Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • newbler cpu core usage

    Hi, I'm trying to run newbler in ubuntu server (8 cores, 8G ram) and can make it use more than one core.

    I have mpich installed. And I've tried with:

    export GS_LAUNCH_MODE=MULTI
    export GS_CACHEDIR=/data

    and:

    export GS_LAUNCH_MODE=GSRPM
    export GS_CACHEDIR=/data

    I also tried run it using mpirun newbler project. It runs but only using one core...

    I set 4 cores in the assembly XML file. So frustrating because I can not find good documentation about this issue.



  • #2
    The environment variables you are playing with are for the gsRunProcesser, they have nothing to do with newbler (now officially called gsAssembler). Only the latest version of gsAssembler (2.3) is able to utilize multiple CPUs. While earlier versions of the assembler wrote a <numCPU> tag to the 454AssemblyProject.xml file, I suspect it was just anticipating future functionality. gsAssembler can use multiple cpus/cores on a single machine, not across a cluster so MPI is irrelevant.

    Comment


    • #3
      Thanks, now I see. I will get gsAssembler 2.3

      PS: They were anticipating the new functionallity too early...Documantation shows that cpu number parameter is working.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      7 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      7 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      66 views
      0 likes
      Last Post seqadmin  
      Working...
      X