[Genabel-commits] r1470 - in pkg/OmicABELnoMM: . doc examples src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Dec 16 09:40:26 CET 2013
Author: lckarssen
Date: 2013-12-16 09:40:25 +0100 (Mon, 16 Dec 2013)
New Revision: 1470
Added:
pkg/OmicABELnoMM/doc/
pkg/OmicABELnoMM/doc/howtocompile.txt
pkg/OmicABELnoMM/examples/
pkg/OmicABELnoMM/examples/CreateData.R
pkg/OmicABELnoMM/examples/XL.fvd
pkg/OmicABELnoMM/examples/XL.fvi
pkg/OmicABELnoMM/examples/XR.fvd
pkg/OmicABELnoMM/examples/XR.fvi
pkg/OmicABELnoMM/examples/Y.fvd
pkg/OmicABELnoMM/examples/Y.fvi
pkg/OmicABELnoMM/src/
pkg/OmicABELnoMM/src/AIOwrapper.cpp
pkg/OmicABELnoMM/src/AIOwrapper.h
pkg/OmicABELnoMM/src/Algorithm.cpp
pkg/OmicABELnoMM/src/Algorithm.h
pkg/OmicABELnoMM/src/Definitions.h
pkg/OmicABELnoMM/src/Utility.cpp
pkg/OmicABELnoMM/src/Utility.h
pkg/OmicABELnoMM/src/main.cpp
Removed:
pkg/OmicABELnoMM/AIOwrapper.cpp
pkg/OmicABELnoMM/AIOwrapper.h
pkg/OmicABELnoMM/Algorithm.cpp
pkg/OmicABELnoMM/Algorithm.h
pkg/OmicABELnoMM/CreateData.R
pkg/OmicABELnoMM/Definitions.h
pkg/OmicABELnoMM/Utility.cpp
pkg/OmicABELnoMM/Utility.h
pkg/OmicABELnoMM/XL.fvd
pkg/OmicABELnoMM/XL.fvi
pkg/OmicABELnoMM/XR.fvd
pkg/OmicABELnoMM/XR.fvi
pkg/OmicABELnoMM/Y.fvd
pkg/OmicABELnoMM/Y.fvi
pkg/OmicABELnoMM/howtocompile.txt
pkg/OmicABELnoMM/main.cpp
Log:
Created subdirectories in OmicABELnoMM and moved files to their respective locations.
Deleted: pkg/OmicABELnoMM/AIOwrapper.cpp
===================================================================
--- pkg/OmicABELnoMM/AIOwrapper.cpp 2013-12-16 08:37:15 UTC (rev 1469)
+++ pkg/OmicABELnoMM/AIOwrapper.cpp 2013-12-16 08:40:25 UTC (rev 1470)
@@ -1,778 +0,0 @@
-#include "AIOwrapper.h"
-
-
-
-AIOwrapper::AIOwrapper()
-{
- Fhandler = &FHandler;
- io_overhead = "*";
-}
-
-AIOwrapper::~AIOwrapper()
-{
-
-}
-
-
-void AIOwrapper::initialize(struct Settings ¶ms)
-{
-
-
- pthread_mutex_init( &(FHandler.m_more), NULL);
- pthread_mutex_init( &(FHandler.m_read), NULL);
- pthread_mutex_init( &(FHandler.m_buff_upd), NULL);
-
- pthread_cond_init(&(FHandler.condition_more), NULL);
- pthread_cond_init(&(FHandler.condition_read), NULL);
-
- pthread_barrier_init(&(FHandler.finalize_barrier),NULL,2);
-
-
- Fhandler->fakefiles = params.use_fake_files;
-
- databel_fvi* Yfvi;
- databel_fvi* ALfvi;
- databel_fvi* ARfvi;
-
- if(!Fhandler->fakefiles)
- {
- Fhandler->fnameAL = params.fnameAL;
- Fhandler->fnameAR = params.fnameAR;
- Fhandler->fnameY = params.fnameY;
- Fhandler->fnameOutB = params.fnameOutB;
-
- databel_fvi* Yfvi = load_databel_fvi( (Fhandler->fnameY+".fvi").c_str() );
- databel_fvi* ALfvi = load_databel_fvi( (Fhandler->fnameAL+".fvi").c_str() );
- databel_fvi* ARfvi = load_databel_fvi( (Fhandler->fnameAR+".fvi").c_str() );
- params.n = ALfvi->fvi_header.numObservations;
- params.m = ARfvi->fvi_header.numVariables/params.r;
- params.t = Yfvi->fvi_header.numVariables;
- params.l = ALfvi->fvi_header.numVariables;
-
- //block size to keep mem under 1 gigabyte
- int opt_block = params.n/(4*1000^3)*(1/(2*params.r));
- int opt_tb = 1000;
- int opt_mb = 1000;
-
- params.mb = min(params.m,opt_tb);
- params.tb = min(params.t,opt_mb);
- }
- else
- {
-
- }
-
- params.p = params.l + params.r;
-
-
- //block size to keep mem under 1 gigabyte
-// int opt_block = params.n/(4*1000^3)*(1/(2*params.r));
-// int opt_tb = max(4*2000,opt_block);
-// int opt_mb = max(2000,opt_block);
-//
-// params.mb = min(params.m,opt_tb);
-// params.tb = min(params.t,opt_mb);
-
- prepare_B();
- prepare_AL(params.l,params.n);
- prepare_AR( params.mb, params.n, params.m, params.r);
- prepare_Y(params.tb, params.n, params.t);
-
-
-
-
-
-}
-
-void AIOwrapper::finalize()
-{
- //cout << "f";
- void *status;
-
- Fhandler->not_done = false;
- pthread_mutex_lock(&(Fhandler->m_more));
- pthread_cond_signal( &(Fhandler->condition_more ));
- pthread_mutex_unlock(&(Fhandler->m_more));
-
- pthread_barrier_wait(&(Fhandler->finalize_barrier));
- finalize_Y();
- finalize_AR();
- finalize_AL();
- finalize_B();
-
- pthread_attr_destroy(&(Fhandler->attr));
-
- pthread_mutex_destroy(&(Fhandler->m_more));
- pthread_cond_destroy(&(Fhandler->condition_more));
-
- pthread_mutex_destroy(&(Fhandler->m_read));
- pthread_cond_destroy(&(Fhandler->condition_read));
-
-
-}
-
-
-void AIOwrapper::prepare_B()
-{
- Fhandler->fp_B = fopen((Fhandler->fnameOutB+".fvd").c_str(), "w+b");
- if(Fhandler->fp_B == 0)
- {
- cout << "Error Opening File B " << Fhandler->fnameOutB << endl;
- exit(1);
- }
-}
-
-
-void AIOwrapper::finalize_B()
-{
- fclose(Fhandler->fp_B);
-}
-
-
-void* AIOwrapper::async_io( void *ptr )
-{
- //cout << "async_io\n" << flush;
- type_fileh* Fhandler = (type_fileh *)ptr;
- int size_buff,tmp_y_blockSize,tmp_ar_blockSize;
-
- struct timespec timeToWait;
- FILE* fp_Y;
-
- FILE* fp_Ar;
- if(!Fhandler->fakefiles)
- {
- fp_Y = fopen((Fhandler->fnameY+".fvd").c_str(), "rb");
- if(fp_Y == 0)
- {
- cout << "Error Reading File Y " << Fhandler->fnameY << endl;
- exit(1);
- }
-
- fp_Ar = fopen((Fhandler->fnameAR+".fvd").c_str(), "rb");
- if(fp_Ar == 0)
- {
- cout << "Error Reading File Xr " << Fhandler->fnameAR << endl;
- exit(1);
- }
-
-
- }
- else
- {
-// fp_Y = fopen("tempY.bin", "w+b");
-// if(fp_Y == 0)
-// {
-// cout << "Error creating temp File Y " << Fhandler->fnameY << endl;
-// exit(1);
-// }
-// fwrite(Fhandler->Yb, sizeof(type_precision), Fhandler->n*Fhandler->y_blockSize, fp_Y);
-// fclose(fp_Y);
-//
-//
-// fp_Ar = fopen("tempAR.bin", "w+b");
-// if(fp_Ar == 0)
-// {
-// cout << "Error creating temp File Y " << Fhandler->fnameY << endl;
-// exit(1);
-// }
-// fwrite(Fhandler->Yb, sizeof(type_precision), Fhandler->n*Fhandler->y_blockSize, fp_Ar);
-// fclose(fp_Ar);
-//
-// fp_Y = fopen("tempY.bin", "rb");
-// if(fp_Y == 0)
-// {
-// cout << "Error Reading File Y " << Fhandler->fnameY << endl;
-// exit(1);
-// }
-//
-// fp_Ar = fopen("tempAR.bin", "rb");
-// if(fp_Ar == 0)
-// {
-// cout << "Error Reading File Xr " << Fhandler->fnameAR << endl;
-// exit(1);
-// }
-
- }
-
-
- Fhandler->not_done = true;
- Fhandler->reset_wait = false;
-
- //cout << "c" << flush;
-
- while(Fhandler->not_done)
- {
-
- while(!Fhandler->empty_buffers.empty() && Fhandler->y_to_readSize)
- {
-
- tmp_y_blockSize = Fhandler->y_blockSize;
- if(Fhandler->y_to_readSize < Fhandler->y_blockSize)
- tmp_y_blockSize = Fhandler->y_to_readSize;
-
- Fhandler->y_to_readSize -= tmp_y_blockSize;
- size_buff = Fhandler->n * tmp_y_blockSize;
- //cout << Fhandler->y_to_readSize << endl;
-
- pthread_mutex_lock(&(Fhandler->m_buff_upd));
- //cout << " pre;" << Fhandler->full_buffers.size() << ";" << Fhandler->empty_buffers.size() << endl;
- type_buffElement* tobeFilled = Fhandler->empty_buffers.front();
- Fhandler->empty_buffers.pop();
- //pthread_mutex_unlock(&(Fhandler->m_buff_upd));
-
- tobeFilled->size = tmp_y_blockSize;
-
- if(Fhandler->fakefiles)
- {
- //fread (tobeFilled->buff,sizeof(type_precision),size,fp_Y);
- //fseek ( fp_Y , 0 , SEEK_SET );
- int old_seed = Fhandler->seed;
- srand (old_seed);
- re_random_vec(tobeFilled->buff, size_buff );
- re_random_vec_nan(tobeFilled->buff, size_buff );
- Fhandler->seed += 75;
- }
- else
- {
- fread (tobeFilled->buff,sizeof(type_precision),size_buff,fp_Y);
- if(Fhandler->y_to_readSize <= 0)
- {
- fseek ( fp_Y , 0 , SEEK_SET );
- }
- }
-
-
- //pthread_mutex_lock(&(Fhandler->m_buff_upd));
- Fhandler->full_buffers.push(tobeFilled);
- // cout << "\nStoring " << tobeFilled << endl;
- //cout << " post;" << Fhandler->full_buffers.size() << ";" << Fhandler->empty_buffers.size() << endl;
- pthread_mutex_unlock(&(Fhandler->m_buff_upd));
-
- pthread_mutex_lock(&(Fhandler->m_read));
- pthread_cond_signal( &(Fhandler->condition_read ));
- pthread_mutex_unlock(&(Fhandler->m_read));
-
- }
-
- while(!Fhandler->ar_empty_buffers.empty() && Fhandler->Ar_to_readSize)
- {
- tmp_ar_blockSize = Fhandler->Ar_blockSize;
- if(Fhandler->Ar_to_readSize < Fhandler->Ar_blockSize)
- tmp_ar_blockSize = Fhandler->Ar_to_readSize;
-
- Fhandler->Ar_to_readSize -= tmp_ar_blockSize;
- size_buff = Fhandler->n * tmp_ar_blockSize*Fhandler->r;
-
- pthread_mutex_lock(&(Fhandler->m_buff_upd));
- type_buffElement* tobeFilled = Fhandler->ar_empty_buffers.front();
- Fhandler->ar_empty_buffers.pop();
-
-
- tobeFilled->size = tmp_ar_blockSize;
-
- if(Fhandler->fakefiles)
- {
- //fread (tobeFilled->buff,sizeof(type_precision),size,fp_Ar);
- //fseek ( fp_Ar , 0 , SEEK_SET );
- re_random_vec(tobeFilled->buff , Fhandler->n * tmp_ar_blockSize*Fhandler->r );
- re_random_vec_nan(tobeFilled->buff , Fhandler->n * tmp_ar_blockSize*Fhandler->r );
-
- }
- else
- {
- fread (tobeFilled->buff,sizeof(type_precision),size_buff,fp_Ar);
- if(Fhandler->Ar_to_readSize <= 0)
- {
- fseek ( fp_Ar , 0 , SEEK_SET );
- }
- }
-
- Fhandler->ar_full_buffers.push(tobeFilled);
- // cout << "\nStoring " << tobeFilled << endl;
- pthread_mutex_unlock(&(Fhandler->m_buff_upd));
-
- pthread_mutex_lock(&(Fhandler->m_read));
- pthread_cond_signal( &(Fhandler->condition_read ));
- pthread_mutex_unlock(&(Fhandler->m_read));
-
- }
-
-
-
-
-#ifdef WINDOWS
- SYSTEMTIME time;
- GetSystemTime(&time);
-
- timeToWait.tv_sec = time.wSecond + 500/1000;
- long int morenanos = (500%1000)*1000000;
- timeToWait.tv_nsec = time.wMilliseconds*1000 + morenanos ;
-#else
- clock_gettime(CLOCK_REALTIME, &timeToWait);
- timeToWait.tv_nsec += 150;
-#endif
-
- pthread_mutex_lock(&(Fhandler->m_more));
- pthread_cond_timedwait( &(Fhandler->condition_more), &(Fhandler->m_more), &timeToWait );
- pthread_mutex_unlock( &(Fhandler->m_more ));
-
- pthread_mutex_lock(&(Fhandler->m_read));
- pthread_cond_signal( &(Fhandler->condition_read ));
- pthread_mutex_unlock(&(Fhandler->m_read));
-
- if(Fhandler->reset_wait)
- {
- pthread_barrier_wait(&(Fhandler->finalize_barrier));
- //wait for main thread to reset everything
- pthread_barrier_wait(&(Fhandler->finalize_barrier));
- }
-
-
- }
- //cout << "k" << flush;
- //barrier
- pthread_barrier_wait(&(Fhandler->finalize_barrier));
-
- type_buffElement* tmp;
- while(!Fhandler->full_buffers.empty())
- {
- tmp= Fhandler->full_buffers.front();
- Fhandler->full_buffers.pop();
- delete []tmp->buff;
- delete tmp;
- }
-
- while(!Fhandler->empty_buffers.empty())
- {
- tmp= Fhandler->empty_buffers.front();
- Fhandler->empty_buffers.pop();
- delete []tmp->buff;
- delete tmp;
- }
-
- while(!Fhandler->ar_full_buffers.empty())
- {
- tmp= Fhandler->ar_full_buffers.front();
- Fhandler->ar_full_buffers.pop();
- delete tmp->buff;
- delete tmp;
- }
-
- while(!Fhandler->ar_empty_buffers.empty())
- {
- tmp= Fhandler->ar_empty_buffers.front();
- Fhandler->ar_empty_buffers.pop();
- delete []tmp->buff;
- delete tmp;
- }
-
- //
-
- //pthread_exit(NULL);
-
- if(!Fhandler->fakefiles)
- {
- fclose(fp_Y);
- fclose(fp_Ar);
-
- }
- else
- {
- fclose(fp_Y);
- fclose(fp_Ar);
- }
-
-//
-// //!induce realistic fileread delay
-
-}
-
-void AIOwrapper::load_ARblock(type_precision** Ar, int &Ar_blockSize)
-{
-
- int status;
- int createstatus = 0;
- //cout<<"^";
-
- while(Fhandler->ar_full_buffers.empty())
- {
- pthread_mutex_lock(&(Fhandler->m_more));
- pthread_cond_signal( &(Fhandler->condition_more ));
- pthread_mutex_unlock(&(Fhandler->m_more));
-
- io_overhead = "#";
-
- pthread_mutex_lock(&(Fhandler->m_read));
- pthread_cond_wait( &(Fhandler->condition_read), &(Fhandler->m_read ));
- pthread_mutex_unlock(&(Fhandler->m_read));
- }
-
-
- //!read new rdy buffer
- pthread_mutex_lock(&(Fhandler->m_buff_upd));
- if(Fhandler->Ar_currentReadBuff)
- {
- Fhandler->ar_empty_buffers.push(Fhandler->Ar_currentReadBuff);
- }
-
- Fhandler->Ar_currentReadBuff = Fhandler->ar_full_buffers.front();
- Fhandler->ar_full_buffers.pop();
-
- //cout << "\nReading " << Fhandler->Ar_currentReadBuff << endl;
- Fhandler->Ar = Fhandler->Ar_currentReadBuff->buff;
- Ar_blockSize = Fhandler->Ar_currentReadBuff->size;
-
- pthread_mutex_unlock(&(Fhandler->m_buff_upd));
-
-
-
- pthread_mutex_lock(&(Fhandler->m_more));
- pthread_cond_signal( &(Fhandler->condition_more ));
- pthread_mutex_unlock(&(Fhandler->m_more));
-
-
-
-//secueantial
-// int tmp_ar_blockSize = Fhandler->Ar_blockSize;
-// if(Fhandler->Ar_to_readSize < Fhandler->Ar_blockSize)
-// tmp_ar_blockSize = Fhandler->Ar_to_readSize;
-//
-// Fhandler->Ar_to_readSize -= tmp_ar_blockSize;
-// int size_buff = Fhandler->n * tmp_ar_blockSize * Fhandler->r;
-// re_random_vec(Fhandler->Ar,size_buff);
-//Ar_blockSize=tmp_ar_blockSize;
-
-
- (*Ar) = Fhandler->Ar;
-
-
-
-
-
-
-}
-
-void AIOwrapper::load_Yblock(type_precision** Y, int &y_blockSize)
-{
-
- int status;
- int createstatus = 0;
-
- while(Fhandler->full_buffers.empty())
- {
-
- pthread_mutex_lock(&(Fhandler->m_more));
- pthread_cond_signal( &(Fhandler->condition_more ));
- pthread_mutex_unlock(&(Fhandler->m_more));
-
- io_overhead = "!";
-
- pthread_mutex_lock(&(Fhandler->m_read));
- pthread_cond_wait( &(Fhandler->condition_read), &(Fhandler->m_read ));
- pthread_mutex_unlock(&(Fhandler->m_read));
-
- }
-
- //!read new rdy buffer
- pthread_mutex_lock(&(Fhandler->m_buff_upd));
- //cout << " pre," << Fhandler->full_buffers.size() << ";" << Fhandler->empty_buffers.size() << endl;
-
- if(Fhandler->currentReadBuff)
- {
- //memset(Fhandler->currentReadBuff->buff,0,y_blockSize);
- Fhandler->empty_buffers.push(Fhandler->currentReadBuff);
- }
- Fhandler->currentReadBuff = Fhandler->full_buffers.front();
- Fhandler->full_buffers.pop();
-
- //cout << "\nReading " << Fhandler->currentReadBuff << endl;
- Fhandler->Yb = Fhandler->currentReadBuff->buff;
- y_blockSize = Fhandler->currentReadBuff->size;
-
- (*Y) = Fhandler->Yb;
-
- //cout << " post," << Fhandler->full_buffers.size() << ";" << Fhandler->empty_buffers.size() << endl;
-
- pthread_mutex_unlock(&(Fhandler->m_buff_upd));
-
-
-
- pthread_mutex_lock(&(Fhandler->m_more));
- pthread_cond_signal( &(Fhandler->condition_more ));
- pthread_mutex_unlock(&(Fhandler->m_more));
-
- //matlab_print_matrix("Y",Fhandler->n,y_blockSize,*Y);
-
-
-}
-
-void AIOwrapper::write_B(type_precision* B, int p, int blockSize)
-{
- fwrite (B , sizeof(type_precision), p*blockSize, Fhandler->fp_B);
-}
-
-void AIOwrapper::prepare_Y(int y_blockSize, int n, int totalY)
-{
- //for fake files
-
- Fhandler->seed = 1337;
- srand (Fhandler->seed);
-
- Fhandler->y_blockSize = y_blockSize;
-
- Fhandler->n= n;
- Fhandler->Y_Amount=totalY;
- Fhandler->y_to_readSize = Fhandler->Y_Amount;
- Fhandler->buff_count = min(2,(totalY+ y_blockSize - 1)/y_blockSize) ;
- //cout << "buffcount " << Fhandler->buff_count;
-
-
- Fhandler->currentReadBuff = 0;
- type_buffElement* tmp;
-
- for(int i = 0; i< Fhandler->buff_count ; i++)
- {
- tmp = new type_buffElement();
- tmp->buff = new type_precision[Fhandler->n*Fhandler->y_blockSize];
- tmp->size = y_blockSize;
-// for( int i = 0; i < Fhandler->n*Fhandler->y_blockSize; i++)
-// {
-// (tmp->buff)[i] = 0;
-// }
- Fhandler->empty_buffers.push(tmp);
- }
- Fhandler->Yb = tmp->buff;
-
-
-
- pthread_mutex_init(&(Fhandler->m_buff_upd), NULL);
- pthread_mutex_init(&(Fhandler->m_more), NULL);
- pthread_mutex_init(&(Fhandler->m_read), NULL);
-
- pthread_attr_init(&(Fhandler->attr));
- pthread_attr_setdetachstate(&(Fhandler->attr), PTHREAD_CREATE_JOINABLE);
-
- pthread_create( &(Fhandler->iothread),&(Fhandler->attr), AIOwrapper::async_io, (void*)Fhandler);
-
-
-
-}
-
-void AIOwrapper::reset_Y()
-{
- void *status;
-
- Fhandler->seed = 1337;
-
- //cout << "ry" << flush;
-
- Fhandler->reset_wait = true;
- pthread_barrier_wait(&(Fhandler->finalize_barrier));
-
- pthread_mutex_lock(&(Fhandler->m_buff_upd));
- Fhandler->y_to_readSize = Fhandler->Y_Amount;
-
- if(Fhandler->currentReadBuff)
- {
- Fhandler->full_buffers.push(Fhandler->currentReadBuff);
- Fhandler->currentReadBuff=0;
- }
-
- while(!Fhandler->full_buffers.empty())
- {
- Fhandler->empty_buffers.push(Fhandler->full_buffers.front());
- for( int i = 0; i < Fhandler->n*Fhandler->y_blockSize; i++)
- {
- ((Fhandler->full_buffers.front())->buff)[i] = 0;
- }
- Fhandler->full_buffers.pop();
- }
- pthread_mutex_unlock(&(Fhandler->m_buff_upd));
-
- Fhandler->reset_wait = false;
-
- pthread_barrier_wait(&(Fhandler->finalize_barrier));
-
- pthread_mutex_lock(&(Fhandler->m_more));
- pthread_cond_signal( &(Fhandler->condition_more ));
- pthread_mutex_unlock(&(Fhandler->m_more));
-
-
-}
-
-void AIOwrapper::reset_AR()
-{
- void *status;
-
-
- //cout << "ra" << flush;
-
- Fhandler->reset_wait = true;
- pthread_barrier_wait(&(Fhandler->finalize_barrier));
-
- pthread_mutex_lock(&(Fhandler->m_buff_upd));
- Fhandler->Ar_to_readSize = Fhandler->Ar_Amount;
-
- if(Fhandler->Ar_currentReadBuff)
- {
- Fhandler->ar_full_buffers.push(Fhandler->Ar_currentReadBuff);
- Fhandler->Ar_currentReadBuff=0;
- }
-
- while(!Fhandler->ar_full_buffers.empty())
- {
- Fhandler->ar_empty_buffers.push(Fhandler->ar_full_buffers.front());
-// for( int i = 0; i < Fhandler->n*Fhandler->r*Fhandler->Ar_blockSize; i++)
-// {
-// ((Fhandler->ar_full_buffers.front())->buff)[i] = 0;
-// }
- Fhandler->ar_full_buffers.pop();
- }
- pthread_mutex_unlock(&(Fhandler->m_buff_upd));
-
- Fhandler->reset_wait = false;
-
- pthread_barrier_wait(&(Fhandler->finalize_barrier));
-
- pthread_mutex_lock(&(Fhandler->m_more));
- pthread_cond_signal( &(Fhandler->condition_more ));
- pthread_mutex_unlock(&(Fhandler->m_more));
-
-
-}
-
-void AIOwrapper::finalize_Y()
-{
-
-
-}
-
-void AIOwrapper::prepare_AR( int desired_blockSize, int n, int totalR, int columnsAR)
-{
-
- Fhandler->Ar = new type_precision[desired_blockSize*columnsAR*n];
- Fhandler->Ar_blockSize = desired_blockSize;
- Fhandler->r = columnsAR;
- Fhandler->Ar_Amount = totalR;
- Fhandler->Ar_to_readSize = Fhandler->Ar_Amount;
-
- int buff_count = min(2,(totalR+ desired_blockSize - 1)/desired_blockSize);
-
- Fhandler->Ar_currentReadBuff = 0;
- type_buffElement* tmp;
-
- for(int i = 0; i< buff_count ; i++)
- {
- tmp = new type_buffElement();
- tmp->buff = new type_precision[n*desired_blockSize*columnsAR];
- tmp->size = desired_blockSize;
-// memset(tmp->buff,-9,n*desired_blockSize*columnsAR);
-
- Fhandler->ar_empty_buffers.push(tmp);
- }
- Fhandler->Ar = tmp->buff;
-
-}
-
-
-void AIOwrapper::finalize_AR()
-{
-
-}
-
-
-void AIOwrapper::load_AL(type_precision** AL)
-{
- if(Fhandler->fakefiles)
- {
- re_random_vec(Fhandler->AL,Fhandler->n*Fhandler->l);
- re_random_vec_nan(Fhandler->AL,Fhandler->n*Fhandler->l);
- (*AL) = Fhandler->AL;
- }
- else
- {
- FILE *fp;
- fp = fopen((Fhandler->fnameAL+".fvd").c_str(), "rb");
- if(fp == 0)
- {
- cout << "Error Reading File " << Fhandler->fnameAL << endl;
- exit(1);
- }
-
- fread (Fhandler->AL,sizeof(type_precision),Fhandler->l*Fhandler->n,fp);
- fclose(fp);
- }
-
-
-
- (*AL) = Fhandler->AL;
-
- //matlab_print_matrix("AL",Fhandler->n,Fhandler->l,*AL);
-}
-
-void AIOwrapper::prepare_AL( int columnsAL, int n)
-{
- Fhandler->AL = new type_precision[columnsAL*n];
- Fhandler->l=columnsAL;
-}
-
-void AIOwrapper::finalize_AL()
-{
- delete []Fhandler->AL;
-}
-
-void AIOwrapper::free_databel_fvi( struct databel_fvi **fvi )
-{
- free ((*fvi)->fvi_data);
- free (*fvi);
- *fvi = NULL;
-}
-
-FILE * AIOwrapper::fgls_fopen( const char *path, const char *mode )
-{
- FILE * f;
- char err[100];
-
- f = fopen( path, mode );
- if ( f == NULL )
- {
- cout << "\nerror on fgls_fopen\n";
- exit( 1 );
- }
- return f;
-}
-
-void * AIOwrapper::fgls_malloc_impl( const char* file, long line, size_t size )
-{
- void *buf;
-
- if ( (buf = malloc( size )) == NULL ) {
- cout<< "\nCouldn't allocate %ld bytes of memory in %s:%ld\n";
- exit(1);
- }
-
- return buf;
-}
-
-struct databel_fvi * AIOwrapper::load_databel_fvi( const char *path )
-{
- FILE *f;
- databel_fvi *fvi;
- size_t data_size;
-
- f = fgls_fopen( path, "r" );
-
- fvi = (databel_fvi*) fgls_malloc( sizeof(databel_fvi) );
- // Header
- fread( &fvi->fvi_header, sizeof(databel_fvi_header), 1, f );
- // Labels
- data_size = (fvi->fvi_header.numVariables +fvi->fvi_header.numObservations ) *
- fvi->fvi_header.namelength * sizeof(char);
- fvi->fvi_data = (char *) fgls_malloc ( data_size );
- // Load labels
- fread( fvi->fvi_data, 1, data_size, f );
-
- fclose( f );
-
- return fvi;
-}
Deleted: pkg/OmicABELnoMM/AIOwrapper.h
===================================================================
--- pkg/OmicABELnoMM/AIOwrapper.h 2013-12-16 08:37:15 UTC (rev 1469)
+++ pkg/OmicABELnoMM/AIOwrapper.h 2013-12-16 08:40:25 UTC (rev 1470)
@@ -1,178 +0,0 @@
-#ifndef AIOWRAPPER_H
-#define AIOWRAPPER_H
-
-#include "Definitions.h"
-#include "Utility.h"
-
-typedef struct BufferElement type_buffElement;
-
-struct BufferElement
-{
- type_precision* buff;
- int size;
-};
-
-typedef struct fileh type_fileh;
-
-
-
-struct fileh
-{
- string fnameAL;
- string fnameAR;
- string fnameY;
- string fnameOutB;
-
- FILE* fp_B;
-
- bool doublefileType;
- bool fakefiles;
-
- type_precision* Yb;
- type_precision* Ar;
- type_precision* AL;
- type_buffElement* currentReadBuff;
- type_buffElement* Ar_currentReadBuff;
- int buff_count;
-
- queue<type_buffElement*> empty_buffers;
- queue<type_buffElement*> full_buffers;
-
- queue<type_buffElement*> b_empty_buffers;
- queue<type_buffElement*> b_full_buffers;
-
- queue<type_buffElement*> ar_empty_buffers;
- queue<type_buffElement*> ar_full_buffers;
-
- int index;
-
- int n;
- int r;
- int l;
-
- int Ar_Amount;
- int Ar_blockSize;
- int Ar_to_readSize;
-
- int Y_Amount;
- int y_blockSize;
- int y_to_readSize;
-
- bool not_done;
- bool reset_wait;
-
- int seed;
- int Aseed;
-
- pthread_mutex_t m_more ;
- pthread_cond_t condition_more ;
- pthread_mutex_t m_read ;
-
- pthread_cond_t condition_read ;
- pthread_mutex_t m_buff_upd ;
-
- pthread_t iothread;
- pthread_attr_t attr;
-
- //barrier
- pthread_barrier_t finalize_barrier;
-
-
-};
-
-#define fgls_malloc(size) fgls_malloc_impl(__FILE__, __LINE__, size)
-
-enum datatype{ UNSIGNED_SHORT_INT_TYPE = 1,
- SHORT_INT_TYPE,
- UNSIGNED_INT_TYPE,
- INT_TYPE,
- FLOAT_TYPE,
- DOUBLE_TYPE,
- SIGNED_CHAR_TYPE,
- UNSIGNED_CHAR_TYPE };
-
-#define NAMELENGTH 32
-#define RESERVEDSPACE 5
-
-typedef struct databel_fvi_header
-{
- unsigned short int type;
- unsigned int nelements;
- unsigned int numObservations;
- unsigned int numVariables;
- unsigned int bytesPerRecord;
- unsigned int bitsPerRecord;
- unsigned int namelength;
- unsigned int reserved[RESERVEDSPACE];
-} databel_fvi_header;
-
-typedef struct databel_fvi
-{
- databel_fvi_header fvi_header;
- char *fvi_data;
-} databel_fvi;
-
-class AIOwrapper
-{
- public:
- AIOwrapper();
- ~AIOwrapper();
-
- void initialize(struct Settings ¶ms);
- void finalize();
-
-
- void load_AL(type_precision** AL);
- void load_ARblock(type_precision** Y, int &blockSize);
- void load_Yblock(type_precision** Y, int &blockSize);
- void reset_Y();
- void reset_AR();
-
- void write_B(type_precision* B, int p, int blockSize);
-
- string io_overhead;
-
-
- protected:
-
- private:
-
-
- void prepare_AR( int desired_blockSize, int n, int totalR, int columnsR);
- void finalize_AR();
-
-
- void prepare_Y(int desired_blockSize, int n, int totalY);
- void finalize_Y();
-
- void prepare_AL( int columns, int n);
- void finalize_AL();
-
- void prepare_B();
- void finalize_B();
-
-
- static void* async_io(void *ptr );
-
- struct databel_fvi * load_databel_fvi( const char *path );
- void free_databel_fvi( struct databel_fvi **fvi );
- FILE * fgls_fopen( const char *path, const char *mode );
-
- void * fgls_malloc_impl( const char* file, long line, size_t size );
-
- type_fileh FHandler;
- type_fileh* Fhandler;
-
-
-
-
-
-
-
-
-
-
-
-};
-
-#endif // AIOWRAPPER_H
Deleted: pkg/OmicABELnoMM/Algorithm.cpp
===================================================================
--- pkg/OmicABELnoMM/Algorithm.cpp 2013-12-16 08:37:15 UTC (rev 1469)
+++ pkg/OmicABELnoMM/Algorithm.cpp 2013-12-16 08:40:25 UTC (rev 1470)
@@ -1,1714 +0,0 @@
-#include "Algorithm.h"
-
-Algorithm::Algorithm()
-{
- //ctor
-}
-
-Algorithm::~Algorithm()
-{
- //dtor
-}
-
-
-void Algorithm::solve(struct Settings params, struct Outputs &out, int type)
-{
- switch (type)
- {
- case FULL_NEQ:
- fullNEQ(params,out);
- break;
- case P_NEQ:
- partialNEQ(params,out);
- break;
- case P_NEQ_B_OPT:
- partialNEQ_Blocked_STL(params,out);
- break;
- case FULL_QR:
- fullQR(params,out);
- break;
- case P_QR:
- partialQR(params,out);
- break;
- case P_QR_B_OPT:
- partialQR_Blocked_Rtl(params,out);
- break;
- case P_NEQ_B_OPT_MD:
- partialNEQ_Blocked_STL_MD(params,out);
- break;
-
- default:
- break;
- }
-
-}
-
-void Algorithm::extract_subMatrix(type_precision* source, type_precision* dest,int dim1_source, int dim2_source,
- int dim1_ini,int dim1_end,int dim2_ini,int dim2_end)
-{
-
- int i,j,idx=0;
- int size, source_ini;
- for(i = dim2_ini; i<dim2_end; i++)
- {
- j = dim1_ini;
- source_ini = i*dim1_source+j;
- size = dim1_end-dim1_ini;
- memcpy( (type_precision*)&dest[idx], (type_precision*)&source[source_ini], size * sizeof(type_precision) );
-// for(j = dim1_ini; j<dim1_end; j++)
-// {
-// dest[idx] = source[i*dim1_source+j];
-// idx++;
-// }
- idx += size;
- }
-
-}
-
-void Algorithm::prepare_Bfinal(type_precision* bfinal, type_precision* top,type_precision* bot,int dim1_b, int dim2_b,int dim1_b_bot)
-{
- //memcpy are faster version of the fors
- int i,k,w,top_idx,bot_idx,max = dim1_b*dim2_b;
- int size;
- top_idx = 0;
- bot_idx = 0;
- for(k = 0; k < dim2_b; k++)
- {
- size = k*dim1_b+(dim1_b-dim1_b_bot)-(k*dim1_b);
- memcpy( (type_precision*)&bfinal[k*dim1_b], (type_precision*)&top[top_idx], size * sizeof(type_precision) );
-// for(i = k*dim1_b; i < k*dim1_b+(dim1_b-dim1_b_bot); i++)
-// {
-// bfinal[i] = top[top_idx];
-// top_idx++;
-// }
- top_idx += size;
- i = k*dim1_b + size;
- w=i;
-
- size = w+dim1_b_bot - w;
- memcpy( (type_precision*)&bfinal[w], (type_precision*)&bot[bot_idx], size * sizeof(type_precision) );
-// for(i = w; i < w+dim1_b_bot; i++)
-// {
-// bfinal[i] = bot[bot_idx];
-// bot_idx++;
-// }
- bot_idx += size;
- }
-
-}
-
-void Algorithm::prepare_QY(type_precision* qy, type_precision* top,type_precision* bot,int dim1_QY, int dim2_QY,int dim1_qy_bot,int bot_blocks )
-{
-
- int i,k,w,top_idx,bot_idx,max = dim1_QY*dim2_QY;
- top_idx = 0;
- bot_idx = 0;
- for(k = 0; k < dim2_QY; k++)
- {
- for(i = k*dim1_QY; i < (k+1)*dim1_QY-dim1_qy_bot; i++)
- {
- qy[i] = top[top_idx];
- top_idx++;
- }
- w=i;
-
- for(i = w; i < w+dim1_qy_bot; i++)
- {
- qy[i] = bot[bot_idx];
- bot_idx++;
- }
- bot_idx+=(bot_blocks-1)*dim1_qy_bot;
- }
-
-}
-
-type_precision* Algorithm::extract_R(type_precision* A,int dim1_A, int dim2_A)
-{
- type_precision* R = (type_precision*)calloc(dim2_A*dim2_A,sizeof(type_precision));
- int i,j;
-
- int R_idx=0;
-
- for(i = 0; i < dim2_A; i++)
- {
- for(j = 0; j <= i; j++)
- {
- R[R_idx] = A[j+i*dim1_A];
- R_idx++;
- }
- R_idx = dim2_A*(i+1);
- }
- return R;
-}
-
-type_precision* Algorithm::prepare_R(type_precision* RL,int dim1_A, int dim2_AL,int dim2_AR)
-{
- int R_dim = (dim2_AR+dim2_AL);
- type_precision* R = new type_precision[R_dim*R_dim];
-
- int i,j;
-
- int RL_idx=0;
- int R_idx=0;
-
- for(i = 0; i < dim2_AL; i++)
- {
- for(j = 0; j <= i; j++)
- {
- RL_idx = i*dim1_A + j;
- R_idx = i*R_dim + j;
- R[R_idx] = RL[RL_idx];
-
- }
-
- }
- return R;
-}
-
-void Algorithm::update_R(type_precision* R, type_precision* topRr, type_precision* botRr,int dim1, int dim2, int r)
-{
- int i,j,w;
- int max = dim1*dim2;
- int rtr_idx=0;
- int rbr_idx=0;
- for( j = r; j > 0 ; j--)
- {
- for(i = max-dim1*j; i < max-dim1*j+dim2-r; i++)
- {
- R[i] = topRr[rtr_idx];
- rtr_idx++;
- }
- w = i;
- for(i = w; i < w+r; i++)
- {
- R[i] = botRr[rbr_idx];
- rbr_idx++;
- }
-
- }
-
-}
-
-
-void Algorithm::build_S(type_precision* S,type_precision* Stl,type_precision* Str,type_precision* Sbr,int l,int r)
-{
- int Sidx;
- int p = l+r;
- for(int i = 0; i < l; i++)
- {
- Sidx = i*p;
- for(int j= 0; j <= i; j++)
- {
- S[Sidx] = Stl[j+i*l];
- Sidx++;
- }
- }
- for(int i = 0; i < r; i++)
- {
- Sidx = l*p+p*i;
- for(int j= 0; j < l; j++)
- {
- S[Sidx] = Str[j+i*l];
- Sidx++;
- }
- }
-
- for(int i = 0; i < r; i++)
- {
- Sidx = l*p+l+p*i;
- for(int j= 0; j <= i; j++)
- {
- S[Sidx] = Sbr[j+i*r];
- Sidx++;
- }
- }
-
-
-
-}
-
-void Algorithm::check_result(type_precision* AL, type_precision* AR,int rowsA,int colsA, int rhs,int colsAR,
- type_precision* y, type_precision* res)
-{
- type_precision* A = (type_precision*)malloc(rowsA*colsA*sizeof(type_precision));
-
- int i,ar_idx=0;
- for(i = 0; i <rowsA*(colsA-colsAR) ; i++)
- {
- A[i] = AL[i];
- }
-
- for(i = rowsA*(colsA-colsAR); i <rowsA*colsA ; i++)
- {
- A[i] = AR[ar_idx];
- ar_idx++;
- }
-
-
-
- type_precision* ynew = replicate_vec(y,rowsA*rhs);
- type_precision* new_sol = (type_precision*)malloc(colsA*rhs*sizeof(type_precision));
-
- lapack_int info = LAPACKE_sgels(STORAGE_TYPE,'N',rowsA,colsA,rhs,A,rowsA,ynew,rowsA);
- assert(info == 0,"Error Check");
-
-
-
-
-
- int index=0;
- int index_new = 0;
- for(i = 0; i < rhs; i++)
- {
- copy_vec( &ynew[index], &new_sol[index_new], colsA);
- index += rowsA;
- index_new += colsA;
- }
-
-
-// if(PRINT)
-// printf("\n Btop=(Rtl\\(Ql'*Y))-(Rtl\\Rtr)*(Rbr\\(Qr'*Y)); \n [Btop ; Rbr\\Qr'*Y] - bcomputed \n");
-
- cblas_saxpy(rhs*colsA, -1.0, res, 1,new_sol,1);
- type_precision u_norm=cblas_snrm2(rhs*colsA,new_sol,1);
- //
- if(abs(u_norm) >= 0.0001 || isnan(u_norm))
- {
-
-
- fflush(stdout);
- matlab_print_matrix("AL",rowsA,colsA-colsAR,AL);
- matlab_print_matrix("AR",rowsA,colsAR,AR);
- matlab_print_matrix("Y",rowsA,rhs,y);
- printf("\nA = [AL AR]; [Q,R] = qr(A,0); rr=R\\(Q'*Y)\n");
- matlab_print_matrix("bcomputed",colsA,rhs,res);
- matlab_print_matrix("newsol",colsA,rhs,ynew);
- printf("\n%%\tnrom: %0.2g", u_norm);
- exit(1);
- }
- else
- {
- matlab_print_matrix("bcomputed",colsA,rhs,res);
- matlab_print_matrix("newsol",colsA,rhs,ynew);
- printf("\n%%\tnrom: %0.2g", u_norm);
- }
-
-
-
- //cout << "\t**************";
-
-
- free(ynew);
- free(new_sol);
- free(A);
-
-
-
-
-
-
-}
-
-///////////////////////////////
-
-
-
-void Algorithm::partialNEQ_Blocked_STL_MD(struct Settings params, struct Outputs &out)
-{
- int max_threads = params.threads;
-
-
- srand (time(NULL));
-
- blas_set_num_threads(max_threads);
-
-
- type_precision *Ytemp;
- lapack_int info,n,lda,ldy,l,r,k,p;
-
- int i,j,w;
- int m;
-
- cputime_type start_tick,start_tick2, end_tick;
-
- AIOfile.initialize(params);
-
- n = params.n; l=params.l; r=params.r; p = l+r;
-
- int y_amount = params.t;
- int y_block_size = params.tb;//kk
-
- int a_amount = params.m;
- int a_block_size = params.mb;
-
- int a_iters = (a_amount + a_block_size - 1) / a_block_size;
-
- int y_iters = (y_amount + y_block_size - 1) / y_block_size;
-
-
- lda = n; ldy = n;
- k = p;
-
- for(int j = 0; j < y_iters; j++)
- {
-
- if(y_iters >= 40 && (i%(y_iters/40))==0)
- {
- cout << "*" << flush;
-
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/genabel -r 1470
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