Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Server hardware - when are too many cores too much

    Hello!

    our dept. wants to buy a new server for our computational biology needs. We work in the field of metagenomics, so our biggest workloads usually include assembly of large metagenomes (spades, megahit), phylogenetic tree reconstruction (raxml, iqtree) and short read mapping/processing (bbmap, bowtie2, samtools, blast).

    I've discussed some specs with our IT department and they came up some preliminary specs (4 x 16-core xeon CPUs, 3 TB RAM, large SSD scratch disks). Here, we discussed the possibility of increasing the number of cores (e.g. 4 x 24-core CPUs) since many of our programs would benefit from an increase in core count given the available RAM. In other words - our assemblies rarely use more than 500 GB of RAM, which would theoretically allow to run 6 assemblies in parallel. This would mean that each assembly gets "only" ~ 11 cores / 22 threads. We would like to bump this but our IT department mentioned that the cores might be memory bandwidth starved if we increase the cores per CPU. So, what is your opinion/experience regarding this? When is too many cores per CPU too much for the programs we use?

    Main specs:

    CPU: 4 x Xeon Gold 5218, 2.30 GHz, 16-Core; alternative 4 x Xeon Platinum 8268, 2.90 GHz, 24-Core

    RAM: 3072GB (48x 64GB) DDR4 PC2933

  • #2
    Listen to your IT recommendations. It is one thing to have cores but if you don't have storage infrastructure to support the I/O needs then that will always be the bottleneck. When you run these assemblies you would not notice the 20min more it may take to complete a job especially if it is running overnight.

    Highest core count xeons are hideously expensive and you can save a good bit of money by dropping that core count to second/third best.

    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
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    51 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X