IPSJ SIG Technical Report Vol.2015-HPC-148 No /3/3 I/O 1 2 Gerofi Balazs 2 Guo-Yuan Lien netcdf API 2 File I/O Arbitr
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1 I/O Gerofi Balazs Guo-Yuan Lien netcdf API File I/O Arbitrator (FARB) MPI I/O.6 I/O File I/O Arbitrator Middleware for Real-Time Severe Weather Prediction System Tomoyuki Saito Yutaka Ishikawa Gerofi Balazs Guo-Yuan Lien Takemasa Miyoshi Shigenori Otsuka Hirofumi Tomita Seiya Nishizawa Abstract: A high-resolution -minute numerical weather prediction system, using weather observable data that is available every seconds, is being developed. In this system, -case ensemble simulations and data assimilation of results and observed data are performed every seconds to predict minute weather. Because the simulation and data assimilation programs are independently developed, data is exchanged via files. The middle-ware of a file I/O arbitrator, called FARB, is proposed to reduce the data exchange overhead between simulations and data assimilation. FARB extends the netcdf API, widely used as file I/O API in weather/climate applications, so that data is directory transferred between two jobs. FARB has been implemented using the MPI communication library. It performs more than three times faster than file I/O operations, and it reduces more than.6 second I/O processing time [] * * CREST i) ii) iii) I/O I/O RDMA (Remote Direct Memory Access) c 5 Information Processing Society of Japan
2 (a) (7.6MB/parameter) LES SCALE[] NHM LETKF [5] MPI Km x Km 8 6.7GiB 8 6 8Byte =.7GiB (b) File I/O FARB FARB netcdf API[] FARB FARB MPI netcdf POSIX I/O FARB.. (a) [].TiB ( (b)) MPI MPI MPI :N: SCALE I/O netcdf[] LETKF , 8, c 5 Information Processing Society of Japan
3 API nc put vara init nc get vara init nc startall nc waitall FARB API. (8 x) 8, x 8 x 8 x 8 x Byte = 89 KB 8 8 x 8 x 8 x 8 x 8 x 8 x 8 99 x 8. FARB netcdf API API MPI (Persistent Communication) API netcdf / API nc create nc open NC FARB NC FARB c 5 Information Processing Society of Japan
4 netcdf 6 FARB 5 netcdf FARB API netcdf 5 netcdf nc put vara nc get vara 6 FARB nc put vara init API nc startall API API nc waitall API 7 5 FARB nc get vara init API nc startall API API nc waitall API 8 FARB, 7 FARB 8 FARB LLC(Low Level Communication Library)[6] LLC RDMA one sided two sided LLC PC Infiniband FX Tofu FARB LLC FARB MPI c 5 Information Processing Society of Japan
5 Oakleaf-FX Specifications CPU (SPARC6 TM IXfx) Number of Cores 6 Clock.88 GHz Memory GB Memory Bandwidth 85 GB/s Interconnect (Tofu Interconnect) Bisection Bandwidth 5 GB/s Topology 6-D Mesh/Torus. 9 C(,,, X). C(E, N, M, X) C(E, N, M, X) E: N : M : X : C(, 8,, 89KB) C(,,, 89KB) x 8 C(,,, 89KB) C(, 8,, 89KB). FARB Oakleaf-FX FX FARB Oakleaf-FX 9 C(,,, X) where 6kiB X MiB S(KB) T(msec) unpack unpack distribute distribute comm comm read read Time (seconds) pack.7s pack write write.s.87s.s MPI FARB FILE NETCDF C(,,, 89KB) T = S/ S=89KB msec msec C(,,, 89KB) MPI FARB / API MPI FILE MPI netcdf netcdf I/O netcdf MPI.7. 8 c 5 Information Processing Society of Japan 5
6 C(, 8,, 89KB) FARB C(,,, 89KB) FILE netcdf FARB FX FARB Model Coupling Toolkit (MCT)[7], [8] OASIS [9] O-PALM [] FARB [] ( ) MCT OASIS O-PALM API FARB netcdf API ( ) regrid FARB (regrid) ( ) OASIS [9] O- PALM [] OASIS Driver Driver FARB 5. POSIX IO API FARB netcdf netcdf POSIX IO API[] POSIX IO API API POSIX IO API FARB POSIX IO API 6. FARB MPI FARB I/O I/O.87. FARB FARB I/O FARB CREST c 5 Information Processing Society of Japan 6
7 [] IEEE, T. and Group, T. O.: The Open Group Base Specifications Issue 7. [] Balazs, G. Vol. -HPC-(), pp. 6 (). [] Li, J., Liao, W.-k., Choudhary, A., Ross, R., Thakur, R., Gropp, W., Latham, R., Siegel, A., Gallagher, B. and Zingale, M.: Parallel netcdf: A High-performance Scientific I/O Interface, Supercomputing, ACM/IEEE Conference, IEEE, pp. 9 9 (online), available from choudhar/publications/liliaa.pdf (). [] Ushio, T., Wu, T. and Yoshida, S.: Review of Recent Progress in Lightning and Thunderstorm Detection Techniques in Asia, Atmospheric Research, Vol. 5, pp. 89 (5). [] Tomita, H.: SCALE-LES: Strategic development of large eddy simulation suitable to the future HPC, Solution of Partial Differential Equations on the Sphere (). [5] Takemasa, Miyoshi, Yamane, S. and Enomoto, T.: Localizing the Error Covariance by Physical Distances within a Local Ensemble Transform Kalman Filter (LETKF), Scientific Online Letters on the Atmosphere (SOLA), Vol. (7). [6] Balazs, G. Vol. -OS-5(), pp. 7 (). [7] Larson, J., Jacob, R. and Ong, E.: The Model Coupling Toolkit: A New Fortran9 Toolkit for Building Multiphysics Parallel Coupled Models, International Journal of High Performance Computing Applications, Vol. 9, No., pp (online), available from (5). [8] Jacob, R., Larson, J. and Ong, E.: M N Communication and Parallel Interpolation in Community Climate System Model Version Using the Model Coupling Toolkit, International Journal of High Performance Computing Applications, Vol. 9, No., pp. 9 7 (online), available from (5). [9] Redler, R., Valcke, S. and Ritzdorf, H.: OASIS a coupling software for next generation earth system modelling, Geoscientific Model Development, Vol., No., pp. 87 (). [] Piacentini, A., Morel, T., Thévenin, A. and Duchaine, F.: O-PALM: An Open Source Dynamic Parallel Coupler, Proceedings of the IV International Conference on Computational Methods for Coupled Problems in Science and Engineering Coupled Problems (). [] Valcke, S. Balaji, V. Craig, A. DeLuca, C. Dunlap, R. Ford, R. Jacob, R. Larson, J. RO Kuinghttons Riley, G. Coupling Technologies for Earth System Modelling, Geoscientific Model Development, (online), available from (). c 5 Information Processing Society of Japan 7
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