The document discusses a novel approach for efficient support of non-contiguous I/O in high-performance computing (HPC) that guarantees atomicity while improving throughput. It introduces a dedicated interface using versioning and shadowing techniques, avoiding traditional locking methods, to manage concurrent access effectively. Experimental results demonstrate superior performance compared to locking-based approaches, highlighting the potential for integration with existing MPI-I/O middleware and parallel file systems.

1. Efficient Support for MPI-I/O Atomicity
Based on Versioning
Viet-Trung Tran1, Bogdan Nicolae2, Gabriel Antoniu2, Luc Bougé1
KerData Research Team
1
ENS Cachan, IRISA, France
2
INRIA, IRISA, Rennes, France
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2. Context: Data Intensive Large-scale HPC
Simulations
 Large-scale simulations of natural phenomena
 Highly parallel platform
 I/O challenges
 High I/O performance
 Huge data sizes (~PB)
 Highly concurrency
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3. Data Access Pattern
 Spatial splitting in parallelization
 Ghost cells
 Application data model vs storage model

•Sequence of bytes
 Concurrent overlapping non-contiguous I/O
 Require atomicity guarantees
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4. Goal:
High throughput non-contiguous I/O
under atomicity guarantees
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5. State of The Art
 Locking-based approaches to ensure atomicity
 3 level of implementations
 Application
 MPI-I/O Application (Visit, Tornado simulation)
 Storage
Data model (HDF5, NetCDF)
MPI-IO middleware
Parallel file systems (PVFS, GPFS, Lustre)
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6. Our Approach
 Dedicated interface for atomic non-contiguous I/O
 Provide atomicity guarantees at storage level
 No need to translate MPI consistency to storage consistency model
 Shadowing as a key to enhance data access under concurrency
 No locking
 Concurrent overlapped writes are allowed
 Atomicity guarantees
 Data striping
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7. Building Block: BlobSeer
 A KerData project (blobseer.gforge.inria.fr)
 Data striping
 Versioning-based concurrency control
 Distributed metadata management
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8. Building Block: BlobSeer (continued)
 Distributed metadata management
 Organized as a segment tree [0, 8]
 Distributed over a DHT
[0, 4] [0, 4] [4, 4]
 Two phases I/O Metadata trees
 Data access
[0, 2] [0, 2] [2, 2] [2, 2] [4, 2]
 Metadata access
[0, 1] [1, 1] [1, 1] [2, 1] [2, 1] [3, 1] [4, 1]
Blob
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9. Proposal for A Non-contiguous,
Versioning Oriented Access Interface
 Non-contiguous Write
 vw = NONCONT_WRITE(id, buffers[], offsets[], sizes[])
 Non-contiguous Read
 NONCONT_READ(id, v, buffers[], offsets[], sizes[])
 Challenges
 Noncontiguous I/O must be atomic
 Efficient under concurrency
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10. 1st challenge: Non-contiguous I/O Must Be Atomic
 Shadowing techniques
 Isolate non-contiguous update into one single consistent snapshot
 Done at metadata level
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11. 2nd challenge: Efficiency Under Concurrent Accesses
 Advantages of Shadowing
Our Locking-
 Parallel data I/O phases approach based
approach
 Parallel Metadata I/O
Overlapping Parallel No
phases ? Data I/O
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12. Minimize Ordering Overhead
 Ordering is done at metadata level
 Arbitrary order
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13. Avoid Synchronization for Concurrent Segment Tree
Generation
 Delegate the generation of shadowing tree to client side
 Shadowing tree are generated in parallel thank to predictable
metadata node ID
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14. Lazy Evaluation During Border Node Calculation
 Building metadata tree in bottom-up fashion
 Optimized for non-contiguous pattern
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15. Sumary: Overlapping Non-contiguous I/O
Our approach Locking-based
approaches
Data I/O phases Parallel Serialization
Metadata I/O phases Close to parallel thanks to Serialization
1- Arbitrary ordering
2- Metadata level’s ordering
3- Client side’s shadowing in parallel
4- Lazy evaluation
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16. Leveraging Our Versioning-Oriented Interface in
Parallel I/O Stack
Application (Visit, Tornado simulation)
Data model (HDF5, NetCDF)
MPI-IO middleware
Storage optimized for atomic MPI-I/O
Integrating BlobSeer to MPI-I/O middleware is straightforward
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17. Experimental Evaluation
• Our machines: Reservation on Grid'5000 platform
– 80 nodes
– Pentium-4 CPU@2.6Ghz, 4GB RAM, Gigabit Ethernet
– Measured bandwidth: 117.5 MB/s for MTU=1500B
• 3 sets of experiments:
– Scalability of non-contiguous I/O
– Scalability under concurrency
– MPI-tile-I/O
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18. Scalability of Non-contiguous I/O
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19. Scalability Under Concurrency
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20. MPI-tile-I/O: 128 KB Chunk Size
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21. MPI-tile-IO: 1MB Chunk Size
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22. Conclusion
• Experiments show promising results
• We outperform locking-based approaches
• Key features: shadowing, dedicated API for atomic non-contiguous I/O
• Comparison to Lustre file system
• High throughput non-contiguous I/O under atomicity guarantees
• Future work
• Exposing versioning-interface to MPI-I/O applications
• Potential improvement for producer-consumer workflow
• Pyramid: A large-scale array-oriented active storage system
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23. Context
Application (Visit, Tornado simulation)
Data model (HDF5, NetCDF)
MPI-IO middleware
Parallel file systems
•Parallel file systems do not provide atomic non-contiguous I/O interface
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24. 2nd challenge: Efficiency under concurrent
accesses
 Minimize ordering overhead
 Ordering is done at metadata level
 Arbitrary order
 Avoid synchronization for concurrent segment tree generation
 Delegate the generation of shadowing tree to client side
 Shadowing tree are generated in parallel
 Lazy evaluation during border node calculation
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