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The Crunchomics’ Documentation

Crunchomics: The Genomics Compute Environment for SILS and IBED

Cruchomics has 1 application server, a web server, a head node and 5 compute nodes. A storage system is mounted in which all users have a fast 25 GB SSD home directory and a 500 GB home directory. Volumes from the faculty server can be mounted on the system.

  • CPU: AMD EPYC Rome 7302 32 cores, 64 threads, 3GHz
  • Compute cluster: 160 cores, 320 threads
  • Infiniband internal connection
  • Local storage compute cluster: 8TB (SSD/NVMe): /scratch
    • /scratch is emptied after month of inactivity
  • Memory:
    • Web server: 256 GB
    • Application server: 1024 GB
    • Head node and compute nodes: 512 GB
  • Storage: gross 504 TB operated in RAID-Z2: net approx. 220 TB.
    • If one disk fails: no data loss
    • Snapshots taken: some protection against unintentional file deletions
    • No backups made!
  • File systems are mounted on all nodes.
  • OS: CentOS 7
  • Help: w.c.deleeuw@uva.nl / j.rauwerda@uva.nl

self intro_crunchomics.rst miniconda.rst slurm_overview.rst slurm_jobs.rst slurm_indirect.rst nvme_clusters.rst containers.rst

Indices and tables

  • genindex
  • search