Light-Weight Parallel I/O Analysis at Scale

Input/output (I/O) operations can represent a significant proportion of the run-time when large scientific applications are run in parallel. Although there have been advances in the form of file-format libraries, file system design and I/O hardware, a growing divergence exists between the performance of parallel file systems and compute processing rates. In this paper we utilise RIOT, an input/output tracing toolkit being developed at the University of Warwick, to assess the performance of three standard industry I/O benchmarks and mini-applications. We present a case study demonstrating the tracing and analysis capabilities of RIOT at scale, using MPI-IO, Parallel HDF-5 and MPI-IO augmented with the Parallel Log-structured File System (PLFS) middle-ware being developed by the Los Alamos National Laboratory.

[1]  Jianwei Li,et al.  Parallel netCDF: A High-Performance Scientific I/O Interface , 2003, ACM/IEEE SC 2003 Conference (SC'03).

[2]  M. Polte,et al.  Fast log-based concurrent writing of checkpoints , 2008, 2008 3rd Petascale Data Storage Workshop.

[3]  William Gropp,et al.  Implementing MPI on the BlueGene/L Supercomputer , 2004, Euro-Par.

[4]  Marco Danelutto,et al.  Euro-Par 2004 Parallel Processing , 2004, Lecture Notes in Computer Science.

[5]  P. Nowoczynski,et al.  Zest Checkpoint storage system for large supercomputers , 2008, 2008 3rd Petascale Data Storage Workshop.

[6]  Nicholas J. Wright,et al.  Effective Performance Measurement at Petascale Using IPM , 2010, 2010 IEEE 16th International Conference on Parallel and Distributed Systems.

[7]  David Kaeli,et al.  Source level transformations to improve I/O data partitioning , 2003, SNAPI '03.

[8]  Leonid Oliker,et al.  Parallel I/O performance: From events to ensembles , 2010, 2010 IEEE International Symposium on Parallel & Distributed Processing (IPDPS).

[9]  John Shalf,et al.  Characterizing and predicting the I/O performance of HPC applications using a parameterized synthetic benchmark , 2008, 2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis.

[10]  David H. Bailey,et al.  The Nas Parallel Benchmarks , 1991, Int. J. High Perform. Comput. Appl..

[11]  Karsten Schwan,et al.  ...and eat it too: high read performance in write-optimized HPC I/O middleware file formats , 2009, PDSW '09.

[12]  Message P Forum,et al.  MPI: A Message-Passing Interface Standard , 1994 .

[13]  Message Passing Interface Forum.  MPI: A message - passing interface standard , 1994 .

[14]  John Shalf,et al.  Using IOR to analyze the I/O Performance for HPC Platforms , 2007 .

[15]  Robert Latham,et al.  24/7 Characterization of petascale I/O workloads , 2009, 2009 IEEE International Conference on Cluster Computing and Workshops.

[16]  David R. Kaeli,et al.  Profile-guided I/O partitioning , 2003, ICS '03.

[17]  Jack Dongarra,et al.  Recent Advances in Parallel Virtual Machine and Message Passing Interface, 15th European PVM/MPI Users' Group Meeting, Dublin, Ireland, September 7-10, 2008. Proceedings , 2008, PVM/MPI.

[18]  Michael Zingale,et al.  Flash code: studying astrophysical thermonuclear flashes , 2000, Comput. Sci. Eng..

[19]  William Gropp,et al.  MPICH2: A New Start for MPI Implementations , 2002, PVM/MPI.

[20]  B. Fryxell,et al.  FLASH: An Adaptive Mesh Hydrodynamics Code for Modeling Astrophysical Thermonuclear Flashes , 2000 .

[21]  Russ Rew,et al.  NetCDF: an interface for scientific data access , 1990, IEEE Computer Graphics and Applications.

[22]  John Bent,et al.  PLFS: a checkpoint filesystem for parallel applications , 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis.

[23]  Stephen A. Jarvis,et al.  RIOT - A Parallel Input/Output Tracer , 2011 .

[24]  George Bosilca,et al.  Open MPI: Goals, Concept, and Design of a Next Generation MPI Implementation , 2004, PVM/MPI.

[25]  B. Wolman,et al.  IOBENCH: a system independent IO benchmark , 1989, CARN.

[26]  Rajeev Thakur,et al.  Users guide for ROMIO: A high-performance, portable MPI-IO implementation , 1997 .