Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Where is Casava's Demux Multithreaded?

    I am trying to get CASAVA setup on my fancy computer but I am having trouble verifying that the code is muddleheaded. Specifically my test files run, but I cannot see the threading for my single lane example. See http://www.biostars.org/post/show/46...hreaded/#46477

    On my 32 core machine I see 3% cpu utilization (1/32 threads).

    I have been exploring the source with artistically placed "grep" commands and I cannot find where the threading occurs.

    1. Is this step parallel?

    2. Where is the CPP associated with the process called "demultiplexBcls"

  • #2
    Most of the time, you will launch CASAVA commands using 'make -j <number of processes>.

    So yes CASAVA is parallel in the Makefile layer.

    I don't know if it uses OpenMP or pthread.

    Sébastien


    Originally posted by lednakashim View Post
    I am trying to get CASAVA setup on my fancy computer but I am having trouble verifying that the code is muddleheaded. Specifically my test files run, but I cannot see the threading for my single lane example. See http://www.biostars.org/post/show/46...hreaded/#46477

    On my 32 core machine I see 3% cpu utilization (1/32 threads).

    I have been exploring the source with artistically placed "grep" commands and I cannot find where the threading occurs.

    1. Is this step parallel?

    2. Where is the CPP associated with the process called "demultiplexBcls"

    Comment


    • #3
      Thanks!

      I came to the conclusion that the BCL to Fastq was Parallel in the makefile, although other steps are parallel with pthreads in addition to the make file.

      This approach is not necessarily optimal, in my case the CPU is grossly underutilized, and I am considering making some source changes to correct it.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Essential Discoveries and Tools in Epitranscriptomics
        by seqadmin




        The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
        04-22-2024, 07:01 AM
      • seqadmin
        Current Approaches to Protein Sequencing
        by seqadmin


        Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
        04-04-2024, 04:25 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 04-30-2024, 12:17 PM
      0 responses
      13 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-29-2024, 10:49 AM
      0 responses
      19 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-25-2024, 11:49 AM
      0 responses
      24 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-24-2024, 08:47 AM
      0 responses
      23 views
      0 likes
      Last Post seqadmin  
      Working...
      X