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NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Early Experiences with Datastar: A 10TF Power4 + Federation.

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Presentation on theme: "NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Early Experiences with Datastar: A 10TF Power4 + Federation."— Presentation transcript:

1 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Early Experiences with Datastar: A 10TF Power4 + Federation system Giri Chukkapalli SDSC

2 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Outline Datastar specs and setup Porting issues from BH to DS Initial setup difficulties and current DS status Initial science highlights Benchmark codes Results Conclusions

3 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER SDSC National NSF center with compute and data resources allocated freely through peer review process Transitioning from NPACI to CyberInfrastructure through Teragrid SDSC’s emphasis and contribution to the national CI initiative is Data intensive computing Acquired Datastar at the beginning of the year to replace Bluehorizon as the main compute engine

4 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER DataStar 10.1 TF, 1760 processors total way 1.7 GHz IBM p690s 2 nodes 64 GB memory for login and interactive use 6 nodes 128 GB memory for scientific computation 2 nodes 128 GB memory for database, DiscoveryLink 1 node 256 GB memory for batch scientific computation All p690s connected to Gigabit Ethernet with 10 GE coming soon way 1.5 GHz IBM p GB memory Batch scientific computation All nodes Federation switch attached All nodes SAN attached

5 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER SDSC DataStar 187 Total Nodes 11 p p (5) (171) (7)

6 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER SANergy Data Movement Orion Teragrid Network SAM-QFS DISK 2Gb 1Gb x 4 p690 Federation Switch SAN Switch Infrastructure 2Gb x 4 SANergy MDC Metadata operations, NFS Data operations SANergy client

7 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER ~400 Sun FC Disk Arrays (~4100 disks, 540 TB total) 32 FC Tape Drives Sun Fire 15K DataStar 176 P655s SAM-QFSETF DBSAN-GPFS 5 x Brocade (1408 2Gb ports) DataStar 11 P690s SANergy Client SANergy Server Force HPSS

8 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Porting issues We moved from default 32bit to default 64bit Fairly easy to port from BH to DS Mixed Fortran + C/C++ codes give some trouble

9 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Initial Setup and difficulties Substantial jump in weight, power and cooling load from BH to DS Memory and performance leak Fixed through NFS automounts Removing unnecessary daemons Problems related to GPFS over SAN IBM FC adapters, Brocade switches and SUN disks Loss of processors, memory, cache HMC issues Federation issues

10 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Large scale preproduction computing 100k to 200k hours per project Onuchic, UCSD: Study the folding kinetics of a beta hairpin at room temperature in explicit water Yeung **3 turbulence run Goodrich, BU - 3D calculation of the shearing and eruption of solar active regions on 201 x 251 x 251 mesh Richard Klein, UCB: dynamical evolution, gravitational collapse and fragmentation of large turbulent molecular cloud in the galaxy NREL, Cornell: Cellulose project, 1 million atom CHARMM simulation of protein interactions

11 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Performance analysis All codes are 64bit compiled Still some problems, so the results may not be the best All the runs are done on 1.5GHz P655s Communication performance NAS benchmarks CG, FT, LU and MG Applications ENZO and CHARMM

12 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Latency and Bandwidth comparison MPI Latencies (usec) Bandwidth (MB/s) BH DS BH DS Intra-node Inter-node

13 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Bisection bandwidth

14 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Barrier performance (Federation)

15 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER MPI broadcast performance

16 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Unusual Bcast behavior

17 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER MPI_Alltoall

18 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Understanding the raw MPI call performance (message size, No. of PEs) is useful to interpret real application MPI traces

19 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER GPFS performance Metadata performance File read, write performance MPI_tile_io, IOR, Pallas MPI I/O, MDTEST Each processor writes one rectangular tile 16 bytes per element each tile is 1000 x 1000 elements 1024PE run writes 32X32 tiles: 16GB file

20 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER GPFS Performance (MPI I/O)

21 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER NAS Benchmarks: Strong scaling

22 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER NAS benchmarks: strong scaling

23 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER NAS benchmarks: strong scaling DS %peak is more flatter than BH owing to the better bandwidth Initially %peak increases due to cache effects and then drops due to communication over heads Sparse matrix codes give the worst %peak and dense matrix codes gives the best %peak

24 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Application benchmarks ENZO: Astrophysics code Consumes 1 Million hours on Datastar CHARMM: MD chemistry code Both are Community codes

25 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Original Enzo performance on DS,BG/L

26 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER Improved Enzo performance on BH and DS

27 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER CHARMM performance 64bit compilation Rarely been run beyond a single node Previously it didn’t scale beyond 32 PEs Short hand written FFTs need to be optimized further Initiated a tuning project with the developers targeting large scale simulations

28 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER summary Datastar is rapidly becoming stable with good performance. Switch routing issues remaining

29 NATIONAL PARTNERSHIP FOR ADVANCED COMPUTATIONAL INFRASTRUCTURE SAN DIEGO SUPERCOMPUTER CENTER


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