Summary of processes
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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

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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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