replying to @cmuratori

          Thank for answering! I am going to look all these up. Let me take the chance to thank you for your inspiring work! I look forward to Star Code Galaxy.

          0 replies 0 retweets 2 likes
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        2. s‏ @idoccor Oct 27
          Replying to @cmuratori @umtassio

          Compress the file with LZ4 HC (or use btrfs + compression) and use iotop to figure out how close you're getting to the available disk bandwidth. There's no point optimizing past what a fast NVME drive can do unless you're planning on RAID'ing them or something.

          1 reply 0 retweets 1 like
        3. s‏ @idoccor Oct 27
          Replying to @idoccor @cmuratori @umtassio

          And if you do multithreaded or multiprocess access, it will often look like random reads to the disk scheduler and drive firmware. For most NVME drives, the random IO is about 1/3rd as fast as sequential. But that might be fine if you're more CPU-bound.

          0 replies 0 retweets 0 likes
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