NA-MIC National Alliance for Medical Image Computing ITK Workshop October 5-8, 2005 Multi-Threading

National Alliance for Medical Image Computing ITK Workshop – Multi-Threading Multi-Threading –The portable Multi-ThreaderThe portable Multi-Threader –Mutual ExclusionMutual Exclusion –ThreadedGenerateDataThreadedGenerateData –BeforeThreadedGenerateDataBeforeThreadedGenerateData –AfterThreadedGenerateDataAfterThreadedGenerateData –SetNumberOfThreadsSetNumberOfThreads –The Evil legacy of FORTRANThe Evil legacy of FORTRAN

National Alliance for Medical Image Computing The Concept of Multi-Tasking Insight Toolkit - Advanced Course

National Alliance for Medical Image Computing The Multi-Tasking Concept Task A Processor Task BTask C The Operating System assigns processor time to each task

National Alliance for Medical Image Computing Tasks have independent memory spaces They cannot communicate with each other unless they use sockets or files Insight Toolkit - Advanced Course

National Alliance for Medical Image Computing The Concept of Multi-Threading Insight Toolkit - Advanced Course

National Alliance for Medical Image Computing The Multi-Threading Concept Task A Processor A Threading library creates threads and assigns processor time to each thread T0 T1 T2

National Alliance for Medical Image Computing Threads from a common Task have the same memory space (Shared Memory) They can simultaneously access variables that were instantiated before creating the threads. Insight Toolkit - Advanced Course

National Alliance for Medical Image Computing The Multi-Threading in Multi-Processors Task A Processor 1 T0 T1 T2 Processor 2 Processor 3 Processor 4

National Alliance for Medical Image Computing Different Threading libraries are available in different platforms Insight Toolkit – Multi-Threading Libraries PThreads SProc Win32 Threads

National Alliance for Medical Image Computing ITK Provides a class for hiding the differences between threading libraries Insight Toolkit – Multi-Threading Libraries itk::MultiThreader Win32 Threads PThreadsSProc

National Alliance for Medical Image Computing Using the itk::MultiThreader Insight Toolkit - Advanced Course Declare a Callback Instantiate an itk::MultiThreader Set the number of Threads Set the callback Invoke SingleMethodExecute()

National Alliance for Medical Image Computing #include itkMultiThreader.h int main( int argc, char * argv[] ) { typedef itk::MultiThreader ThreaderType; ThreaderType::Pointer threader = ThreaderType::New(); const unsigned int numberOfThreads = atoi( argv[1] ); threader->SetNumberOfThreads( numberOfThreads ); threader->SetSingleMethod( ThreaderCallback, NULL ); threader->SingleMethodExecute(); } Using the Multi-Threader

National Alliance for Medical Image Computing Defining the Theader Callback #include itkMultiThreader.h ITK_THREAD_RETURN_TYPE ThreaderCallback( void * arg ) { typedef itk::MultiThreader::ThreadInfoStruct ThreadInfoType; ThreadInfoType * infoStruct = static_cast ( arg ); const unsigned int threadId = infoStruct->ThreadID; std::cout << Thread = << threadId << std::endl; ITK_THREAD_RETURN_TYPE value; return value; }

National Alliance for Medical Image Computing Exercise 31a Insight Toolkit - Advanced Course Run the Multi-Caster for different numbers of Threads

National Alliance for Medical Image Computing DONT PUSH THIS BUTTON ! Insight Toolkit - Advanced Course

National Alliance for Medical Image Computing DONT TRY TO WRITE TO SHARED DATA FROM MULTIPLE THREADS Insight Toolkit - Advanced Course

National Alliance for Medical Image Computing Exercise 31b Insight Toolkit - Advanced Course Do the wrong thing on purpose: Attempt to write to a static variable simultaneously from different Threads

National Alliance for Medical Image Computing Defining the WRONG Theader Callback #include itkMultiThreader.h static unsigned long int Counter = 0; ITK_THREAD_RETURN_TYPE ThreaderCallback( void * arg ) { typedef itk::MultiThreader::ThreadInfoStruct ThreadInfoType; ThreadInfoType * infoStruct = static_cast ( arg ); const unsigned int threadId = infoStruct->ThreadID; Counter++; std::cout << Thread = << threadId; std::cout << Counter = << Counter << std::endl; ITK_THREAD_RETURN_TYPE value; return value; }

National Alliance for Medical Image Computing IF YOU REALLY REALLY WANT TO PUSH THIS BUTTON Insight Toolkit - Advanced Course

National Alliance for Medical Image Computing Exercise 31c Insight Toolkit - Advanced Course Prevent the possible simultaneous access to share memory by introducion Mutual Exclusion

National Alliance for Medical Image Computing Defining the RIGHT Theader Callback #include itkMultiThreader.h #include itkSimpleFastMutexLock.h static unsigned long int Counter = 0; static itk::SimpleFastMutexLock mutex; ITK_THREAD_RETURN_TYPE ThreaderCallback( void * arg ) { mutex.Lock(); Counter++; mutex.UnLock(); std::cout << Counter = << Counter << std::endl; ITK_THREAD_RETURN_TYPE value; return value; }

National Alliance for Medical Image Computing Exercise 31d Insight Toolkit - Advanced Course Use the itk::RealTimeClock to measure how fast (or how slow) the Mutual exclusion

National Alliance for Medical Image Computing Timing the Mutual Exclusion Class #include itkSimpleFastMutexLock.h #include itkRealTimeClock.h static unsigned long int Counter = 0; static itk::SimpleFastMutexLock mutex; int main() { const unsigned int N = L; itk::RealTimeClock clock; const double T1 = clock.GetTimestamp(); for(unsigned long i=0; i < N; i++) { mutex.Lock(); Counter++; mutex.UnLock(); } const double TT = clock.GetTimestamp() – T1; std::cout << Time = << TT / N << td::endl; ITK_THREAD_RETURN_TYPE value; return value; }

National Alliance for Medical Image Computing Writing a Multi-Threading Filter Insight Toolkit - Advanced Course

National Alliance for Medical Image Computing Insight Toolkit – Filters Hierarchy itk::ProcessObject public: MultiThreader * GetThreader(); private: MultiThreader m_Threader int m_NumberOfThreads

National Alliance for Medical Image Computing Insight Toolkit – Filters Hierarchy itk::ImageSource public: virtual void BeforeThreadedGenerateData(); virtual void AfterThreadedGenerateData(); virtual void ThreadedGenerateData( const OutputImageRegionType & region, int threadId );

National Alliance for Medical Image Computing Insight Toolkit – GenerateData() BeforeThreadedGenerateData AfterThreadedGenerateData TGD

National Alliance for Medical Image Computing END Insight Toolkit - Advanced Course