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Cluster C omponents

Cluster C omponents. Compute Server Disk Storage Image Server. Compute Server: Stanford Research Computing Facility (RCF). Accessible only to Stanford faculty and authorized sub users for their research 128 nodes provided by the provost

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Cluster C omponents

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  1. Cluster Components • Compute Server • Disk Storage • Image Server

  2. Compute Server:Stanford Research Computing Facility (RCF) • Accessible only to Stanford faculty and authorized sub users for their research • 128 nodes provided by the provost • 8 cores each (16 threads), 64GB RAM, Infiniband card • Ivy Bridge V2 with 1866GHz memory • 1024 cores, 2048 threads, 8TB RAM total in the initial cluster • Cluster re-evaluated every 2-3 years for upgrade/expansion

  3. Compute Server:Stanford Research Computing Facility (RCF) • 1PB of scratch space (not backed up) • Must push data to the local storage prior to running jobs • Home directories allocated to individual users (~10-15GB/user), but may be combined among users within a group • Expansion units will be available for purchase later on • Two additional nodes with 1.5TB RAM each • Jobs running on these machines must meet minimum RAM requirements or else they will be terminated and sent to the general cluster • Infiniband56Gbits/sec Ethernet lines

  4. Purchasing into the RCF: Hardware • Purchasers will always have access to the main cluster • Base system purchase • 8 cores (16 threads), 64GB RAM (4GB/thread), Infiniband card, $5000 • Custom systems can be purchased • i.e., 8 cores (16 threads), 128GB RAM (8GB/thread), ~$7000 • Flexible configurations can be made to purchased machines • i.e., 4 active threads (12 “wasted” threads, 128GB RAM with 32GB/thread) • Can be changed as long as DIMM configuration remains optimal

  5. Purchasing into the RCF: Administration • Can assign priority of jobs among authorized users that have access to a purchased machine. • Server administration is included in purchase price. No annual fees. • Purchase announcements made ~3 times per year. • May have to wait a couple months before purchased machine is available. • Other users’ access to purchased machines that are idle is TBD • Compliance/audit issues remain

  6. Loading Software on the RCF cluster • Can request to have software packages on the general cluster • More likely to be installed if widely used • Matlab is on the list to be added, but is currently a source of frustration • Can install software on a purchased machine • Recommended for software that is not widely used (i.e., offline.recon) • Need to evaluate current licenses for transfer to purchased machines (i.e., COMSOL, SEMCAD, etc.)

  7. RCF Timeline • February • Designated “friendly” users to begin testing • One each from Rutt group and McNabgroup • March • Cluster becomes available for general use • April-June? • 1st round of purchased machines available

  8. RCF Considerations • May be advantageous to purchase early due to our high RAM requirements • Purchase costs may increase next year • Unclear if purchased machines are available to other users • Job priority rules are still being decided

  9. Compute Server Action Items • Leaning towards RCF purchase of 2 x 128GB systems to be used as a mini cluster. • Jennifer’s group gets top priority on one machine and Brian’s group gets top priority on other. • Users from both groups are authorized to use both machines. • ASAP:Designate friendly users for RCF testing. One each from Brian’s group and Jennifer’s group. • Jason/Simone + Grant Yang

  10. Disk Storage • Synology desktop NAS or rack-mounted • RAID6 configuration • Main Unit: 48TB capacity  40TB actual storage • Expansion Units: 48TB capacity  48TB actual storage • Must decide maximum expansion capacity prior to purchasing main unit • Main + 2xExpansion = 144TB system  136TB RAID6 • Main + 1xExpansion = 96TB system  88TB RAID6

  11. Desktop vs. Rack Storage vs. Max Capacity

  12. Image Server • Want a multi-user DICOM server and database • Need a way for people to be able to view and pull DICOM images remotely • Adding all these users as recognized DICOM nodes is cumbersome • A web interface is an effective way to accomplish this

  13. OsiriX • Has a fairly basic web layout • Rudimentary search • Organized by albums (which cannot be managed through the website, I think) • Excellent image viewer • Can be customized to our heart’s content though • Advanced user management with customized access rights for each individual • Try it out: http://171.65.72.243:3333/ • Just press login

  14. OsiriX – Main Page

  15. OsiriX – Album Page • Download options • “OsiriX remote transfer” • Zip of DICOMs • Weasis remote view

  16. OsiriX – Exam Page

  17. OsiriX – Series View

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