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(warning) (warning) (warning) Read the Hydra-5 Migration Notes and Reset Your Password  (warning) (warning) (warning)

The Hydra cluster has been upgraded as follows:

  • Software
    • Upgrade OS to CentOS 7.6,
    • Change our management tool (from Rocks 6.x to Bright Cluster, aka BCM 8.2),
    • Switch from SGE to UGE (Univa) version 8.6.6, a commercially supported version of SGE (backward compatible).
  • Hardware
    • Added 16 new nodes (40c/380GB) for a total of 640 cores,
    • Decommissioned oldest nodes (old compute-6* and compute-4-*),
    • Add ed1.5PB of high performance storage (parallel file system GPFS, aka Spectrum Scale),
    • This is in addition to the 500TB of NetApp and the  950TB of near-line storage (NAS),
    • The /scratch disk has been moved to the GPFS and increase in size from 100TB to 900TB (450TB+450TB for /scratch/genomics and /scratch/sao)
    • Moved all the nodes to a 10Gb/s Ethernet connection (was 1Gb/s).


Please Note

  • While we made every effort to set up the new configuration as backward compatible as possible, there are changes.
  • Read the migration notes!
  • The upgrade will take place from August 26th through September 2nd, 2019.
  • During this time, Hydra will be inaccessible to users and as of 9am on Monday August 26th any remaining running jobs will be killed.
  • We hope to have Hydra back up before September 2nd, but that decision won’t be made until the upgrade work is completed.
  • During the down time, access to files stored on Hydra will be limited, and at times unavailable. Note that none of your files will be deleted.

Plan your use of Hydra accordingly.

(lightbulb) Please read this page carefully, and after the upgrade, do not hesitate to contact us (at SI-HPC-Admin@si.edu) if something is not working as it should any longer.

  • For biology and genomics software issues and/or incompatibilities that arise, please contact SI-HPC@si.edu,
  • SAO users please contact Sylvain at hpc@cfa.harvard.edu.

List of Software Changes 

  • Switching from Rocks to BCM
    • BCM locates things differently from Rocks;
      • for example /opt  is no longer used, instead BCM uses /cm  
    • If you use modules, everything should work the same;
      • but if you hardwired locations, things may no longer work the same;
    • The compute nodes will be renamed as follows:
      • compute-NN-MM, 
      • i.e. the "N", or logical rack number, and
      • M the node index are both two-digit numbers;
    • You should use modules as much as possible.
  • Job Scheduler
    • We switched to UGE, or Univa Grid Engine; that
      • is backward compatible with SGE;
      • offers some additional features;
      • although the output of some commands will look different, and
      • some have different options .

  •  The list of queues and their limits will not changed,
    • a few complex values will change (to use local SSD and GPU usage)
    • (warning) One important change (warning) is that 

      the memory reservation value will no longer be specified per slots, but per jobs:
      the specification  "-pe mthread 10 -l mres=20G,h_data=20G,h_vmem=20G,himem"
      must be changed to "-pe mthread 10 -l mres=200G,h_data=20G,h_vmem=20G,himem"
      to reserve 200GB of memory for this job, asking the scheduler to start on a node that has 20G per thread of free memory
  • Compilers
    • The default compiler versions has changes, and
    • they had to be reloaded.
    • For MPI jobs the compiler/flavor/version combos has also changed.
  • Local tools
    • The tools accessible with the tools/local module have been split into two groups and
    • some of the names have been changed or simplified
    • Use module help tools/local and module help tools/local+ to see what the split is and what the names are.
    • Use module help tools/local-bc to see the correspondence
    • Loading tools/local-bc will
      • load tools/local and tools/local+ and
      • create aliases to be backward compatible (-bc)
    • (lightbulb)use the new names whenever possible



Last updated   SGK.


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