Kernel-level Measurement for Integrated

Parallel Performance Views

KTAU: Kernel - TAU

Aroon Nataraj

Performance Research LabUniversity of Oregon

KTAU: Outline Introduction Motivations Objectives Architecture / Implementation Choices Experimentation – the performance views Perturbation Study Future work and directions Acknowledgements

Introduction : ZeptoOS and TAU DOE OS/RTS for Extreme Scale Scientific

Computation(Fastos) Conduct OS research to provide effective OS/Runtime for

petascale systems

ZeptoOS (under Fastos) Scalable components for petascale architectures Joint project Argonne National Lab and University of Oregon ANL: Putting light-weight kernel (based on Linux) on BG/L and

other platforms (XT3)

University of Oregon Kernel performance monitoring, tuning KTAU

Integration of TAU infrastructure with Linux Kernel Integration with ZeptoOS, installation on BG/L Port to 32-bit and 64-bit Linux platforms

KTAU: Motivation Application Performance

user-level execution performance + OS-level operations performance

Domains: Time and Hardware Perf. Metrics

PAPI (Performance Application Programming Interface) Exposes virtualized hardware counters

TAU (Tuning and Analysis Utility) Measures a lot of interesting user-level entities: parallel

application, MPI, libraries … Time domain Uses PAPI to correlate counter information with source

KTAU: Motivation

Simple Parallel Model

KTAU: Motivation

Simple Parallel Model - Scale

As HPC systems continue to scale to larger processor counts Application performance more sensitive

New OS factors become performance bottlenecks (E.g. [Petrini’03, Jones’03, other works…])

Isolating these system-level issues as bottlenecks is non-trivial

Comprehensive performance understanding Observation of all performance factors

Relative contributions and interrelationship: can we correlate?

KTAU: Motivation

Effects of Scale

KTAU: MotivationProgram - OS Interactions Program OS Interactions - Direct vs. Indirect Entry Points

Direct - Applications invoke the OS for certain services Syscalls (and internal OS routines called directly from syscalls)

Indirect - OS takes actions without explicit invocation by application

Preemptive Scheduling (HW) Interrupt handling OS-background activity (keeping track of time and timers, bottom-

half handling, etc)

Indirect interactions can occur at any OS entry (not just when entering through Syscalls)

KTAU: Motivation

Program - OS Interactions

KTAU: Motivation

Program - OS Interactions Direct Interactions easier to handle

Synchronous with user-code and in process-context

Indirect Interactions more difficult to handle Usually asynchronous and in interrupt-context: Hard to measure

and harder to correlate/integrate with app. measurements

Indirect interactions may be unrelated to current task E.g. Kernel-level packet processing for another process But related in terms of time to current process

KTAU: Motivation

Program - OS Interactions(Partial)

KTAU: Motivation Kernel-wide vs. Process-centric Kernel-wide - Aggregate kernel activity of all active

processes in system Understand overall OS behavior, identify and remove kernel

hot spots. Cannot show what parts of app. spend time in OS and why

Process-centric perspective - OS performance within context of a specific application’s execution Virtualization and Mapping performance to process Interactions between programs, daemons, and system services Tune OS for specific workload or tune application to better

conform to OS config. Expose real source of performance problems (in the OS or the

application)

KTAU: Motivation Kernel-wide vs. Process-centric

KTAU: Motivation Existing Approaches User-space Only measurement tools

Many tools only work at user-level and cannot observe system-level performance influences

Kernel-level Only measurement tools Most only provide the kernel-wide perspective – lack proper

mapping/virtualization Some provide process-centric views but cannot integrate OS and

user-level measurements Combined or Integrated User/Kernel Measurement Tools

A few powerful tools allow fine-grained measurement and correlation of kernel and user-level performance

Typically these focus only on Direct OS interactions. Indirect interactions not merged.

Using Combinations of above tools Without better integration, does not allow fine-grained correlation

between OS and App. Many kernel tools do not explicitly recognize Parallel workloads

(e.g. MPI ranks) Need an integrated approach to parallel perf. observation, analyses

KTAU: High-Level Objectives

Support low-overhead OS performance measurement at multiple levels of function and detail

Provide both kernel-wide and process-centric perspectives of OS performance

Merge user-level and kernel-level performance information across all program-OS interactions

Provide online information and the ability to function without a daemon where possible

Support both profiling and tracing for kernel-wide and process-centric views in parallel systems

Leverage existing parallel performance analysis tools Support for observing, collecting and analyzing parallel data

KTAU: Outline Introduction Motivations Objectives Architecture / Implementation Choices Experimentation – the performance views Perturbation Study ZeptoOS – KTAU on Blue Gene / L Future work and directions Acknowledgements

KTAU Architecture

KTAU: Arch. / Impl. Choices Instrumentation

Static Source instrumentation Macro Map-ID: Map block of code and process-context to

unique index (dense id-space) – easy array lookup. Macro Start, Stop – provide the mapping index and process-

context is implicit Measurement

Differentiate between ‘local/self’ and ‘inter-context’ access. HPC codes primarily use ‘self’.

Store performance data in PCB (task_struct) Integrating Kernel/User Performance state

Don’t assume synchronous kernel-entry or process-context Have to use memory mapping between kernel and appl. State Pinning shared state in memory Kernel Call Groups – program-OS interactions summary

Analyses and Visualization – Use TAU facilities

KTAU: Controlled Experiments Controlled Experiments

Exercise kernel in controlled fashion Check if KTAU produces the expected correct and meaningful

views

Test machines Neutron: 4-CPU Intel P3 Xeon 550MHz, 1GB RAM, Linux

2.6.14.3(ktau) Neuronic: 16-node 2-CPU Intel P4 Xeon 2.8GHz, 2GB RAM/node,

Redhat Enterprise Linux 2.4(ktau)

Benchmarks NPB LU application [NPB]

Simulated computational fluid dynamics (CFD) application. A regular-sparse, block lower and upper triangular system solution.

LMBENCH [LMBENCH]

Suite of micro-benchmarks exercising Linux kernel A few others not shown (e.g. SKAMPI)

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KTAU: Controlled Examples continued…Tracing

Merging App / OS Traces

MPI_Send OS Routines

Fine-grained Tracing

Shows detail inside interrupts and bottom halves

Using VAMPIR Trace Visualization [VAMPIR]

KTAU: Controlled Examples continued…Tracing

Correlating CIOD and RPC-IOD Activity

KTAU: Larger-Scale Runs Run parallel benchmarks on larger-scale (128 dual-cpu nodes)

Identify (and remove) system-level performance issues Understand perturbation overheads introduced by KTAU

NPB benchmark: LU Application [NPB]

Simulated computational fluid dynamics (CFD) application. A regular-sparse, block lower and upper triangular system solution.

ASC benchmark: Sweep3D [Sweep3d]

Solves a 3-D, time-independent, neutron particle transport equation on an orthogonal mesh.

Test machine: Chiba-City Linux cluster (ANL) 128 dual-CPU Pentium III, 450MHz, 512MB RAM/node, Linux

2.6.14.2 (ktau) kernel, connected by Ethernet

KTAU: Larger-Scale Runs Experienced problems on Chiba by chance Initially ran NPB-LU and Sweep3D codes on 128x1

configuration Then ran on 64x2 configuration Extreme performance hit (72% slower!) with the

64x2 runs Used KTAU views to identify and solve issues

iteratively Eventually brought performance gap to 13% for LU

and 9% for Sweep.

KTAU: Larger-scale Runs

Two ranks - relatively very low MPI_Recv() time.

Two ranks - MPI_Recv() diff. from Mean in

OS-SCHED.

User-level MPI_Recv MPI_Recv OS Interactions

KTAU: Larger-scale Runs

Two ranks have very low voluntary

scheduling durations.

(Same) Two ranks have very large

preemptive scheduling.

Voluntary Scheduling Preemptive Scheduling

Note: x-axis log scale

KTAU Larger-scale Runs

NPB LU processes PID:4066, PID:4068

active. No other significant activity!

Why the Pre-emption?

64x2 Pinned: Interrupt Activity Bimodal across MPI ranks.

ccn10 Node-level View Interrupt Activity

KTAU Larger-scale Runs

Many more OS-TCP CallsApprox. 100% longer

100% More background OS-TCP activity in Compute

phase.More imbalance!

Use ‘Merged’ performance data to identify imbalance.Why does purely compute bound region have lots of I/O?

TCP within Compute : Time TCP within Compute : Calls

KTAU Larger-scale Runs

OS-TCP in SMP Costlier

IRQ-Balancing blindly distributes interrupts and bottom-halves. E.g.: Handling TCP related BH in CPU-0 for LU-process on CPU-1

Cache issues! [COMSWARE]

Cost / Call of OS-level TCP

KTAU Perturbation Study Five different Configurations

Base: Vanilla kernel, un-instrumented benchmark Ktau-Off: Kernel patched with Ktau and instrumentations compiled-

in. But all instrumentations turned Off (boot-time control) Prof-All: All kernel instrumentations turned On. Prof-Sched: Only scheduler subssystem’s instrumentations turned

on Prof-All+TAU: ProfAll, but also with user-level Tau instrumentation

enabled

NPB LU application benchmark: 16 nodes, 5 different configurations, Mean over 5 runs each

ASC Sweep3D: 128 nodes, Base and Prof-All+TAU, Mean over 5 runs each.

Test machine: Chiba-City ANL

KTAU Perturbation Study

Disabled probe effect. Single

instrumentation very cheap.

E.g. Scheduling.

Complete Integrated Profiling Cost under

3% on Avg. and as low as 1.58%.

Sweep3d on 128 Nodes

Base ProfAll+TAU

Elapsed Time: 368.25 369.9

% Avg Slow.: 0.49%

KTAU: Outline Introduction Motivations Objectives Architecture / Implementation Choices Experimentation – the performance views Perturbation Study Future work and directions Acknowledgements

KTAU: Future Work Dynamic measurement control - enable/disable events w/o

recompilation or reboot Improve performance data sources that KTAU can access - E.g.

PAPI

Improve integration with TAU’s user-space capabilities to provide even better correlation of user and kernel performance information full callpaths, phase-based profiling, merged user/kernel traces

Integration of Tau, Ktau with Supermon (possibly MRNet?), TAUg (next)

Porting efforts: IA-64, PPC-64 and AMD Opteron

ZeptoOS: Planned characterization efforts BGL I/O node Dynamically adaptive kernels

Acknowledgements

Prof. Allen D Malony

Dr. Sameer Shende, Senior Scientist

Alan Morris, Senior Software Engineer, PRL

Suravee Suthikulpanit , MS Student (Graduated)

Support Acknowledgements

Department of Energy’s Office of Science (contract no. DE-FG02-05ER25663) and

National Science Foundation (grant no. NSF CCF 0444475)

References

[petrini’03]:F. Petrini, D. J. Kerbyson, and S. Pakin, “The case of the missing supercomputer performance: Achieving optimal performance on the 8,192 processors of asci q,” in SC ’03

[jones’03]: T. Jones and et al., “Improving the scalability of parallel jobs by adding parallel awareness to the operating system,” in SC ’03

[PAPI]: S. Browne et al., “A Portable Programming Interface for Performance Evaluation on Modern Processors”. The International Journal of High Performance Computing Applications, 14(3):189--204, Fall 2000.

[VAMPIR]: W. E. Nagel et. al., “VAMPIR: Visualization and analysis of MPI resources,” Supercomputer, vol. 12, no. 1, pp. 69–80, 1996.

[ZeptoOS]: “ZeptoOS: The small linux for big computers,” http://www.mcs.anl.gov/zeptoos/

[NPB]: D.H. Bailey et. al., “The nas parallel benchmarks,” The International Journal of Supercomputer Applications, vol. 5, no. 3, pp. 63–73, Fall 1991.

References

[Sweep3d]: A. Hoise et. al., “A general predictive performance model for wavefront algorithms on clusters of SMPs,” in International Conference on Parallel Processing, 2000

[LMBENCH]: L. W. McVoy and C. Staelin, “lmbench: Portable tools for performance analysis,” in USENIX Annual Technical Conference, 1996, pp. 279–294

[TAU]: “TAU: Tuning and Analysis Utilities,” http://www.cs.uoregon.edu/research/paracomp/tau/

[KTAU-BGL]: A. Nataraj, A. Malony, A. Morris, and S. Shende, “Early experiences with ktau on the ibm bg/l,” in EuroPar’06, European Conference on Parallel Processing, 2006.

[KTAU]: A. Nataraj et al., “Kernel-Level Measurement for Integrated Parallel Performance Views: the KTAU Project” (under submission)