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Similaire à OpenCAPI-based Image Analysis Pipeline for 18 GB/s kilohertz-framerate X-ray Camera at the Swiss Light Source synchrotron
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OpenCAPI-based Image Analysis Pipeline for 18 GB/s kilohertz-framerate X-ray Camera at the Swiss Light Source synchrotron
- 1. WIR SCHAFFEN WISSEN – HEUTE FÜR MORGEN OpenCAPI-based image analysis pipeline for 18 GB/s kHz-framerate X- ray camera at the SLS synchrotron Filip Leonarski :: Beamline Data Scientist :: Macromolecular Crystallography Page 1
- 2. • Introduction: Macromolecular crystallography at synchrotrons and X-ray detectors • Technology: POWER + OpenCAPI • Solution: Jungfraujoch Plan Page 2
- 3. X-ray 1901 Nobel Prize W. Röentgen Discovery of X-rays
- 4. X-ray macromolecular crystallography (MX) Page 4 1901 Nobel Prize W. Röentgen Discovery of X-rays (Photo 51 by R. Gosling and R. Franklin) 1962 Nobel Prize F. Crick, J. Watson and M. Wilkins Structure of DNA double helix solved with X-rays
- 5. X-ray macromolecular crystallography (MX) Page 5 1901 Nobel Prize W. Röentgen Discovery of X-rays (Photo 51 by R. Gosling and R. Franklin) 1962 Nobel Prize F. Crick, J. Watson and M. Wilkins Structure of DNA double helix solved with X-rays 2009 Nobel Prize V. Ramakrishnan*, T. Steiz, A. Yonath* Structure of ribosome (*) some of their structures were solved at PSI
- 6. Wikipedia: X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three- dimensional picture of the density of electrons within the crystal. X-ray macromolecular crystallography (MX) Page 6
- 7. • Particle accelerators are source of the brightest X-ray beam (multiple orders of magnitudes as compared to conventional X- ray tubes), when charged particles travel through magnetic field - Effect is nuisance for high energy physics (undesirable energy loss), - but it is a blessing for structural science => modern storage rings are build exclusively as light sources. • Synchrotrons provide continuous X-ray beam, while X-ray free electron lasers produce femtosecond long bright pulses MX at synchrotron Page 7
- 8. Paul Scherrer Institute Page 8 SwissFEL Swiss Light Source Swiss Alps
- 9. • 3 experimental stations at the synchrotron • 1 experimental station at the SwissFEL • Beamtime is shared between academic and industrial users - Industrial customers are mostly pharmaceutical companies looking for drug binding to potential drug targets - Academic users are universities and scientific institutes worldwide doing basic research in structural biology MX at Swiss Light Source and SwissFEL Page 9
- 10. • New storage ring to be installed in 2024-2025 • Flux (photons/second) will increase by order of magnitude • Measurements can be done 10x faster • Enabling fragment screening method – i.e. single protein target is crystallized with hundredths or thousands of molecular fragments to find best drug - This is like molecular docking, but fully experimentally Major upgrade in 2024/2025 for SLS 2.0 Page 10
- 11. • PSI is major detector developer - Hybrid pixel detectors developed for CERN high energy physics experiments - Design could be used for X-ray cameras – first PILATUS in 2000s - PSI start-up Dectris, commercialized PILATUS and EIGER detectors, most synchrotrons are equipped with their detectors • Currently PSI is rolling out new generation: JUNGFRAU Page 11 New detector for SwissFEL and SLS 2.0
- 12. • Silicon sensor converts X-ray to electric charge • Bump bonded to sensor is ASIC, with dedicated electronics for each pixel • Pixel has three capacitors allowing different amplification • They are dynamically switched during exposure to adjust for incoming charge Page 12 Adaptive gain detector to increase dynamic range Aim: measure reliably from 1 to 20,000,000 photons per second
- 13. Page 13 Adaptive gain detector to increase dynamic range 0001010111110011 Pixel output in JF: 0001010111110011 Gain: 00:G0 01:G1 11:G2 ADC value: 0001010111110011 Photon number: = !"# $ %&'&()*+ ,*-.∗%01)1. &.&2,3 Gain and pedestal factors are specific for pixel and gain setting Prior calibration Dedicated dark run
- 14. • Detector is modular • 524,288 pixels per module • 2.2 kHz * 524,288 pixels * 16 bit = 2.3 GB/s - 2 x 10 Gbit/s links • 4 Mpixel detector (2020) - 16 x 10 Gbit/s • 10 Mpixel (2022) - 40 x 10 Gbit/s Page 14 Modular detector 4 Mpixel (2020) 10 Mpixel (2022)
- 15. Page 15 MX detector data rates double every 2 years 0.1 1 10 100 2006 2008 2010 2012 2014 2016 2018 2020 2022 2024 Frame rate [GB/s] Year 2007 PSI PILATUS 6 Mpixel 12.5 Hz 0.2 GB/s 2014 Dectris EIGER 16 Mpixel 133 Hz 3.4 GB/s 2019 Dectris EIGER 2 XE 16 Mpixel 400 Hz 13.5 GB/s 2020 PSI JUNGFRAU 4 Mpixel 2200 Hz 18.4 GB/s 2022 PSI JUNGFRAU 10 Mpixel 2200 Hz 46.1 GB/s
- 16. • Detector is streaming frames over UDP - Receiver using Linux Datagram Socket • Conversion of pixel read-out - CPU SIMD code • Compression - CPU compression First approach: scale conventional architecture Page 16
- 17. • Detector is streaming frames over UDP - Receiver using Linux Datagram Socket • Conversion of pixel read-out - CPU SIMD code • Compression - CPU compression First approach: scale conventional architecture Page 17 Aim 20 GB/s Reached 5 GB/s
- 18. WIR SCHAFFEN WISSEN – HEUTE FÜR MORGEN POWER / OpenCAPI / FPGA architecture Page 18
- 19. • Real-time performance - FPGA design is cycle-accurate, with fixed latency and throughput • Large memory throughput - FPGAs with HBM2 have 460 GB/s bandwidth to 8 GB large memory • Ethernet on-board - FPGA are made to work with network, often having dedicated “hard” cores for ethernet • Development of FPGAs is difficult and time consuming - Hardware description languages - PCI Express • Virtex Ultrascale+ HBM (XCVU33P and XCVU35P) - Availble as low-profile half-length 75W cards FPGA are perfect devices for data acquisition Page 19
- 20. • C/C++ compiler to produce hardware design language (Verilog or VHDL) • All code is valid C++ code, it can be executed on CPU and functionally is generally equivalent • Dedicated pragma to guide FPGA synthesis • It is generally understandable for software developers, but may contain strange/inoptimal constructs from software point of view High-level synthesis Page 20 Bitshuffle for 16-bit numbers
- 21. • For VU33/35P: - Size: 8 GB - Bandwidth: up to 460 GB/s - Latency: up to 120 cycles @ 200 MHz • Complex architecture - 32 x 256-bit AXI3 interfaces - Either operating as 32 separate memories - Or as single memory with crossbar (at the cost of up to 50% throughput) • 256-bit is a problem, as data are 512-bit (PCIe Gen3 x16) or 1024-bit (OpenCAPI, PCIe Gen4 x16) • Simulation only with special tools (Cadence Xcelium), impossible with Xilinx tools High-bandwidth memory Page 21
- 22. • PCI Express is CPU-centric bus, as it is design to support peripherals • This is good model, when FPGA is a coprocessor to CPU – which sends data, and waits for reply => but for data acquisition, it is FPGA that is producing the data, CPU has no prior knowledge which packet will be processed at the time • DMA is operating on physical addresses: virtual addresses need to be pinned by kernel (so are not swapped and moved) Þ need to maintain own driver Þ address translation cache possible on FPGA, but requires memory PCI Express DMA Page 22 Xilinx QDMA is a robust but highly complex solution for PCI Express – used to interface FPGAs with x86 AMD and Intel CPUs
- 23. • IBM POWER9 showed great numbers for I/O and memory throughput in Summit and Sierra supercomputers • IBM designed own memory coherent interface for accelerators (CAPI/OpenCAPI), which has advantages over PCIe POWER architecture Page 23 Source: Wikipedia
- 25. OpenCAPI Page 25 FPGA board POWER9 CPU OpenCAPI cable • Predecessor CAPI => proprietary IBM • Communication over PCIe physical lines (but different protocol) • OpenCAPI => consortium model • Dedicated cabling (8 x 25 Gbit/s lines) • For POWER10 – this will be default memory interface, (allowing to have any type of memory attached to CPU + to “share” memory over network)
- 26. • Similar difference what 80286/80386 virtual mode brought to software development • In OpenCAPI one needs single kernel operation => Attach accelerator to running process • Then, accelerator has access to virtual address space of running process – it is FPGA that is initiating the communication => Address translation is handled by TLB and OS => FPGA sees memory in a fully cache-coherent way • All security/reliability/efficiency mechanisms in CPU and kernel are also present in OpenCAPI Page 26 What difference brings OpenCAPI? Source: Wikipedia
- 27. • Main function for the action contains a pointer to virutal address space - On device the pointer will be synthesized as 1024-bit master memory-mapped AXI interface - On CPU this pointer has to be just set to zero (which is first address of virtual address space) • Any cell in virtual memory is just accessed as offset from this pointer • Only requirement is that memory is aligned to 128-bytes - No special memory allocator, malloc or mmap is fine - No pinning/registering • The same memory buffer class for both simulation and working with device • For configuration, there is also 4 MiB memory-maped I/O space (like BAR in PCIe) - On device implemented as slave AXI-lite (32-bit) How to develop with OpenCAPI? Page 27
- 28. • Open source “shell” mantained by IBM • http://github.com/OpenCAPI/oc-accel • Provides ready made tool to work with OpenCAPI (from transceiver setup to AXImm bridge) • Provides preconfigured interfaces for I/O peripherals (HBM, 100G, NVMe) • Provides simulation environment - One can simulate both SW and HW in a single simulation (both user FPGA design and software are not modified from their “real” implementation) OC-Accel Page 28
- 29. WIR SCHAFFEN WISSEN – HEUTE FÜR MORGEN Jungfraujoch – FPGA implementation Page 29
- 30. Page 30 Jungfraujoch server Ethernet UDP/IP Dark current Conversion Strong pixel finder Bitshuffle Memory writer FPGA board with OpenCAPI interface - Data acquisition - Initial data analysis - Pre-compression (2.5 Mpixel/board for JF) Up to 50 GB/s acquisition and data analysis in a single 2U IBM POWER9 server with 1-4 FPGA boards Frame summation
- 31. Page 31 Jungfraujoch FGPA streaming design Modular design • Stream of data handled by successive cores doing work in parallel à throughput and latency of each core is determined by the hardware design • Extra stages can be relatively simply added, option to bypass cores • All cores are C++ functions, connected with AXI-Stream FIFOs • As buffering is expensive on FPGA, it is best suited for algorithm that have limited dependencies between frames Ethernet UDP/IP Dark current Conversion Strong pixel finder Bitshuffle Memory writer Frame summation
- 32. Page 32 Jungfraujoch Ethernet UDP/IP core Processes ethernet packets from network, ignores unnecessary packets, reads frame header to get frame number, module number, etc. Ethernet UDP/IP Dark current Conversion Strong pixel finder Bitshuffle Memory writer Frame summation
- 33. Page 33 Jungfraujoch Dark current core This cores is responsible for calculating moving average of detector frames. Calculated value is used as dark current (pedestal) for subsequent frames. Ethernet UDP/IP Dark current Conversion Strong pixel finder Bitshuffle Memory writer Frame summation
- 34. Page 34 Jungfraujoch Conversion core This cores translates JUNGFRAU read-out into units of energy or photon counts. It benefits from very fast HBM2 memory within the FPGA (460 GB/s). Data leaving this core can be used for processing by data analysis software. Ethernet UDP/IP Dark current Conversion Strong pixel finder Bitshuffle Memory writer Frame summation
- 35. Page 35 Jungfraujoch Frame summation core (work in progress) As data that left gain correction core are on linear scale, they can be summed to reduce downstream data rate, if lower frame rate is needed, as compared to detector. Ethernet UDP/IP Dark current Conversion Strong pixel finder Bitshuffle Memory writer Frame summation
- 36. Page 36 Jungfraujoch Strong pixel finder core This is first step of spot finding algorithm (for example COLSPOT). It identifies pixels that are stronger than given number of standard deviations of their neighborhood. Ethernet UDP/IP Dark current Conversion Strong pixel finder Bitshuffle Memory writer Frame summation
- 37. Page 37 Jungfraujoch Bitshuffle FPGAs are bit order agnostic. Therefore exchanging bit order in popular compression prefilter is pretty much for free on FPGA. Ethernet UDP/IP Dark current Conversion Strong pixel finder Bitshuffle Memory writer Frame summation
- 38. Page 38 Jungfraujoch Host memory write Address in host memory buffer is calculated and data forwarded to host memory via OpenCAPI. Additional image statistics are saved as well. Ethernet UDP/IP Dark current Conversion Strong pixel finder Bitshuffle Memory writer Frame summation
- 39. Page 39 Jungfraujoch implementation on VU33P FPGA Spot finding HBM Gain Pedestal Write data OpenCAPI 100G UDP
- 40. Jungfraujoch FPGA power usage is 18 W/board for the whole streaming functionality Page 40 Xilinx Vivado Power Report 2 boards for 4 Mpixel JUNGFRAU and 4 boards for 10 Mpixel JUNGFRAU
- 41. • VU33P or VU35P with 8 GB of HBM2 • OpenCAPI link and PCIe Gen3 x16 (or two PCIe Gen4 x8) • Small flash (2 kb) to store MAC address, board IR • QSFP-DD optical socket (same as QSFP28, but with 8 lanes for 2x100G) => compatible with QSFP28 transceivers • Up to 75W Alpha Data 9H3 board Page 41
- 42. • Software tests – Catch2 - 8 min - Among other software tests includes 13 FPGA action tests (whole SLS code) - Automated tests cover 95% lines of high- level synthesis code - Covers most of the functionality correctness – including address calculation - Main limitation is debugging of FIFOs parallel behavior (deadlocks, etc.) • Hardware simulation – Cadence Xcelium - 4 hours - Collection of 8 frames from single module - Checks if hardware description is correct, can find problems with synchronization, and other, very rare, issues - Too slow to verify functionality OpenCAPI programming - testing Page 42
- 43. • Detector and data acquisition system was sent in November for an experiment in Photon Factory, KEK • More than 2,000 datasets collected for protein targets, few real-life native-SAD structures solved • Due to pandemic, detector support and development (including deployment of new FPGA design) was done fully remotely from Switzerland Commissioning in KEK (Jan – May 2021) Page 43 BL-1A Photon Factory JUNGFRAU detector (up) tested in helium chamber for native-SAD measurements with 3.75 keV X-rays
- 44. Page 44 Structure of Nucleocapsid Phosphoprotein from SARS-CoV-2 solved in 1 second • Crystal was previously measured with conventional setup at our beamline – with measurement taking longer than one minute • With JUNGFRAU detector and OpenCAPI readout, 2000 images collected in one second allowed to solve structure of this protein • Experimental team: Filip Leonarski, Sylvain Engilberge, Vincent Olieric, Meitian Wang (MX Group), Aldo Mozzanica (PSI Detector Group) • SARS-CoV-2 protein was produced by Zinzula, L., Basquin, J., Bracher, A., Baumeister, W. (MPI, Martinsried)
- 45. Possible gain from using FPGA based system Page 45 Courtesy: B. Mesnet (IBM)
- 46. Possible gain from using FPGA based system Page 46 Courtesy: B. Mesnet (IBM)
- 47. MX Group (PSI) • Vincent Olieric • Takashi Tomizaki • Chia-Ying Huang • Sylvain Engilberg • Justyna Wojdyła • Meitian Wang Detector Group (PSI) • Aldo Mozzanica • Martin Brückner • Carlos Lopez-Cuenca • Bernd Schmitt Science IT (PSI) • Leonardo Sala Controls (PSI) • Andrej Babic • Leonardo Hax-Damiani SLS management (PSI) • Oliver Bunk Photon Factory, KEK • Naohiro Matsugaki • Yusuke Yamada • Masahide Hikita MAX IV • Jie Nan • Zdenek Matej Uni Konstanz • Kay Diederichs LBL • Aaron Brewster DLS • Graeme Winter • DIALS Team ESRF • Jerome Kieffer IBM Systems (France) • Alexandre Castellane • Bruno Mesnet InnoBoost SA • Lionel Clavien Acknowledgements Page 47