The Memory Intensive System

Transcription

1 The Memory Intensive System The DiRAC-2.5x Memory Intensive system at Durham in partnership with Dell Dr Lydia Heck, Technical Director ICC HPC and DiRAC Technical Manager 1

2 DiRAC Who we are: a U.K. National HPC facility distributed over four academic institutions Managed by Scientists for their Science Areas DiRAC Services support a significant portion of STFC s science programme, providing simulation and data modelling resources for the UK Frontier Science theory community in Particle Physics, astroparticle physics, Astrophysics, cosmology, solar system & planetary science... Dirac web pages. A partner in the National e-infrastructure under the umbrella of IRIS. We have a full management structure Management team: Director, technical director, innovation director, project scientist, technical manager programme management board (PMB): management team + scientists Oversight Committee (OSC): independent, external. Fully refereed resource allocation through the DiRAC Resource Allocation committee (RAC): managed by STFC, chaired by scientists from both Astrophysics and Particle Physics 2

3 DiRAC - History 2009 DiRAC-1: 13 Installations ( 13M) Part of DiRAC-1 COSMA4 in Durham installed in 2010 with 2976 cores Intel Westmere 2.67 GHz and 14.8 Tbyte of RAM DiRAC-2 : ( 15M) 4 sites and 5 installations: Funded by the U.K. government Department for Business, Innovation & Skills (BIS) OPEX funded by the U.K. Science and Technology Facilities Council (STFC) The procurements (OJEU) were done in less than 100 days. DiRAC-2 installations with a total peak performance of 2 PFlops From North to South: Edinburgh Bluegene (UK-QCD) QCD simulations; some astrophysical calculations were ported (IBM) 20 th of Top 500, June 2012 Durham (ICC) - COSMA Intel SandyBridge cluster Cosmological simulations; Solar system and planetary modelling; gravitational waves; Beam optimisation simulations (IBM) 134 th of Top 500, June 2012 Cambridge Cosmos Shared Memory SGI system; cosmological data modelling (SGI) Cambridge Darwin Intel SandyBridge cluster QCD, cosmological and astrophysical simulations; solar and planetary physics (Dell) 93 rd of Top 500, June 2012 Leicester Complexity Intel SandyBridge Cluster - astrophysical simulations; solar and planetary physics; cosmological and astrophysical simulations; star formation (HP) 3

4 DiRAC - History 2016 DiRAC-2.5 Edinburgh: transfer of the Bluegene-Q system from the Hartree Centre at Daresbury as spare parts ( 30k) Durham (ICC) COSMA6 - repurposing of the Blue Wonder cluster (114 th in Top 500, June 2012) gift from the Hartree Centre and rebuilt in partnership with OCF and DDN and a lot of willing hands from the ICC adding 8000 cores to the existing system: total of cores ( 400k) Cambridge new installation (Dell): 13% of CSD3 (768 nodes; 24,576 cores, Intel Omnipath), CSD3-GPU (360 nodes; 1440 GPUs, Mellanox EDR) and CSD3-KNL (342 nodes; 342 KNL, Intel Omnipath). Leicester Complexity repurposing local HPC cluster to add 3000 Intel SandyBridge cores: to a total of

5 DiRAC-2.5x Autumn 2017 Total spend: 9M - 3 competitive tenders. Edinburgh to replace ailing Bluegene Q Extreme Scaling Durham to add a system with 100 Tbyte of RAM and fast checkpointing i/o system Memory Intensive Leicester to replace the DiRAC-2.5 add-on with modern competitive cores and adding substantial shared memory systems Data Leicester Investigations into Cloud Computing how could Public Cloud benefit DiRAC and how could DiRAC offer cloud Investigations in optimal ways of transferring data 5

6 Edinburgh Extreme Scaling (ES) Delivered and installed by HPE (680 Tflops) The Extreme Scaling Service is hosted by the University of Edinburgh. DiRAC Extreme Scaling (also know as Tesseract) is available to industry, commerce and academic researchers. Intel Xeon Skylake 4116 processors, 844 nodes, 12 cores per socket, two sockets per node, FMA AVX512, 2.2GHz base, 3.0Ghz turbo, 96GB RAM Hypercube Intel Omnipath Interconnect 2.4PB Lustre DDN storage This system is configured for good to excellent strong scaling and vectorised codes and has High Performance I/O and Interconnect. Edinburgh Castle Public Body for Scotland's Historic EnvironmentHistoric Environment Scotland 6

7 Durham - Memory Intensive (MI) COSMA5 (2012): (IBM/Lenovo/DDN) 6,400 Intel SandyBridge, 2.6 GHz, 51 Tbyte of RAM; Mellanox FDR10 interconnect in 2:1 blocking; 2.5 Pbyte of GPFS data storage COSMA6 ( 2016): (IBM/Lenovo/DDN) 8192 Intel SandyBridge, 2.6 GHz, 65 Tbyte of RAM; Mellanox FDR10 interconnect in 2:1 blocking; 2.5 Pbyte of Lustre data storage COSMA7 (Dell, 2018): 4116 Intel Skylake 5120 cores, Mellanox EDR in a 2:1 blocking configuration with islands of 24 nodes; a total of 110 Tbyte of RAM; a fast checkpointing i/o system (343 Tbyte) with peak performance of 185 Gbyte/second write and read; a data storage of 1.8 Pbyte. The system was delivered by Dell 7

8 Cambridge Data Intensive (DiC) DiRAC has a 13% share of the CSD3 petascale HPC platform (Peta4 & Wilkes2), hosted at Cambridge University (Dell) Peta4 The Peta4 system provides 1.5 petaflops of compute capability: 342 C6320p node Intel KNL Cluster (Intel Xeon Phi CPU with 96GB of RAM per node. 768 Skylake nodes each with 2 x Intel Xeon Skylake 6142 processors, 2.6GHz 16-core (32 cores per node 384 nodes with 192 GB memory 384 nodes with 384 GB memory The HPC interconnect is Intel OmniPath in 2:1 Blocking The storage consists of 750 TB of disk storage offering a Lustre parallel filesystem and 750 GB of Tape. Wilkes2 The Wilkes2 system provides 1.19 petaflops of compute capability: 360 NVIDIA GPU cluster with four NVIDIA Tesla P100 GPUs, in 90 Dell EMC server nodes, each with 96GB memory connected by Mellanox EDR Infiniband, providing 1.19 petaflops of computational performance. 13% of 8

9 Leicester Data Intensive Delivered and installed by HPE, 2018 Data Intensive 2.5x (DiL) The DI system has two login nodes, Mellanox EDR interconnect in a 2:1 blocking setup and 3PB Lustre storage. Main Cluster 136 dual-socket nodes with Intel Xeon Skylake 6140, two FMA AVX512, 2.3GHz; 36 cores, 192 GB RAM cores in total. Large-Memory 1 x 6TB server with 144 cores X6154@ 3.0GHz base 3 x 1.5TB server with 36 cores X6140@ 2.3GHz base The DI System at Leicester is designed to offer fast, responsive I/O. Data Intensive 2 (formerly Complexity ) 272 Intel Xeon Sandybridge nodes with 128 GB RAM per node, 4352 cores (95Tflop/s) connected via non-blocking Mellanox FDR interconnect. This cluster features an innovative Switching architecture designed, built and delivered by Leicester University and Hewlett Packard. The total storage available to both systems is in excess of 1PB. 9

10 Durham MI COSMA7 (Dell, 2018) 4116 Intel Skylake 5120 cores, Mellanox EDR in a 2:1 blocking configuration with islands of 24 nodes; 2 x 1.5 Tbyte login nodes 1 x 3 Tbyte 4 socket for Durham Astrophysics a total of 110 Tbyte of RAM; a fast checkpointing i/o system (343 Tbyte) with peak performance of 185 Gbyte/second write and read; a data storage of 1.8 Pbyte. 10

11 Durham MI The system was delivered by Dell in March 2018; Installed by Alces The DiRAC service started on 1 May 2018 Industrial engagement: Aligns closely with the Industrial Strategy of the Department for Business, Energy and Industrial Strategy (BEIS). funding leads to industrial engagement; this results in innovation, both leading to benefits academia and the wider industry. 11

12 How is MI different? a fast checkpointing i/o system (343 Tbyte) with peak performance of 185 Gbyte/second write and read; 15 Lustre Object Storage Servers on Dell 640 nodes each with 2 x Intel Skylake 5120 processors 192 Gbyte of RAM 8 x 3.2 TB NVMe SFF drives. 1 Mellanox EDR card A user code benchmark produced 180 Gbyte/second write and read This is almost wire-speed! This is currently the fastest filesystem in production in Europe 12

13 Kilo Watt hours over 5 years How is DiRAC@Durham MI different? Power usage for snapshots with different performance solutions 3,000,000 2,500,000 2,000,000 1,500,000 1,000, , hour 12-hour 6-hour 4-hour 2-hour 1-hour Axis Title 30GB/sec 120GB/sec 140GB/sec 13

14 How is MI different? Snapshot period 24-hour 12-hour 6-hour 4-hour 2-hour 1-hour hours/snap 30GB/sec 7,087,597 14,175,194 28,350,388 42,525,582 85,051, ,102, GB/sec 1,771,899 3,543,799 7,087,597 10,631,396 21,262,791 42,525, GB/sec 1,518,771 3,037,542 6,075,083 9,112,625 18,225,250 36,450, total number of cores 4,096 years of running 5 Total number of available cpu hours per year: 36,056,160 14

15 Durham MI industrial engagement Dell partners: Alces integrator and offer for a CDT placement Intel collaboration on proofs of concept; extension of IPCC at Durham ICC; Mellanox student placement to optimize SWIFT for Mellanox interconnect; optimized openmpi for Mellanox infrastructure; membership of Centre of Excellence; Nvidia a 2 day Nvidia Hackerton in September More involvement as the partnerships are building 15

16 Science on MI The system has been designed to allow for effective large scale cosmological structure calculations EAGLE likes fewer cores and more RAM per node. SWIFT should not really mind, however in order to do the detailed simulations lots of RAM is required. In both cases there are long run times. The Universe is close to 14 billion years old! Science aims: A run about 30 times bigger than the EAGLE run: The EAGLE run parameters: 1500^3 dark matter mass particles = 3.375* 10^9 1500^3 (= * 10^9 ) baryonic (visible) matter particles Volume of the Eagle run: 100 Mega Parsec (1 parsec = 3.2 light years ) 10,000 particles per Milky Way galaxy 20 TB of RAM 16

17 Science on MI Visible Matter Astrophysics: Galaxy formation, super nova, star formation 10^6 solar masses per mass particle; 10,000 mass particles per galaxy which is an effective resolution of 1000 parsec (or of the order of 3000 light years) Super Nova events create a lot of energy. Using previous methods this energy would be distributed to heat every particle. In EAGLE, this energy would heat a tiny fraction to 10^7 K with a hundred neighbours. The cooling rate would be low. To do this better the resolution has to improve by a factor of 10 at least to a resolution of 100 light years. It would be even better to go down to 1 light year. The stars in the milky way have a total of 5*10^10 solar masses. At a resolution of 10^6 solar masses/per mass particle this means that all stars are modelled by only about mass particles. (There are 250 +/- 150 x 10^9 stars in the galaxy). Gas in the present galaxy simulation is very limited features. The real galaxy has a complex intergalactic medium with dense cold gas clouds, warmer and diffuse hot gas and ionized gas. In more finer grain calculations, these could be modelled much more realistically. The first galaxies were are of the order 100 light years across. With the current resolution, these cannot be modelled. Our Milky Way is about 50,000 light years across. 17

18 Science on MI Volume of the visible universe of the order of 10^31 cubic lightyears; the linear distance is of the order of 3x 10^10 light years. A run about 30 times bigger than the EAGLE run to investigate Verifying Einstein s Gravity laws scale out in volume keeping the same resolution. The evolution of the structure of the universe can calculated without a significant influence of the baryonic physics (less than 1%). This is only possible on larger scales where gravity of dark matter dominates the baryonic physics. The EAGLE run model a volume of about 10^25 lightyears, which is 1/1,000,000 of the real universe The largest objects have not yet been found/modelled. 18

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