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  • genometools parallel

    Hi, I am using genometools and find it quite slow with an 1G fasta file.
    When running:
    $ gt suffixerator ...
    It simply used one cpu and was quite slow. Then I tried:
    $ gt -j 4 suffixerator ...
    But nothing changed.
    So I'm really confused whether gt could use parallel processors to accelerate working, just like RepeatMasker (who has -pa to set number of parallel processors)?

  • #2
    Originally posted by hugh_hang View Post
    Hi, I am using genometools and find it quite slow with an 1G fasta file.
    When running:
    $ gt suffixerator ...
    It simply used one cpu and was quite slow. Then I tried:
    $ gt -j 4 suffixerator ...
    But nothing changed.
    So I'm really confused whether gt could use parallel processors to accelerate working, just like RepeatMasker (who has -pa to set number of parallel processors)?
    I'm curious how you decided to use the "-j" option for gt suffixerator because I have never seen that and it does not appear to be documented. Depending on what task you are trying accomplish, there are ways of running jobs in parallel but I'm not aware of any genometools applications that will use multiple processors.

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    • #3
      Originally posted by SES View Post
      I'm curious how you decided to use the "-j" option for gt suffixerator because I have never seen that and it does not appear to be documented. Depending on what task you are trying accomplish, there are ways of running jobs in parallel but I'm not aware of any genometools applications that will use multiple processors.
      I saw '-j' in LTRdigest User’s Manual where write:
      To run the protein domain search in a parallel fashion, use the -j parameter to gt to specify the number of concurrent threads to use:
      gt -j 3 ltrdigest [options] GFF3 file indexname
      I thought '-j' is an option of 'gt' command that can be added into all gt tools. Maybe I was so naive for it can only added into the command of 'gt ltrdigest'.

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      • #4
        I don't know what genometools does, but maybe it would be possible to parallelize it with gnu parallel. Have a look here to get an idea how it works..
        savetherhino.org

        Comment


        • #5
          Originally posted by rhinoceros View Post
          I don't know what genometools does, but maybe it would be possible to parallelize it with gnu parallel. Have a look here to get an idea how it works..
          It is really awesome. I know what to do next, thanks!

          Comment


          • #6
            Originally posted by hugh_hang View Post
            I saw '-j' in LTRdigest User’s Manual where write:

            I thought '-j' is an option of 'gt' command that can be added into all gt tools. Maybe I was so naive for it can only added into the command of 'gt ltrdigest'.
            LTRdigest uses HMMER for the protein domain search, so I think that "-j" option applies specifically to that routine of the LTRdigest tool.

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            • #7
              Originally posted by SES View Post
              LTRdigest uses HMMER for the protein domain search, so I think that "-j" option applies specifically to that routine of the LTRdigest tool.
              Thanks, I suddenly realized.

              Comment


              • #8
                Currently LTRdigest is the only tool to use the parallelization option -j for now, but that might change in the future.

                Comment


                • #9
                  Originally posted by sst View Post
                  Currently LTRdigest is the only tool to use the parallelization option -j for now, but that might change in the future.
                  do you know if the change will occur in the newest version in 2014?

                  Comment


                  • #10
                    Originally posted by hugh_hang View Post
                    do you know if the change will occur in the newest version in 2014?
                    Currently there are no plans multithreading the existing tools -- what I am saying is that there might be new tools using that option if they use multithreading -- sorry if my comment was misleading

                    Comment

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