Difference between revisions of "User:Barre/ITK Registration Optimization"
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===Suggested Benchmarks=== | ===Suggested Benchmarks=== | ||
| − | + | All tests should cout two values | |
| − | + | * the time required | |
| − | time | + | * an measure of the error (0 = no error; 1 = 100% error) |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
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| − | + | Tests to be developed and suggested parameter settings | |
| − | < | + | * LinearInterpTest <numThreads> <dimSize> <factor> [<outputImage>] |
| − | + | ** NumThreads = 1, 2, 4, and #OfCoresIf>4 (for every platform) | |
| − | + | ** DimSize = 100, 200 (meaning: 100^3 and 200^3 images) | |
| − | + | ** Factor = 1.5, 2, 3 (thereby producing up to 600^3 images) | |
| − | + | ** = 24 tests (approx time on dual-core for all tests = 1.5 minutes) | |
| − | + | * BSplineInterpTest <numThreads> <dimSize> <factor> [<outputImage>] | |
| − | + | ** NumThreads = 1, 2, 4, and #OfCoresIf>4 (for every platform) | |
| − | < | + | ** DimSize = 100, 200 (meaning: 100^3 and 200^3 images) |
| + | ** Factor = 1.5, 2, 3 (thereby producing up to 600^3 images) | ||
| + | ** = 24 tests (approx time on dual-core for all tests = ??) | ||
| + | * SincInterpTest <numThreads> <dimSize> <factor> [<outputImage>] | ||
| + | * BSplineTransformLinearInterpTest <numThreads> <dimSize> <nodes> [<outputImage>] | ||
| + | * MeanReciprocalSquaredDifferenceMetricTest | ||
| + | * MeanSquaresMetricTest | ||
| + | * NormalizedCorreltationMetricTest | ||
| + | * GradientDifferentMetricTest | ||
| + | * MattesMutualInformationMetricTest | ||
| + | * MutualInformationMetricTest | ||
| + | * NormalizedMutualInformationMetricTest | ||
| + | * MutualInformationHistogramMetricTest | ||
| + | * NormaalizedMutualInformationHistogramMetricTest | ||
===Potential Issues with Timing=== | ===Potential Issues with Timing=== | ||
Revision as of 14:04, 29 March 2007
ITK Registration Optimization (BW NAC) Project
My (Sebastien Barre) notes so far. Once the dust settles, the relevant sections will be moved to the project pages listed below.
Project
The ultimate specific goal is B-Spline registration optimization for linux and windows on multi-core and multi-processor, shared memory machines. [...] Also, setup tools and a reporting mechanism for ITK speed to be monitored and reported by us and others. BWH is the driving force behind this work.
- Non Rigid Registration at NA-MIC
- ITK Registration Optimization at NA-MIC
- Slicer3:Performance Analysis at NA-MIC
- User:Barre/ITK Registration Optimization at NA-MIC (this page)
Contacts
Quick Links
- Google Performance Tools
- kcachegrind, The KCachegrind Handbook, Running Kcachegrind on Mac OSX 10.4
- Also check my BW-NAC Google Notebook for fresher links.
Source Code
Testing Data
- NAMIC: Deformable registration speed optimization (DSpace @ Insight-Journal)
Suggested Benchmarks
All tests should cout two values
- the time required
- an measure of the error (0 = no error; 1 = 100% error)
Tests to be developed and suggested parameter settings
- LinearInterpTest <numThreads> <dimSize> <factor> [<outputImage>]
- NumThreads = 1, 2, 4, and #OfCoresIf>4 (for every platform)
- DimSize = 100, 200 (meaning: 100^3 and 200^3 images)
- Factor = 1.5, 2, 3 (thereby producing up to 600^3 images)
- = 24 tests (approx time on dual-core for all tests = 1.5 minutes)
- BSplineInterpTest <numThreads> <dimSize> <factor> [<outputImage>]
- NumThreads = 1, 2, 4, and #OfCoresIf>4 (for every platform)
- DimSize = 100, 200 (meaning: 100^3 and 200^3 images)
- Factor = 1.5, 2, 3 (thereby producing up to 600^3 images)
- = 24 tests (approx time on dual-core for all tests = ??)
- SincInterpTest <numThreads> <dimSize> <factor> [<outputImage>]
- BSplineTransformLinearInterpTest <numThreads> <dimSize> <nodes> [<outputImage>]
- MeanReciprocalSquaredDifferenceMetricTest
- MeanSquaresMetricTest
- NormalizedCorreltationMetricTest
- GradientDifferentMetricTest
- MattesMutualInformationMetricTest
- MutualInformationMetricTest
- NormalizedMutualInformationMetricTest
- MutualInformationHistogramMetricTest
- NormaalizedMutualInformationHistogramMetricTest
Potential Issues with Timing
- Repository was updated so that it can compile on Unix.
__rtdsc()
CallMonWin includes <intrin.h> to call __rdtsc(), a header that does not exist in Microsoft compilers prior to Visual Studio 8/2005. It seems however that one can call __rdtsc() directly from assembly:
- GameDev.net forum, see third comment by Evil Steve (!)
- CPUID for x64 Platforms and Microsoft Visual Studio* .NET 2005
- High Resolution Elapsed Timer
A few articles advises against the use of __rdtsc(), especially in a multicore/multithread context:
The suggested alternative is to use Performance Counters. Hardware counters are actually not an OS feature per se, but a CPU feature that has been around for some time. They provide high-resolution timers that can be used to monitor a wide range of resources:
The issue remains on how to access those counters in a cross-platform way:
- PAPI: "The Performance API (PAPI) project specifies a standard API for accessing hardware performance counters".
Stephen/Christian reported that Dual Core CPUs were not supported, but it seems from the release notes for PAPI 3.5 (2006-11-09) that both Intel Core2Duo and Pentium D (i.e. dual core) are indeed supported.
Process Priority
Whatever our choices, several articles also suggest to bump the application's priority to real-time before performing testing to make sure the wall-clock() results are as realistic as possible. It is however very important to set it back to normal (see last paragraph. Example (win32):
DWORD dwPriorityClass = GetPriorityClass(GetCurrentProcess());
int nPriority = GetThreadPriority(GetCurrentThread());
SetPriorityClass(GetCurrentProcess(),REALTIME_PRIORITY_CLASS);
SetThreadPriority(GetCurrentThread(),THREAD_PRIORITY_TIME_CRITICAL);
[...]g
SetThreadPriority(GetCurrentThread(),nPriority);
SetPriorityClass(GetCurrentProcess(),dwPriorityClass);
Thread Affinity
We should consider using SetThreadAffinityMask to make sure that the starting time is recorded on the same thread as the ending time (Win32). Will that constrain the rest of the program to run on a single thread, very good question. Also check Sleep(0), reported in a few discussions, including this long one.
Test Platforms
The primary target platform at the 8, 16, and 32 processor machines at BWH. However, preliminary tests have been performed on KHQ computers.
KHQ
A full software stack was compiled on several machines at Kitware. Each component was build in two flavors, both shared/debug and static/release:
- Tcl/Tk 8.4
- VTK (cvs)
- ITK (cvs)
- ITK Applications (cvs)
- FLTK (1.1 svn)
- BWHItkOptimization (cvs)
All platforms are so far described in the BWHItkOptimization/Results directory:
| Host | #CPU | CPU | Freq | RAM | Arch | OS | Login |
|---|---|---|---|---|---|---|---|
| amber2 | 2 | Pentium Xeon | 2.8 GHz | 4 GB | 64 bits | Linux 2.6 (Red Hat Enterprise 4) | kitware (ssh, vnc; cd ~/barre) |
| fury | 1 | Pentium 4 (hyperthread) | 2.8 GHz | 1 GB | 32 bits | Linux 2.6 (Fedora Core 4) | barre, jjomier, aylward |
| panzer | 1 | Intel Core Duo (dual core) | 1.66 GHz | 1 GB | 32 bits | Mac OS X 10.4.8 | barre, jjomier, aylward |
| sanakhan | 1 | Pentium M | 1.8 GHz | 1 GB | 32 bits | Windows XP SP2 | barre |
| tetsuo | 1 | Pentium D (dual core) | 3.2 GHz | 2 GB | 32 bits | Windows XP SP2 | barre |
Tests
- LinearInterp: (to describe)
BWH
I have not yet access to the machines at BWH. Stephen has, and will let me know.
Status
- kcachegrind and timing are being performed on amber2. Stay tuned.
- valgrind is not supported on x86_64 architecture :( Now using fury instead of amber2.
- RegTests/RunLinearInterpTest.sh.in is configured automatically to run and times LinearInterp with various combinations of threads, size and factor parameters.
- It was run on fury (release static): Results/fury.kitware.timings-rel.txt
- It was run on fury (debug): Results/fury.kitware.timings-dbg.txt
- It was run on amber2 (release static): Results/amber2.kitware.timings-rel.txt
