Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Trinity error around number of CPU's and Java virtual machine

    Hi,

    I have been sending trinity jobs to a cluster under differing conditions. If I request 1 node with one or two processes (CPU's) and 2GB of memory for each process/CPU, the program runs without a hitch.

    However, If I request four processes/CPU's from a single node or from two nodes, the program fails with the following error message:

    initialization of VM
    Error occurred during initialization of VM
    Could not reserve enough space for object heapCould not reserve enough space for object heap

    Could not create the Java virtual machine.
    Could not create the Java virtual machine.

    In all runs, I match the --JM flag and --CPU flag in Trinity with the number of processes and the amount of memory requested from the cluster.

    Each node in the cluster has 8 CPU's and a total of 16GB of memory, so I am by no means overburdening the system. The cluster support team tested this by running Trinity input with a total of 24G of memory and got the same answer.

    Has anyone else had trouble with executing Trinity over more than two CPUs?

  • #2
    Originally posted by gwilymh View Post

    Has anyone else had trouble with executing Trinity over more than two CPUs?
    No. People run Trinity with more than two CPUs all of the time.

    Since you have your cluster support people working with you they would be the best people to troubleshoot your problem since I suspect a cluster setup problem. My first suspicion -- and this is true anytime someone says they are having problems using more the 4GB -- is to look for a 32-bit dependency somewhere. Specifically what version of Java are you using?

    BTW: '-JM' only applies to Jellyfish memory and has nothing to do with Java. Look at the '--bfly*' options for some Java parameters.

    Comment


    • #3
      8 cores and 16G RAM is not a lot, specially if there are other jobs running on that node. Are you using a queuing system to submit the jobs?

      Comment


      • #4
        Thank you all for the responses. Where can one find the documentation for the butterfly-specific (--bfly*) options? There does not seem to be any in the Trinity manual, webpage or --help instructions.

        Also, what exactly is Jellyfish? Is it a specialized program for counting k-mers in Trinity? Or is it used outside of Trinity? Does --JM refer to the overall memory allocation, or to the memory allocation per thread?

        Comment


        • #5
          Originally posted by gwilymh View Post
          Also, what exactly is Jellyfish? Is it a specialized program for counting k-mers in Trinity? Or is it used outside of Trinity? Does --JM refer to the overall memory allocation, or to the memory allocation per thread?
          Nature protocols article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875132/

          Stages within Trinity (http://trinityrnaseq.sourceforge.net...ity_guide.html)

          Stage 1: generate the kmer-catalog using jellyfish
          Stage 2: run Inchworm to generate draft contigs
          Stage 2: Chrysalis clustering of inchworm contigs and mapping reads
          Stage 3: Chrysalis deBruijn graph construction
          Stage 4: Run butterfly, generate final Trinity.fasta file

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Exploring the Dynamics of the Tumor Microenvironment
            by seqadmin




            The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
            07-08-2024, 03:19 PM
          • seqadmin
            Exploring Human Diversity Through Large-Scale Omics
            by seqadmin


            In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
            06-25-2024, 06:43 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 07-10-2024, 07:30 AM
          0 responses
          20 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 07-03-2024, 09:45 AM
          0 responses
          197 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 07-03-2024, 08:54 AM
          0 responses
          207 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 07-02-2024, 03:00 PM
          0 responses
          191 views
          0 likes
          Last Post seqadmin  
          Working...
          X