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Summary of Processes. Rutt offline.recon – memory bound COMSOL – memory bound mcDESPOT and quantitative mapping – CPU bound, voxelwise parallel Zeineh offline.recon ImageJ – memory bound ASHS – CPU bound McNab FSL, bedpost – CPU bound, voxelwise parallel FreeSurfer – serial

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summary of processes
Summary of Processes
  • Rutt
    • offline.recon– memory bound
    • COMSOL – memory bound
    • mcDESPOT and quantitative mapping – CPU bound, voxelwise parallel
  • Zeineh
    • offline.recon
    • ImageJ– memory bound
    • ASHS – CPU bound
  • McNab
    • FSL, bedpost – CPU bound, voxelwise parallel
    • FreeSurfer – serial
    • Probabilistic ICA for resting state fMRI
    • Matlab diffusion simulations – memory intensive
summary of load
Summary of Load
  • Most describe their load as “peaky”
    • Development time and coming up with new ideas dominates
  • However, Michael would like to start up larger studies within 5 yrs.
    • 30-50 subjects
  • Planning on routine thalamic segmentation?
summary hardware
Summary: Hardware
  • Needs
    • High memory – at least 64GB, Michael wants 196GB
    • Unified data storage and backup
  • Wants
    • Prioritize CPU speed over cores as many jobs are not parallelized
  • In general, having enough memory to make the problem feasible at all is most important
    • Faster CPU is just an incremental improvement
summary software
Summary: Software
  • Needs
    • DICOM connectivity
      • How do we get this without OSX/OsiriX?
    • Scheduling and job submission
    • Matlab, FSL, FreeSurfer, etc.
  • Wants
    • Remote desktop
      • Esp. for viewing larger datasets (ImageJ or Trackvis)
      • Not sure if this is an appropriate use of the system
      • Would change the hardware of the terminal node
concerns
Concerns
  • Jennifer looking for a solution ASAP
    • I stated end of Jan purchase date, which she was okay with
  • Administration
    • This could turn out to be a fairly demanding job esp. for many users
  • Sharing and resource management
    • Need to develop a policy for sharing compute time
    • At MGH/Martinos, they have one machine that’s a free for all and others must be reserved/scheduled
hardware proposal
Hardware Proposal
  • If there is some urgency, we should focus on expandability:
    • Get something that meets our core needs now
    • But that can be expanded as users begin to use it more or better understand what their jobs need
  • Terminal node
    • Simple barebones system with minimal CPU power and RAM
    • Functions as the liaison between user and cluster, manages job scheduling & load distribution
    • Used for testing programs and scripts for compatibility
    • Could possibly have remote desktop, but would then need a lot more RAM
  • Data server
    • Minimal CPU power and RAM
    • RAID – 6 (req. 4 drives), 60 (req. 8 drives, more fault recovery)
  • Compute nodes
    • 64GB RAM with as many slots as possible
    • CPU?
    • Ideally diskless
    • Need fast (10Gbps) connection to data server
stanford services and rates
Stanford Services and Rates
  • IT
    • Consulting for planning– free?
    • Basic administration – $3.6k/yr
    • Secured housing for rack, 10Gbps connection to campus backbone – $3k/yr
    • Backup storage – $4-5k/yr per 10TB
  • Med School, IRT
    • Basic administration – $2.4k/yr
    • Secured housing for rack – $4.8k/yr
    • $840/yr per 500GB
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