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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

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Summary of Processes

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  1. 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

  2. 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?

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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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