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Front cover
by Megan Gilge
IBM System Blue Gene Solution Blue Gene/Q Application Development
Front cover
Notices
Trademarks
Preface
Author
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Summary of changes
June 2013, Second Edition
Chapter 1. System overview
1.1 Blue Gene/Q environment overview
1.2 Blue Gene/Q hardware overview
1.3 Blue Gene/Q software overview
1.3.1 System administration and management
1.3.2 Compute Node Kernel and services
1.3.3 I/O node kernel and services
1.3.4 Message Passing Interface
1.3.5 Compilers
1.3.6 Application development and debugging
Chapter 2 Kernel functionality
2.1 Compute Node Kernel
2.1.1 Stateless compute nodes
2.1.2 Firmware
2.2 Role of the I/O node kernel
Chapter 3. Processes
3.1 Importance of process count
3.2 Process creation
3.3 Processes per node
3.4 Determining how many processes per node to use
3.5 Specifying process count
3.6 Support for 64-bit applications
3.7 Object identifiers
3.7.1 Process identifier
3.7.2 Thread identifier
3.7.3 Thread group identifier
3.7.4 T coordinate
3.8 Sub-node jobs
3.9 Threading overview
3.9.1 Hardware thread over-commitment
3.10 Thread scheduler
3.10.1 Thread preemption
3.10.2 Thread yield
3.10.3 Round-robin dispatch
3.11 Thread affinity
3.11.1 Breadth-first assignment
3.11.2 Depth-first assignment
3.11.3 Thread affinity control
3.11.4 Setting affinity with the pthread attribute
3.11.5 Setting affinity with the system call
3.11.6 Extended thread affinity control
3.12 Thread priority
3.12.1 Setting priority through the pthread attribute
3.12.2 Explicit setting of priority
3.12.3 Hardware thread priority
Chapter 4. Memory
4.1 Memory system overview
4.1.1 L1 prefetch cache overview
4.1.2 L2 cache functional overview
4.1.3 Boot eDRAM overview
4.2 Memory management
4.3 Memory protection
4.4 Shared memory
4.5 Persistent memory
4.6 Compute node ramdisk
4.7 Support for the /proc file system
4.8 L1P prefetcher
4.8.1 Linear stream prefetcher overview
4.8.2 Perfect prefetcher overview
4.8.3 L1P prefetcher API descriptions
4.8.4 Performance considerations
4.9 L2 atomic operations
4.10 Speculative execution
4.11 Support for dynamic linking
4.12 Transactional memory
Chapter 5. Compute Node Kernel interfaces
5.1 Lightweight principles
5.2 Kernel access
5.2.1 Application programming interfaces
5.2.2 System programming interface
5.3 System calls
Chapter 6. Parallel paradigms
6.1 Programming model
6.2 Blue Gene/Q MPI implementation
6.2.1 High-performance network for efficient parallel execution
6.2.2 Forcing MPI to allocate too much memory
6.2.3 Not waiting for the MPI_Test function
6.2.4 Flooding the network with messages
6.2.5 Deadlocking the system
6.2.6 Violating MPI buffer ownership rules
6.2.7 Buffer alignment sensitivity
6.3 Blue Gene/Q MPI extensions
6.3.1 Changing class-route usage at run time
6.3.2 Determining hardware properties
6.4 MPI functions
6.5 Compiling MPI programs on the Blue Gene/Q system
6.6 OpenMP
6.6.1 OpenMP implementation for Blue Gene/Q
6.7 Multiple Program, Multiple Data
Chapter 7. Developing applications with Blue Gene/Q compilers
7.1 Programming environment overview
7.2 Compilers for the Blue Gene/Q system
7.2.1 IBM XL compilers
7.2.2 GNU Compiler Collection
7.2.3 Python interpreter
7.2.4 Toolchain tools
7.3 Compiling and linking applications on the Blue Gene/Q system
7.4 Compiler options specific to the Blue Gene/Q system
7.4.1 Options for the Blue Gene/Q system
7.4.2 Unsupported compiler options
7.5 Support for pthreads and OpenMP
7.5.1 Thread stack size for the Blue Gene/Q system
7.6 Creating libraries on the Blue Gene/Q system
7.7 Running dynamically linked applications on the Blue Gene/Q system
7.7.1 Creating a program
7.7.2 Creating a shared library
7.7.3 Running a Blue Gene/Q dynamically linked program on a front end node
7.7.4 Running a dynamically linked program on the Blue Gene/Q system
7.7.5 Tools for dynamic linking
7.8 Mathematical Acceleration Subsystem Libraries
7.9 Engineering and Scientific Subroutine Libraries
7.10 Cross-compilation on the Blue Gene/Q system
7.10.1 Configuring and building on an I/O node used as a front end node
7.10.2 Using implicit program launching from a front end node
7.11 Python support
7.11.1 Using the Python interpreter in a cross-compiled environment
7.11.2 Running the Python interpreter on the Blue Gene/Q system
7.12 Using the QPX floating‑point unit
7.12.1 Using SIMD instructions in applications
Chapter 8. Running and debugging applications
8.1 Running applications
8.1.1 IBM LoadLeveler
8.2 Debugging applications
8.2.1 General debugging architecture
8.2.2 GNU Project Debugger
8.2.3 Coreprocessor debugger
8.2.4 The addr2line utility
8.3 What to do when a job fails
8.4 Debugging jobs
8.4.1 The snapbug tool
8.4.2 The Coreprocessor tool
Appendix A. Mapping
Mapping overview
General guidance
Appendix B. Blue Gene/Q personality
Personality of Blue Gene/Q nodes
Examples of retrieving Blue Gene/Q personality information
Appendix C. PAMI and MPI header files and libraries
Blue Gene/Q applications
Appendix D. MPI and CNK environment variables
Message Passing Interface environment variables
Compute Node Kernel environment variables
Setting environment variables
Appendix E. Using GNU profiling
Using the Blue Gene/Q gmon tool
Profiling with the GNU toolchain
Appendix F. Hardware performance counters
Blue Gene Hardware Performance Monitoring API
Performance Application Programming Interface
Appendix G. Requirements for C++ programming in a failover environment
Related publications
IBM Redbooks
Other publications
Online resources
How to get IBM Redbooks
Help from IBM
References
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Note: Before using this information and the product it supports, read the information in “Notices” on page vii.
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