IT of SPIM Data Storage and Compression. EMBO Course - August 27th! Jeff Oegema, Peter Steinbach, Oscar Gonzalez

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1 IT of SPIM Data Storage and Compression EMBO Course - August 27th Jeff Oegema, Peter Steinbach, Oscar Gonzalez 1

2 Talk Outline Introduction and the IT Team SPIM Data Flow Capture, Compression, and the Data Volume Problem Transfer, Network and Storage Infrastructure Planning for SPIM 2

3 People Involved - IT Staff Peter Steinbach Scientific / HPC Software Development Data Streaming Library Compression and HPC Algorithm Development Ian Henry Scientific Computing Leader Scientific and Project Coordination Collaboration Management Oscar Gonzalez HPC Administrator Cluster Interaction and Queuing High-Performance Storage / Lustre Network Benchmarking and Performance Tuning Matt Boes Infrastructure Team Leader Network Design and Development Fileserver Design and Development Jeff Oegema IT Coordinator Overall Project Coordination External Collaboration Management 3

4 SPIM Dataflow Camera Camera Capture Computer(s) Capture Computer(s) or Dedicated Local Storage Storage System Data Transfer Cluster for Processing Zeiss Windows Software for Processing Data Transfer Longer Term Storage Review Archival Presentation Capture Processing Usage and Archiving 4

5 SPIM Dataflow Camera Camera Capture Computer(s) Capture Computer(s) or Dedicated Local Storage Storage System Data Transfer Cluster for Processing Zeiss Windows Software for Processing Data Transfer Longer Term Storage Review Archival Presentation Capture Processing Usage and Archiving 5

6 Zeiss Lightsheet Z.1 2 x CamLink SPIM System Lightsheet Z.1 Capture Computer Capture Stream 150 MB / sec Storage Computer 8 / 32 TB Storage Drain to network / external storage 10Gb Ethernet 6

7 The Potential Deluge Developmental SPIM - Camera Potential TB / Day Estimated CERN data production / day 82 TB 82 TB - Estimated CERN Data Production / Day 50 GB Single Lightsheet Z1 Capture - 1 day 13 TB 13 TB Confocal Microscope Capture - 1 day GB - Confocal - 1 day 7

8 The Potential Deluge - Multiple Lightsheet Z MB / sec x 4 = 600 MB / sec ~52 TB / day ~364 TB / week Our entire online disk storage (fileserver) currently is 700 TB 8

9 The Potential Deluge - Future Tech 800 MB / sec x 2 cameras = 1.6 GB / sec ~138 TB / day Almost a PB per week CERN produces 30 PB of data annually from LHC experiments* * 9

10 SPIM Dataflow Camera Camera Capture Computer(s) Capture Computer(s) or Dedicated Local Storage Storage System Data Transfer Cluster for Processing Zeiss Windows Software for Processing Data Transfer Longer Term Storage Review Archival Presentation Capture Processing Usage and Archiving 10

11 Transfer Volumes and Times Data Volume / Time 1 Gbit 10 Gbit 150 MB / sec 9 GB / minute 540 GB / hour ~13 TB / day 1.5 sec.15 sec 90 sec 9 sec 1.5 hours 9 minutes 1.5 days 3.6 hours This assumes approximately theoretical maximum line speed - which never happens. Typically we see 60%. 11

12 First : Get the Data Off Camera Camera Capture Host 10 Gb/s 1.25 GB/s Remote Storage Storage network mounted drives (ex. SMB) secure network file transfer (scp/sftp/rsync) unencrypted file transfer (ex. ftp) pro simple secure fast con OS dependent encryption may slow transfer insecure 12

13 Operating Systems & Networking Percentage of Line Speed Extensive Network Streaming Tests Win7, Windows Server 2008 R2 10 Gbit/s fiber network same hardware No disk i/o involved Windows Linux 13

14 Networks are ç a shared resource 14

15 Network File Transfer is necessary ( capture host becomes unusable / full ) protocols are important to keep in mind network is a shared resource 15

16 Second : Bottlenecks again Camera Camera Capture Host Storage Spinning disk based storage Large Volume Comparatively cheap SSD based storage Fast Small Volume Expensive SPIM Operation Capture Transfer Capture Transfer Capture Transfer 16

17 Second : Get it Small Camera Camera Capture Host Storage cropping (only keep what you need) fusion + deconvolution (n stacks become 1) compression Reduce data volume before any network or disk 17

18 Compression : Demonstration Please zip a SPIM dataset of your choice How long did it take? How small is the compressed data? 18

19 Compression : Fast Capture Camera Camera Storage 19

20 Compression : Noise? SPIM data contains a lot of noise 20

21 Compression : Denoised 21

22 Compression : Denoised Original 22 Denoised

23 Compression : Sqeazy pipeline standard compression algorithms fast soon to be open-sourced currently: 3x lossless compression 10x lossy compression 23 Loic Royer initiated by: Martin Weigert

24 SPIM Dataflow Camera Camera Capture Computer(s) Capture Computer(s) or Dedicated Local Storage Storage System Data Transfer Cluster for Processing Zeiss Windows Software for Processing Data Transfer Longer Term Storage Review Archival Presentation Capture Processing Usage and Archiving 24

25 HPC for SPIM Lots of image data 25

26 HPC for SPIM Lots of image data CPU intensive 26

27 HPC for SPIM Lots of image data CPU intensive High memory footprint 27

28 HPC for SPIM Lots of image data CPU intensive High memory footprint High I/O 28

29 HPC for SPIM Lots of image data CPU intensive High memory footprint High I/O GPUs are promising 29

30 HPC for SPIM Lots of image data CPU intensive High memory footprint High I/O GPUs are promising 30

31 31

32 Cluster Architecture Head node Job management Cluster monitoring Clients Export node 10 GbE Worker nodes 40x: * 12 cores * 128 GB RAM * 1 TB HDD 4x: * 12 cores * 128 GB RAM * 1 TB HDD * GPU Disk server 200 TB net space (RAID 6) 10 GB/s InfiniBand non-blocking MB/s (up to saturation) 32

33 MPI-CBG Cluster Storage 10 GbE 10 GbE 10 GbE Export Node Export Node Export Node Lustre Storage 200 TB Total Space Capable of 10 GB/s of up to 600 MB/s streams Also serves the cluster processing nodes Temporary storage Processing Nodes 33

34 Resource Usage The cluster was made available on Feb 2013 Total number of jobs done: 6,852,661 Average throughput: 462 jobs/h CPU time consumed: 151y 46d 10h 59m 12s Average CPU time: 11m 35s 34

35 Lessons Learned Cluster design is very important - think before you buy I/O is critical to move data in and out of the cluster I/O is VERY critical to access data from the cluster Storage requirements are huge, both inside and outside the cluster GPU resources might be useful but you need enough to make it practical 35

36 Workstations If/when a cluster is not an option, check what your WS can do. Example Data PC 12 cores 128 GB 4x 2TB (RAID 5) Pros: Rather cheap Fine for small datasets Convenient for data visualisation Cons: Limited computing resources Limited storage capacity and bandwidth 36

37 SPIM Dataflow Camera Camera Capture Computer(s) Capture Computer(s) or Dedicated Local Storage Storage System Data Transfer Cluster for Processing Zeiss Windows Software for Processing Data Transfer Longer Term Storage Review Archival Presentation Capture Processing Usage and Archiving 37

38 Current Infrastructure 10 Gpbs 8 Gpbs Fileserver Visible network-wide High capacity (900 TB) Robust (no SPOF) Backed up daily Tape library Second copies Long term storage 38

39 Future Plans... Scale-out NAS Highly scalable Very high capacity (10 PB) Very high bandwidth Very robust (no SPOF) 39

40 Taking it Home - External Drives 4TB transfer USB 3.0 (600 MB / sec) Protocol 1.85 hours USB 2.0 (60 MB / sec) 18.5 hours WD Black (130.4 MB / sec) Hitachi Deskstar ( / MB sec) Samsung SSD - 1 TB (550 MB /sec) Drive Speed 8.52 hours hours 2.02 hours The limitation is the slower of the two 40

41 Bottlenecks at Each Stage Capture Network Processing Storage Single Drive RAID Array 1 Gbit 10 Gbit Single Machine HPC Fileserver New Fileserver or Data System Bottlenecks can be addressed but the pipeline can t be made infinitely wide Experiment Design and Data Management become extremely important Compression can help but the issue remains 41

42 IT Planning for SPIM (or things to think about before I capture ) What is the practical output of your SPIM setup? How long are you planning on capturing at a time? What processing do you need to do on your data? How fast do you need to complete the processing? What is the data you will consider primary data for publication? How will you present your data to the world or turn it into movies or results more easily shared? 42

43 Discussion and Questions 43

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