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SDM Center Coupling Parallel IO with Remote Data Access Ekow Otoo, Arie Shoshani, Doron Rotem, and Alex Sim Lawrence Berkeley National Lab.

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Presentation on theme: "SDM Center Coupling Parallel IO with Remote Data Access Ekow Otoo, Arie Shoshani, Doron Rotem, and Alex Sim Lawrence Berkeley National Lab."— Presentation transcript:

1 SDM Center Coupling Parallel IO with Remote Data Access Ekow Otoo, Arie Shoshani, Doron Rotem, and Alex Sim Lawrence Berkeley National Lab.

2 SDM Center SciDAC All Hands Meeting October’052 Outline  Project objectives  Status and accomplishments  Usage in an application  Extensions  Other future work

3 SDM Center SciDAC All Hands Meeting October’053 Project Objectives Development of the MpiioSrm library  mpiiosrm.h libmpiiosrm.a, libmpiiosrm.so Allows near-online access to files on mass storage system (e.g., HPSS), from MPI applications on a linux cluster Access files from local and remote MSS with MPI applications. Applications on a Linux cluster having  Local parallel file system (PVFS2) and  HPSS as the remote mass storage system

4 SDM Center SciDAC All Hands Meeting October’054 Status – 1 Libmpiiosrm Module Dependencies MPI Applications MPI-IOSRM PVFS2GPFSUFSXFSOther BDBOther ADIO HPSS SAM Jasmin Castor High Level Access and Control Record Structured File Access Low Level File System Access pNetCDF HDF5 mpiiosrm

5 SDM Center SciDAC All Hands Meeting October’055 Status – 2 Main Functions Functions in libmpiiosrm.a: 1.MPI_File_srm_proxy_init(); 2.MPI_File_srm_open(); [in place of MPI_File_open()] 3.MPI_File_srm_close(); [in place of MPI_File_close()] 4.MPI_File_srm_delete(); [in place of MPI_File_delete()] 5.MPI_File_srm_proxy_destroy() Functions (2) and (4) take a file name as one of its parameters. Note name changes from last meeting.

6 SDM Center SciDAC All Hands Meeting October’056 Status – 3 Major Changes Since Last AHM Function names revised MPI_File_srm_proxy_init() function starts an SRM client as a detached thread.  Only the process with the proxy_rank spawns this thread. Use of PVFS2 srm_put() implemented for MPI_File_writes, i.e.,  Files can now migrate from PVFS2 to HPSS.  Still being tested.

7 SDM Center SciDAC All Hands Meeting October’057 Usage in an Application Steps for reading remote files:  Prepare an input file for the program A file containing the file names to be read from HPSS if not found in local parallel file system.  Initiate grid-proxy-init(); password, etc. User requires a grid certificate  Start a namesrver, drmServer and a trmServer  Compile the program to be executed  Run “mpiexec –n XX ” to access files given in the input file.

8 SDM Center SciDAC All Hands Meeting October’058 Usage in an Application Input file Layout Implicit layout of parallel files  Uses default PVFS configuration  Alternatively use keys of MPI-IO File hints  Specify only pairs of source and destination URLs Explicit layout specifies for each file:  Pairs of source and destination URL  Start_IO_Node  Striping factor  Striping unit

9 SDM Center SciDAC All Hands Meeting October’059 Usage in an Application Program Skeleton … MPI_Init(); … MPI_Info_create(); MPI_Info_set(); … MPI_File_srm_proxy_init(); … MPI_File_srm_open(); … … MPI_File_srm_close(); MPI_File_srm_proxy_destroy(); … MPI_Finalize();

10 SDM Center SciDAC All Hands Meeting October’0510 Extensions MPI Applications Srm- -Client HPSS SAM Jasmin Castor DRMTRM Srm-Server MPI-IO File Control Data vs File Access Multi-site Access Fault tolerance & Failsafe

11 SDM Center SciDAC All Hands Meeting October’0511 Extensions - 2 Control of Prefetching of File Bundles  Process files, one at a time, by availability  Process files, one at a time, by sequence  Process files by bundles Data Access instead of File Access only  Allow for file filtering at the source SRM  Use of select criteria and indexes to generate only relevant data

12 SDM Center SciDAC All Hands Meeting October’0512 Extension - 3 Multi-Site Access  Extend access to other MSS implementing SRM specs.  Access files from multiple sites in a session  Extensions to Xrootd servers Fault Tolerance and Failsafe Operations  Easier now with multiple srm_client proxies being spawn as threads Access from C++ and Fortran

13 SDM Center SciDAC All Hands Meeting October’0513 Other Future Work Parallel Multidimensional Index Schemes  Repertoire of high and low dimensional indexing methods for scientific applications High dimensions:  Bitmaps (John, Kurt, etc)  Others Low Dimensions (1 ~ 8)  R-Tree, Order Preserving Extendible hashing,  Multi-level Grid File  String Searching Methods – Suffix trees, PATRICIA, etc.

14 SDM Center SciDAC All Hands Meeting October’0514 Other Future Work - cont. Extendible Multidimensional Array Files  With extendibility in all dimensions, not just one  For both dense arrays and sparse arrays  Efficiently accessible in MPI with irregular distributed array method using map arrays.  Multi-resolution array files

15 SDM Center SciDAC All Hands Meeting October’0515 Other Proposed Activities cont. Array Mapping Method for k dims, A[N]…[N] Element Access Ops with E extensions and constant k. Storage Size, element size s, integer size w Conventional Method, Extendible in 1 dimension only O(1)w*k + s*N k Index Array, Extendible in any dimensions O(1)w*N*k*(k+1) + s*N k Index Array Tree, Extendible in any dimensions O(ln E)w*((k+6)*E - 3) + s*N k

16 SDM Center SciDAC All Hands Meeting October’0516 Example of Mapping Function i0i0 i1i < 35 5 < < >= Red-Black-Like Binary Tree

17 SDM Center SciDAC All Hands Meeting October’0517 The End


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