K3b::AudioDataSource* K3b::AudioDataSource::split( const K3b::Msf& pos )
{
if( pos < length() ) {
K3b::AudioDataSource* s = copy();
s->setStartOffset( startOffset() + pos );
s->setEndOffset( endOffset() );
setEndOffset( startOffset() + pos );
s->moveAfter( this );
emitChange();
return s;
}
else
return 0;
}
void K3b::AudioDataSource::fixupOffsets()
{
// no length available yet
if( originalLength() == 0 )
return;
if( startOffset() >= originalLength() ) {
setStartOffset( 0 );
}
if( endOffset() > originalLength() ) {
setEndOffset( 0 ); // whole source
}
if( endOffset() > 0 && endOffset() <= startOffset() ) {
setEndOffset( startOffset() );
}
}
bool K3bAudioCdTrackSource::initParanoia()
{
if( !m_initialized ) {
if( !m_cdParanoiaLib )
m_cdParanoiaLib = K3bCdparanoiaLib::create();
if( m_cdParanoiaLib ) {
m_lastUsedDevice = searchForAudioCD();
// ask here for the cd since searchForAudioCD() may also be called from outside
if( !m_lastUsedDevice ) {
// could not find the CD, so ask for it
QString s = i18n("Please insert Audio CD %1%2")
.arg(m_discId, 0, 16)
.arg(m_cddbEntry.cdTitle.isEmpty() || m_cddbEntry.cdArtist.isEmpty()
? QString::null
: " (" + m_cddbEntry.cdArtist + " - " + m_cddbEntry.cdTitle + ")");
while( K3bDevice::Device* dev = K3bThreadWidget::selectDevice( track()->doc()->view(), s ) ) {
if( searchForAudioCD( dev ) ) {
m_lastUsedDevice = dev;
break;
}
}
}
// user canceled
if( !m_lastUsedDevice )
return false;
k3bcore->blockDevice( m_lastUsedDevice );
if( m_toc.isEmpty() )
m_toc = m_lastUsedDevice->readToc();
if( !m_cdParanoiaLib->initParanoia( m_lastUsedDevice, m_toc ) ) {
k3bcore->unblockDevice( m_lastUsedDevice );
return false;
}
if( doc() ) {
m_cdParanoiaLib->setParanoiaMode( doc()->audioRippingParanoiaMode() );
m_cdParanoiaLib->setNeverSkip( !doc()->audioRippingIgnoreReadErrors() );
m_cdParanoiaLib->setMaxRetries( doc()->audioRippingRetries() );
}
m_cdParanoiaLib->initReading( m_toc[m_cdTrackNumber-1].firstSector().lba() + startOffset().lba() + m_position.lba(),
m_toc[m_cdTrackNumber-1].firstSector().lba() + lastSector().lba() );
// we only block during the initialization because we cannot determine the end of the reading process :(
k3bcore->unblockDevice( m_lastUsedDevice );
m_initialized = true;
kdDebug() << "(K3bAudioCdTrackSource) initialized." << endl;
}
}
return m_initialized;
}
void KeplerBtDynamics::keyPressed(int key)
{
switch (key) {
case 'e': {
btVector3 startOffset(ofRandom(-295,295),ofRandom(100, 500),ofRandom(-295,295));
spawnKepler(startOffset);
}
}
}
void BirdOptimizer::spawnBigBird()
{
btVector3 startOffset(0, 5, 0);
if ((m_giveBirdThisId % kNumBirdsPerGeneration) == 0) {
m_numGeneration++;
evaluateCurrentGenerationBirds();
}
m_currentBirdLocalParam = new BigBirdLocalParams();
m_currentBirdLocalParam->birdId = m_giveBirdThisId++;
m_currentBirdLocalParam->startTransform.setIdentity();
m_currentBirdLocalParam->startTransform.setOrigin(startOffset);
m_currentBirdLocalParam->hoistTransform.setIdentity();
m_currentBirdLocalParam->hoistTransform.setOrigin(startOffset);
m_currentBirdData = new proto::BigBirdConstructionData();
m_currentBirdData->set_hoistanglexy(10.f);
m_currentBirdData->set_hoistanglezxy(90.f);
m_currentBirdData->set_pelvishalflength(0.5f);
m_currentBirdData->set_winghalflength(0.5f);
m_currentBirdData->set_hoistmass(0.0f);
m_currentBirdData->set_pelvismass(2.0f);
m_currentBirdData->set_wingmass(0.5f);
make_Vector3d(btVector3(0.f, 0.f, 0.f), m_currentBirdData->mutable_pelvisrelpostoattachwing());
make_Vector3d(btVector3(0.f, 0.f, 0.f), m_currentBirdData->mutable_featherrelpostoattachfeather());
m_currentBirdData->set_wingflaphingelimit(90.f);
m_currentBirdData->set_featheraoahingelimit(40.f);
m_currentBirdData->set_featheraoamotormaximpulse(0.05f);
m_currentBirdData->set_wingflapmotormaximpulse(1.0f);
m_currentBirdData->set_randseed((unsigned int)time(NULL));
srand(m_currentBirdData->randseed());
int numPoints = kNumSamplesInWingbeat;
if(m_numGeneration == 0) {
fillWithRandomNumbers(m_currentBirdData);
//fillWithRun(m_currentBirdData);
} else if (m_numGeneration > 0 && (m_giveBirdThisId % kNumBirdsPerGeneration) == 0) {
m_currentBirdData->CopyFrom(*m_currentBestInfo);
} else if (m_numGeneration > 0) {
perturbBestResult(*m_currentBestInfo, m_currentBirdData);
}
//std::cout << m_currentBirdData->wingbeatdata().DebugString() << std::endl;
m_currentTrajectoryData = new proto::TrajectoryData();
m_bigbird = new BigBird(m_ownerWorld, *m_currentBirdLocalParam,*m_currentBirdData);
}
void RagdollDemo::initPhysics()
{
// Setup the basic world
setTexturing(true);
setShadows(true);
setCameraDistance(btScalar(5.));
m_collisionConfiguration = new btDefaultCollisionConfiguration();
m_dispatcher = new btCollisionDispatcher(m_collisionConfiguration);
btVector3 worldAabbMin(-10000,-10000,-10000);
btVector3 worldAabbMax(10000,10000,10000);
m_broadphase = new btAxisSweep3 (worldAabbMin, worldAabbMax);
m_solver = new btSequentialImpulseConstraintSolver;
m_dynamicsWorld = new btDiscreteDynamicsWorld(m_dispatcher,m_broadphase,m_solver,m_collisionConfiguration);
//m_dynamicsWorld->getDispatchInfo().m_useConvexConservativeDistanceUtil = true;
//m_dynamicsWorld->getDispatchInfo().m_convexConservativeDistanceThreshold = 0.01f;
// Setup a big ground box
{
btCollisionShape* groundShape = new btBoxShape(btVector3(btScalar(200.),btScalar(10.),btScalar(200.)));
m_collisionShapes.push_back(groundShape);
btTransform groundTransform;
groundTransform.setIdentity();
groundTransform.setOrigin(btVector3(0,-10,0));
#define CREATE_GROUND_COLLISION_OBJECT 1
#ifdef CREATE_GROUND_COLLISION_OBJECT
btCollisionObject* fixedGround = new btCollisionObject();
fixedGround->setCollisionShape(groundShape);
fixedGround->setWorldTransform(groundTransform);
m_dynamicsWorld->addCollisionObject(fixedGround);
#else
localCreateRigidBody(btScalar(0.),groundTransform,groundShape);
#endif //CREATE_GROUND_COLLISION_OBJECT
}
// Spawn one ragdoll
btVector3 startOffset(1,0.5,0);
spawnRagdoll(startOffset);
startOffset.setValue(-1,0.5,0);
spawnRagdoll(startOffset);
clientResetScene();
}
void MotorDemo::initPhysics()
{
setTexturing(true);
setShadows(true);
// Setup the basic world
m_Time = 0;
m_fCyclePeriod = 2000.f; // in milliseconds
// m_fMuscleStrength = 0.05f;
// new SIMD solver for joints clips accumulated impulse, so the new limits for the motor
// should be (numberOfsolverIterations * oldLimits)
// currently solver uses 10 iterations, so:
m_fMuscleStrength = 0.5f;
setCameraDistance(btScalar(5.));
m_collisionConfiguration = new btDefaultCollisionConfiguration();
m_dispatcher = new btCollisionDispatcher(m_collisionConfiguration);
btVector3 worldAabbMin(-10000,-10000,-10000);
btVector3 worldAabbMax(10000,10000,10000);
m_broadphase = new btAxisSweep3 (worldAabbMin, worldAabbMax);
m_solver = new btSequentialImpulseConstraintSolver;
m_dynamicsWorld = new btDiscreteDynamicsWorld(m_dispatcher,m_broadphase,m_solver,m_collisionConfiguration);
m_dynamicsWorld->setInternalTickCallback(motorPreTickCallback,this,true);
// Setup a big ground box
{
btCollisionShape* groundShape = new btBoxShape(btVector3(btScalar(200.),btScalar(10.),btScalar(200.)));
m_collisionShapes.push_back(groundShape);
btTransform groundTransform;
groundTransform.setIdentity();
groundTransform.setOrigin(btVector3(0,-10,0));
localCreateRigidBody(btScalar(0.),groundTransform,groundShape);
}
// Spawn one ragdoll
btVector3 startOffset(1,0.5,0);
spawnTestRig(startOffset, false);
startOffset.setValue(-2,0.5,0);
spawnTestRig(startOffset, true);
clientResetScene();
}
void RagdollApp::initPhysics()
{
// Setup the basic world
m_time = 0;
m_CycPerKnee = 2000.f; // in milliseconds
m_CycPerHip = 3000.f; // in milliseconds
m_fMuscleStrength = 0.5f;
setTexturing(true);
setShadows(true);
setCameraDistance(btScalar(5.));
m_collisionConfiguration = new btDefaultCollisionConfiguration();
m_dispatcher = new btCollisionDispatcher(m_collisionConfiguration);
btVector3 worldAabbMin(-10000,-10000,-10000);
btVector3 worldAabbMax(10000,10000,10000);
m_broadphase = new btAxisSweep3 (worldAabbMin, worldAabbMax);
m_solver = new btSequentialImpulseConstraintSolver;
m_dynamicsWorld = new btDiscreteDynamicsWorld(m_dispatcher,m_broadphase,m_solver,m_collisionConfiguration);
//m_dynamicsWorld->getDispatchInfo().m_useConvexConservativeDistanceUtil = true;
//m_dynamicsWorld->getDispatchInfo().m_convexConservativeDistanceThreshold = 0.01f;
m_dynamicsWorld->setInternalTickCallback( forcePreTickCB, this, true );
m_dynamicsWorld->setGravity( btVector3(0,-0,0) );
// create surface
//createSurface();
//// Setup a big ground box
btCollisionShape* groundShape = new btBoxShape(btVector3(btScalar(200.),btScalar(10.),btScalar(200.)));
m_collisionShapes.push_back(groundShape);
btTransform groundTransform;
groundTransform.setIdentity();
groundTransform.setOrigin(btVector3(0,-10,0));
btCollisionObject* fixedGround = new btCollisionObject();
fixedGround->setCollisionShape(groundShape);
fixedGround->setWorldTransform(groundTransform);
m_dynamicsWorld->addCollisionObject(fixedGround);
// Spawn one ragdoll
btVector3 startOffset(1,0.5,0);
spawnRagdoll(startOffset);
startOffset.setValue(-1,0.1,0);
spawnRagdoll(startOffset);
clientResetScene();
}
bool EFXFixture::saveXML(QDomDocument* doc, QDomElement* efx_root) const
{
QDomElement subtag;
QDomElement tag;
QDomText text;
Q_ASSERT(doc != NULL);
Q_ASSERT(efx_root != NULL);
/* EFXFixture */
tag = doc->createElement(KXMLQLCEFXFixture);
efx_root->appendChild(tag);
/* Fixture ID */
subtag = doc->createElement(KXMLQLCEFXFixtureID);
tag.appendChild(subtag);
text = doc->createTextNode(QString("%1").arg(head().fxi));
subtag.appendChild(text);
/* Fixture Head */
subtag = doc->createElement(KXMLQLCEFXFixtureHead);
tag.appendChild(subtag);
text = doc->createTextNode(QString("%1").arg(head().head));
subtag.appendChild(text);
/* Mode */
subtag = doc->createElement(KXMLQLCEFXFixtureMode);
tag.appendChild(subtag);
text = doc->createTextNode(QString::number(mode ()));
subtag.appendChild(text);
/* Direction */
subtag = doc->createElement(KXMLQLCEFXFixtureDirection);
tag.appendChild(subtag);
text = doc->createTextNode(Function::directionToString(m_direction));
subtag.appendChild(text);
/* Start offset */
subtag = doc->createElement(KXMLQLCEFXFixtureStartOffset);
tag.appendChild(subtag);
text = doc->createTextNode(QString::number(startOffset()));
subtag.appendChild(text);
/* Intensity */
subtag = doc->createElement(KXMLQLCEFXFixtureIntensity);
tag.appendChild(subtag);
text = doc->createTextNode(QString::number(fadeIntensity()));
subtag.appendChild(text);
return true;
}
void SimulationVisual::keyboardCallback(unsigned char key, int x, int y)
{
switch (key)
{
case 'e':
{
btVector3 startOffset(0,2,0);
spawnRagdoll(startOffset);
break;
}
default:
GlutDemoApplication::keyboardCallback(key, x, y);
}
}
bool K3bAudioCdTrackSource::seek( const K3b::Msf& msf )
{
// HACK: to reinitialize every time we restart the decoding
if( msf == 0 && m_cdParanoiaLib )
closeParanoia();
m_position = msf;
if( m_cdParanoiaLib )
m_cdParanoiaLib->initReading( m_toc[m_cdTrackNumber-1].firstSector().lba() + startOffset().lba() + m_position.lba(),
m_toc[m_cdTrackNumber-1].firstSector().lba() + lastSector().lba() );
return true;
}
void RagdollDemo::keyboardCallback(unsigned char key, int x, int y)
{
switch (key)
{
case 'e':
{
btVector3 startOffset(0,2,0);
spawnRagdoll(startOffset);
break;
}
default:
DemoApplication::keyboardCallback(key, x, y);
case 'p':
{
if(pause)
pause = FALSE;
else
pause = TRUE;
}
case 'o':
{
if(oneStep)
{
oneStep = FALSE;
}
else
{
oneStep = TRUE;
}
}
case 'z':
{
//cout << "SIZE: " << sizeof(collisionID)/sizeof(collisionID[0]) << endl;
for(int i = 0; i < sizeof(collisionID)/sizeof(collisionID[0]); i++)
{
/*
cout << i << ": " << collisionID[i]->id;
cout << " | ADDRESS: " << collisionID[i];
cout << " | HIT: " << collisionID[i]->hit;
cout << " | Colliosion Flags: " << collisionID[i]->body->getCollisionFlags() << endl;
*/
}
}
}
}
void ChainBtDynamics::initPhysics()
{
// Setup the basic world
m_collisionConfiguration = new btDefaultCollisionConfiguration();
m_dispatcher = new btCollisionDispatcher(m_collisionConfiguration);
btVector3 worldAabbMin(-10000,-10000,-10000);
btVector3 worldAabbMax(10000,10000,10000);
m_broadphase = new btAxisSweep3 (worldAabbMin, worldAabbMax);
m_solver = new btSequentialImpulseConstraintSolver;
m_dynamicsWorld = new btDiscreteDynamicsWorld(m_dispatcher,m_broadphase,m_solver,m_collisionConfiguration);
//m_dynamicsWorld->setGravity(btVector3(0.0f, -9.8f*GRAVITY_SCALE, 0.0f));
//m_dynamicsWorld->setGravity(btVector3(0.0f, 0.1f*GRAVITY_SCALE, 0.0f));
//m_dynamicsWorld->setGravity(btVector3(0.0f, -3.0f*GRAVITY_SCALE, 0.0f));
m_dynamicsWorld->setGravity(btVector3(0.0f, 0.00f*GRAVITY_SCALE, 0.0f));
//m_dynamicsWorld->getDispatchInfo().m_useConvexConservativeDistanceUtil = true;
//m_dynamicsWorld->getDispatchInfo().m_convexConservativeDistanceThreshold = 0.01f;
// Setup a big ground box
//{
// //btCollisionShape* groundShape = new btBoxShape(btVector3(btScalar(1.5),btScalar(0.1),btScalar(1.5)));
//
// btCollisionShape* groundShape = new btBoxShape(btVector3(btScalar(3000.0f),
// btScalar(600.0f),
// btScalar(3000.0f)));
// m_collisionShapes.push_back(groundShape);
// btTransform groundTransform;
// groundTransform.setIdentity();
// //groundTransform.setOrigin(btVector3(0,-10,0));
// groundTransform.setOrigin(btVector3(0,-600.0f,0));
//
// btCollisionObject* fixedGround = new btCollisionObject();
// fixedGround->setCollisionShape(groundShape);
// fixedGround->setWorldTransform(groundTransform);
// m_groundInfo.isGround = true;
// fixedGround->setUserPointer(&m_groundInfo);
//
// m_dynamicsWorld->addCollisionObject(fixedGround);
//}
btVector3 startOffset(0,100,0);
clientResetScene();
}
void Simulation::initPhysics()
{
// setup the ANN
ANN* neuralNet = new ANN();
neuralNet->loadXML();
// Setup the basic world
m_collisionConfiguration = new btDefaultCollisionConfiguration();
m_dispatcher = new btCollisionDispatcher(m_collisionConfiguration);
btVector3 worldAabbMin(-10000,-10000,-10000);
btVector3 worldAabbMax(10000,10000,10000);
m_broadphase = new btAxisSweep3 (worldAabbMin, worldAabbMax);
m_solver = new btSequentialImpulseConstraintSolver;
m_dynamicsWorld = new btDiscreteDynamicsWorld(m_dispatcher, m_broadphase,
m_solver,m_collisionConfiguration);
//tick = 0;
m_dynamicsWorld->setInternalTickCallback(robotPreTickCallback, this, true);
// Setup a big ground box
{
btCollisionShape* groundShape = new btBoxShape(btVector3(btScalar(200.),
btScalar(10.),btScalar(200.)));
m_collisionShapes.push_back(groundShape);
btTransform groundTransform;
groundTransform.setIdentity();
groundTransform.setOrigin(btVector3(0,-10,0));
btCollisionObject* fixedGround = new btCollisionObject();
fixedGround->setCollisionShape(groundShape);
fixedGround->setWorldTransform(groundTransform);
m_dynamicsWorld->addCollisionObject(fixedGround);
}
// Spawn one ragdoll
btVector3 startOffset(1,0.5,0);
spawnRagdoll(startOffset);
}
void RagdollDemo::keyboardCallback(unsigned char key, int x, int y)
{
switch (key)
{
case 'p':
pause = !pause;
break;
case 'o':
oneStep = true;
break;
case 'e':
{
btVector3 startOffset(0,2,0);
spawnRagdoll(startOffset);
break;
}
default:
DemoApplication::keyboardCallback(key, x, y);
}
}
void Text3D::computeGlyphRepresentation()
{
if (_font.valid() == false) return;
_textRenderInfo.clear();
_lineCount = 0;
if (_text.empty())
{
_textBB.set(0,0,0, 0,0,0);//no size text
TextBase::computePositions(); //to reset the origin
return;
}
// initialize bounding box, it will be expanded during glyph position calculation
_textBB.init();
osg::Vec2 startOfLine_coords(0.0f,0.0f);
osg::Vec2 cursor(startOfLine_coords);
osg::Vec2 local(0.0f,0.0f);
osg::Vec2 startOffset(0.0f,0.0f);
unsigned int previous_charcode = 0;
unsigned int linelength = 0;
bool kerning = true;
unsigned int lineNumber = 0;
for(String::iterator itr=_text.begin(); itr!=_text.end(); )
{
_textRenderInfo.resize(lineNumber + 1);
LineRenderInfo & currentLineRenderInfo = _textRenderInfo.back();
// record the start of the current line
String::iterator startOfLine_itr = itr;
// find the end of the current line.
osg::Vec2 endOfLine_coords(cursor);
String::iterator endOfLine_itr = computeLastCharacterOnLine(endOfLine_coords, itr,_text.end());
// ** position the cursor function to the Layout and the alignement
TextBase::positionCursor(endOfLine_coords, cursor, (unsigned int) (endOfLine_itr - startOfLine_itr));
if (itr!=endOfLine_itr)
{
for(;itr!=endOfLine_itr;++itr)
{
unsigned int charcode = *itr;
Font3D::Glyph3D* glyph = _font->getGlyph(charcode);
if (glyph)
{
const osg::BoundingBox & bb = glyph->getBoundingBox();
// adjust cursor position w.r.t any kerning.
if (previous_charcode)
{
if (_layout == RIGHT_TO_LEFT)
{
cursor.x() -= glyph->getHorizontalAdvance();
}
if (kerning)
{
switch (_layout)
{
case LEFT_TO_RIGHT:
{
cursor += _font->getKerning(previous_charcode, charcode, _kerningType);
break;
}
case RIGHT_TO_LEFT:
{
cursor -= _font->getKerning(charcode, previous_charcode, _kerningType);
break;
}
case VERTICAL:
break; // no kerning when vertical.
}
}
}
else
{
switch (_layout)
{
case LEFT_TO_RIGHT:
{
cursor.x() -= glyph->getHorizontalBearing().x();
break;
}
case RIGHT_TO_LEFT:
{
cursor.x() -= bb.xMax();
break;
}
case VERTICAL:
{
// cursor.y() += glyph->getVerticalBearing().y();
break;
}
}
}
local = cursor;
if (_layout==VERTICAL)
{
local.x() += -glyph->getVerticalBearing().x();
local.y() += -glyph->getVerticalBearing().y();
}
// move the cursor onto the next character.
// also expand bounding box
switch (_layout)
{
case LEFT_TO_RIGHT:
_textBB.expandBy(osg::Vec3(cursor.x() + bb.xMin(), cursor.y() + bb.yMin(), 0.0f)); //lower left corner
_textBB.expandBy(osg::Vec3(cursor.x() + bb.xMax(), cursor.y() + bb.yMax(), 0.0f)); //upper right corner
cursor.x() += glyph->getHorizontalAdvance();
break;
case VERTICAL:
_textBB.expandBy(osg::Vec3(cursor.x(), cursor.y(), 0.0f)); //upper left corner
_textBB.expandBy(osg::Vec3(cursor.x() + glyph->getWidth(), cursor.y() - glyph->getHeight(), 0.0f)); //lower right corner
cursor.y() -= glyph->getVerticalAdvance();
break;
case RIGHT_TO_LEFT:
_textBB.expandBy(osg::Vec3(cursor.x()+bb.xMax(), cursor.y() + bb.yMax(), 0.0f)); //upper right corner
_textBB.expandBy(osg::Vec3(cursor.x()+bb.xMin(), cursor.y()+bb.yMin(), 0.0f)); //lower left corner
break;
}
osg::Vec3 pos = osg::Vec3(local.x(), local.y(), 0.0f);
currentLineRenderInfo.push_back(Text3D::GlyphRenderInfo(glyph, pos));
previous_charcode = charcode;
}
}
}
else
{
++itr;
}
if (itr!=_text.end())
{
// skip over return.
if (*itr=='\n') ++itr;
}
// move to new line.
switch(_layout)
{
case LEFT_TO_RIGHT:
case RIGHT_TO_LEFT:
{
startOfLine_coords.y() -= (1.0 + _lineSpacing) / _font->getScale();
++_lineCount;
break;
}
case VERTICAL:
{
startOfLine_coords.x() += _characterHeight / _font->getScale() / _characterAspectRatio * (1.0 + _lineSpacing);
// because _lineCount is the max vertical no. of characters....
_lineCount = (_lineCount >linelength)?_lineCount:linelength;
break;
}
default:
break;
}
cursor = startOfLine_coords;
previous_charcode = 0;
++lineNumber;
}
_textBB.expandBy(0.0f,0.0f,-1);
TextBase::computePositions();
}
int main(int argc, char **argv)
{
ros::init(argc, argv, "msf_eval");
ros::Time::init();
enum argIndices{
bagfile = 1,
EVAL_topic = 2,
GT_topic = 3,
singleRunOnly = 4
};
//calibration of sensor to vicon
Eigen::Matrix4d T_BaBg_mat;
//this is the Vicon one - SLAM sensor V0
///////////////////////////////////////////////////////////////////////////////////////////
T_BaBg_mat << 0.999706627053000, -0.022330158354000, 0.005123243528000, -0.060614697387000, 0.022650462142000, 0.997389634278000, -0.068267398302000, 0.035557942651000, -0.003589706237000, 0.068397960288000, 0.997617159323000, -0.042589657349000, 0, 0, 0, 1.000000000000000;
////////////////////////////////////////////////////////////////////////////////////////////
ros::Duration dt(0.0039);
const double timeSyncThreshold = 0.005;
const double timeDiscretization = 10.0; //discretization step for different starting points into the dataset
const double trajectoryTimeDiscretization = 0.049; //discretization of evaluation points (vision framerate for fair comparison)
const double startTimeOffset = 10.0;
if (argc < 4)
{
MSF_ERROR_STREAM("usage: ./"<<argv[0]<<" bagfile EVAL_topic GT_topic [singleRunOnly]");
return -1;
}
bool singleRun = false;
if (argc == 5)
{
singleRun = atoi(argv[singleRunOnly]);
}
if(singleRun){
MSF_WARN_STREAM("Doing only a single run.");
}else{
MSF_WARN_STREAM("Will process the dataset from different starting points.");
}
typedef geometry_msgs::TransformStamped GT_TYPE;
typedef geometry_msgs::PoseWithCovarianceStamped EVAL_TYPE;
// output file
std::stringstream matlab_fname;
std::string path = ros::package::getPath("msf_eval");
matlab_fname << path << "/Matlab/matlab_data" << ros::Time::now().sec << ".m";
std::ofstream outfile(matlab_fname.str().c_str());
std::stringstream poses_EVAL;
std::stringstream poses_GT;
assert(outfile.good());
outfile << "data=[" << std::endl;
ros::Duration startOffset(startTimeOffset);
sm::kinematics::Transformation T_BaBg(T_BaBg_mat); //body aslam to body Ground Truth
// open for reading
rosbag::Bag bag(argv[bagfile], rosbag::bagmode::Read);
// views on topics
rosbag::View view_EVAL(bag, rosbag::TopicQuery(argv[EVAL_topic]));
rosbag::View view_GT(bag, rosbag::TopicQuery(argv[GT_topic]));
//check topics
if (view_EVAL.size() == 0)
{
MSF_ERROR_STREAM("The bag you provided does not contain messages for topic "<<argv[EVAL_topic]);
return -1;
}
if (view_GT.size() == 0)
{
MSF_ERROR_STREAM("The bag you provided does not contain messages for topic "<<argv[GT_topic]);
return -1;
}
//litter console with number of messages
MSF_INFO_STREAM("Reading from "<<argv[bagfile]);
MSF_INFO_STREAM("Topic "<<argv[EVAL_topic]<<", size: "<<view_EVAL.size());
MSF_INFO_STREAM("Topic "<<argv[GT_topic]<<", size: "<<view_GT.size());
//get times of first messages
GT_TYPE::ConstPtr GT_begin = view_GT.begin()->instantiate<GT_TYPE>();
assert(GT_begin);
EVAL_TYPE::ConstPtr POSE_begin = view_EVAL.begin()->instantiate<EVAL_TYPE>();
assert(POSE_begin);
MSF_INFO_STREAM("First GT data at "<<GT_begin->header.stamp);
MSF_INFO_STREAM("First EVAL data at "<<POSE_begin->header.stamp);
while (true) // start eval from different starting points
{
rosbag::View::const_iterator it_EVAL = view_EVAL.begin();
rosbag::View::const_iterator it_GT = view_GT.begin();
// read ground truth
ros::Time start;
// Find start time alignment: set the GT iterater to point to a time larger than the aslam time
while (true)
{
GT_TYPE::ConstPtr trafo = it_GT->instantiate<GT_TYPE>();
assert(trafo);
ros::Time time_GT;
time_GT = trafo->header.stamp + dt;
EVAL_TYPE::ConstPtr pose = it_EVAL->instantiate<EVAL_TYPE>();
assert(pose);
ros::Time time_EKF;
time_EKF = pose->header.stamp;
if (time_EKF >= time_GT)
{
it_GT++;
if (it_GT == view_GT.end())
{
MSF_ERROR_STREAM("Time synchronization failed");
return false;
}
}
else
{
start = time_GT;
MSF_INFO_STREAM("Time synced! GT start: "<<start <<" EVAL start: "<<time_EKF);
break;
}
}
// world frame alignment
sm::kinematics::Transformation T_WaBa;
sm::kinematics::Transformation T_WgBg;
sm::kinematics::Transformation T_WgBg_last;
sm::kinematics::Transformation T_WaWg;
// now find the GT/EKF pairings
int ctr = 0; //how many meas did we add this run?
double ds = 0.0; // distance travelled
ros::Time lastTime(0.0);
MSF_INFO_STREAM("Processing measurements... Current start point: "<<startOffset<<"s into the bag.");
for (; it_GT != view_GT.end(); ++it_GT)
{
GT_TYPE::ConstPtr trafo = it_GT->instantiate<GT_TYPE>();
assert(trafo);
// find closest timestamp
ros::Time time_GT = trafo->header.stamp + dt;
EVAL_TYPE::ConstPtr pose = it_EVAL->instantiate<EVAL_TYPE>();
assert(pose);
ros::Time time_EKF = pose->header.stamp;
bool terminate = false;
//get the measurement close to this GT value
while (time_GT > time_EKF)
{
it_EVAL++;
if (it_EVAL == view_EVAL.end())
{
terminate = true;
MSF_INFO_STREAM("done. All EKF meas processed!");
break;
}
pose = it_EVAL->instantiate<EVAL_TYPE>();
assert(pose);
time_EKF = pose->header.stamp;
}
if (terminate){
break;
}
// add comparison value
if (time_GT - start >= startOffset)
{
T_WaBa = sm::kinematics::Transformation(
Eigen::Vector4d(-pose->pose.pose.orientation.x, -pose->pose.pose.orientation.y,
-pose->pose.pose.orientation.z, pose->pose.pose.orientation.w),
Eigen::Vector3d(pose->pose.pose.position.x, pose->pose.pose.position.y, pose->pose.pose.position.z));
T_WgBg = sm::kinematics::Transformation(
Eigen::Vector4d(-trafo->transform.rotation.x, -trafo->transform.rotation.y, -trafo->transform.rotation.z,
trafo->transform.rotation.w),
Eigen::Vector3d(trafo->transform.translation.x, trafo->transform.translation.y,
trafo->transform.translation.z));
// initial alignment
if (ctr == 0)
{
T_WaWg = (T_WaBa) * T_BaBg * T_WgBg.inverse();
T_WgBg_last = T_WgBg;
}
sm::kinematics::Transformation dT = T_WaBa * (T_WaWg * T_WgBg * T_BaBg.inverse()).inverse();
sm::kinematics::Transformation T_WaBa_gt = (T_WaWg * T_WgBg * T_BaBg.inverse());
T_WaBa_gt = sm::kinematics::Transformation(T_WaBa_gt.q().normalized(), T_WaBa_gt.t());
dT = sm::kinematics::Transformation(dT.q().normalized(), dT.t());
// update integral
if (trafo)
{
ds += (T_WgBg.t() - T_WgBg_last.t()).norm();
// store last GT transformation
T_WgBg_last = T_WgBg;
}
else
{
// too noisy
if ((T_WgBg * T_WgBg_last.inverse()).t().norm() > .1)
{
ds += (T_WgBg.t() - T_WgBg_last.t()).norm();
//MSF_INFO_STREAM((T_WgBg*T_WgBg_last.inverse()).t().norm());
// store last GT transformation
T_WgBg_last = T_WgBg;
}
}
Eigen::Vector3d dalpha;
if (dT.q().head<3>().norm() > 1e-12)
{
dalpha = (asin(dT.q().head<3>().norm()) * 2 * dT.q().head<3>().normalized());
}
else
{
dalpha = 2 * dT.q().head<3>();
}
// g-vector alignment
Eigen::Vector3d e_z_Wg(0, 0, 1);
Eigen::Vector3d e_z_Wa = dT.C() * e_z_Wg;
double dalpha_e_z = acos(std::min(1.0, e_z_Wg.dot(e_z_Wa)));
if (fabs((time_GT - time_EKF).toSec()) < timeSyncThreshold
&& (time_EKF - lastTime).toSec() > trajectoryTimeDiscretization)
{
if (startOffset.toSec() == startTimeOffset)
{
poses_EVAL << T_WaBa.t().transpose() << ";" << std::endl;
poses_GT << T_WgBg.t().transpose() << ";" << std::endl;
}
Eigen::Matrix<double, 6, 6> cov = getCovariance(pose);
outfile << (time_GT - start).toSec() << " "
<< ds << " " << (T_WaBa.t() - T_WaBa_gt.t()).norm() << " " //translation
<< 2 * acos(std::min(1.0, fabs(dT.q()[3]))) << " " << dalpha_e_z << " " //orientation
<<cov(0, 0)<<" "<<cov(1, 1)<<" "<<cov(2, 2)<<" " //position covariances
<<cov(3, 3)<<" "<<cov(4, 4)<<" "<<cov(5, 5)<<";" //orientation covariances
<< std::endl;
lastTime = time_EKF; // remember
}
// count comparisons
ctr++;
}
}
MSF_INFO_STREAM("Added "<<ctr<<" measurement edges.");
//where in the bag should the next eval start
startOffset += ros::Duration(timeDiscretization);
if (ctr == 0 || singleRun) //any new measurements this run?
{
break;
}
}
// cleanup
bag.close();
outfile << "];";
outfile << "poses = [" << poses_EVAL.str() << "];" << std::endl;
outfile << "poses_GT = [" << poses_GT.str() << "];" << std::endl;
outfile.close();
return 0;
}
bool EFX::saveXML(QDomDocument* doc, QDomElement* wksp_root)
{
QDomElement root;
QDomElement tag;
QDomElement subtag;
QDomText text;
QString str;
Q_ASSERT(doc != NULL);
Q_ASSERT(wksp_root != NULL);
/* Function tag */
root = doc->createElement(KXMLQLCFunction);
wksp_root->appendChild(root);
root.setAttribute(KXMLQLCFunctionID, id());
root.setAttribute(KXMLQLCFunctionType, Function::typeToString(type()));
root.setAttribute(KXMLQLCFunctionName, name());
/* Fixtures */
QListIterator <EFXFixture*> it(m_fixtures);
while (it.hasNext() == true)
it.next()->saveXML(doc, &root);
/* Propagation mode */
tag = doc->createElement(KXMLQLCEFXPropagationMode);
root.appendChild(tag);
text = doc->createTextNode(propagationModeToString(m_propagationMode));
tag.appendChild(text);
/* Speeds */
saveXMLSpeed(doc, &root);
/* Direction */
saveXMLDirection(doc, &root);
/* Run order */
saveXMLRunOrder(doc, &root);
/* Algorithm */
tag = doc->createElement(KXMLQLCEFXAlgorithm);
root.appendChild(tag);
text = doc->createTextNode(algorithmToString(algorithm()));
tag.appendChild(text);
/* Width */
tag = doc->createElement(KXMLQLCEFXWidth);
root.appendChild(tag);
str.setNum(width());
text = doc->createTextNode(str);
tag.appendChild(text);
/* Height */
tag = doc->createElement(KXMLQLCEFXHeight);
root.appendChild(tag);
str.setNum(height());
text = doc->createTextNode(str);
tag.appendChild(text);
/* Rotation */
tag = doc->createElement(KXMLQLCEFXRotation);
root.appendChild(tag);
str.setNum(rotation());
text = doc->createTextNode(str);
tag.appendChild(text);
/* StartOffset */
tag = doc->createElement(KXMLQLCEFXStartOffset);
root.appendChild(tag);
str.setNum(startOffset());
text = doc->createTextNode(str);
tag.appendChild(text);
/********************************************
* X-Axis
********************************************/
tag = doc->createElement(KXMLQLCEFXAxis);
root.appendChild(tag);
tag.setAttribute(KXMLQLCFunctionName, KXMLQLCEFXX);
/* Offset */
subtag = doc->createElement(KXMLQLCEFXOffset);
tag.appendChild(subtag);
str.setNum(xOffset());
text = doc->createTextNode(str);
subtag.appendChild(text);
/* Frequency */
subtag = doc->createElement(KXMLQLCEFXFrequency);
tag.appendChild(subtag);
str.setNum(xFrequency());
text = doc->createTextNode(str);
subtag.appendChild(text);
/* Phase */
subtag = doc->createElement(KXMLQLCEFXPhase);
tag.appendChild(subtag);
str.setNum(xPhase());
text = doc->createTextNode(str);
subtag.appendChild(text);
/********************************************
* Y-Axis
********************************************/
tag = doc->createElement(KXMLQLCEFXAxis);
root.appendChild(tag);
tag.setAttribute(KXMLQLCFunctionName, KXMLQLCEFXY);
/* Offset */
subtag = doc->createElement(KXMLQLCEFXOffset);
tag.appendChild(subtag);
str.setNum(yOffset());
text = doc->createTextNode(str);
subtag.appendChild(text);
/* Frequency */
subtag = doc->createElement(KXMLQLCEFXFrequency);
tag.appendChild(subtag);
str.setNum(yFrequency());
text = doc->createTextNode(str);
subtag.appendChild(text);
/* Phase */
subtag = doc->createElement(KXMLQLCEFXPhase);
tag.appendChild(subtag);
str.setNum(yPhase());
text = doc->createTextNode(str);
subtag.appendChild(text);
return true;
}
void RagdollDemo::initPhysics()
{
// Setup the basic world
setTexturing(true);
setShadows(true);
setCameraDistance(btScalar(5.));
m_collisionConfiguration = new btDefaultCollisionConfiguration();
m_dispatcher = new btCollisionDispatcher(m_collisionConfiguration);
btVector3 worldAabbMin(-10000,-10000,-10000);
btVector3 worldAabbMax(10000,10000,10000);
m_broadphase = new btAxisSweep3 (worldAabbMin, worldAabbMax);
m_solver = new btSequentialImpulseConstraintSolver;
m_dynamicsWorld = new btDiscreteDynamicsWorld(m_dispatcher,m_broadphase,m_solver,m_collisionConfiguration);
//m_dynamicsWorld->getDispatchInfo().m_useConvexConservativeDistanceUtil = true;
//m_dynamicsWorld->getDispatchInfo().m_convexConservativeDistanceThreshold = 0.01f;
// Setup a big ground box
{
btCollisionShape* groundShape = new btBoxShape(btVector3(btScalar(200.),btScalar(10.),btScalar(200.)));
m_collisionShapes.push_back(groundShape);
btTransform groundTransform;
groundTransform.setIdentity();
groundTransform.setOrigin(btVector3(0,-10,0));
#define CREATE_GROUND_COLLISION_OBJECT 1
#ifdef CREATE_GROUND_COLLISION_OBJECT
btCollisionObject* fixedGround = new btCollisionObject();
fixedGround->setCollisionShape(groundShape);
fixedGround->setWorldTransform(groundTransform);
m_dynamicsWorld->addCollisionObject(fixedGround);
#else
localCreateRigidBody(btScalar(0.),groundTransform,groundShape);
#endif //CREATE_GROUND_COLLISION_OBJECT
}
// Spawn one ragdoll
btVector3 startOffset(1,0.5,0);
//spawnRagdoll(startOffset);
startOffset.setValue(-1,0.5,0);
//spawnRagdoll(startOffset);
CreateBox(0, 0., 2., 0., 1., 0.2, 1.); // Create the box
//leg components
CreateCylinder(1, 2. , 2., 0., .2, 1., 0., 0., M_PI_2); //xleft horizontal
CreateCylinder(2, -2., 2., 0., .2, 1., 0., 0., M_PI_2); //xright (negative) horizontal
CreateCylinder(3, 0, 2., 2., .2, 1., M_PI_2, 0., 0.); //zpositive (into screen)
CreateCylinder(4, 0, 2., -2., .2, 1., M_PI_2, 0., 0.); //znegative (out of screen)
CreateCylinder(5, 3.0, 1., 0., .2, 1., 0., 0., 0.); //xleft vertical
CreateCylinder(6, -3.0, 1., 0., .2, 1., 0., 0., 0.); //xright vertical
CreateCylinder(7, 0., 1., 3.0, .2, 1., 0., 0., 0.); //zpositive vertical
CreateCylinder(8, 0., 1., -3.0, .2, 1., 0., 0., 0.); //znegative vertical
//The axisworldtolocal defines a vector perpendicular to the plane that you want the bodies to rotate in
//hinge the legs together
//xnegative -- right
//two bodies should rotate in y-plane through x--give axisworldtolocal it a z vector
btVector3 local2 = PointWorldToLocal(2, btVector3(-3., 2., 0));
btVector3 local6 = PointWorldToLocal(6, btVector3(-3., 2., 0));
btVector3 axis2 = AxisWorldToLocal(2, btVector3(0., 0., 1.));
btVector3 axis6 = AxisWorldToLocal(6, btVector3( 0., 0., 1.));
CreateHinge(0, *body[2], *body[6], local2, local6, axis2, axis6);
joints[0]->setLimit(btScalar(0.), btScalar(M_PI_2+M_PI_4));
//positive -- left
//give axisworldtolocal a z vector
btVector3 local1 = PointWorldToLocal(1, btVector3(3., 2., 0));
btVector3 local5 = PointWorldToLocal(5, btVector3(3., 2., 0));
btVector3 axis1 = AxisWorldToLocal(1, btVector3( 0., 0., 1.));
btVector3 axis5 = AxisWorldToLocal(5, btVector3(0., 0., 1.));
CreateHinge(1, *body[1], *body[5], local1, local5, axis1, axis5);
joints[1]->setLimit(btScalar(M_PI_4), btScalar(M_PI_4));
//zpositive -- back
//rotates in y-plane through z--give it an x vector
btVector3 local3 = PointWorldToLocal(3, btVector3(0, 2., 3.));
btVector3 local7 = PointWorldToLocal(7, btVector3(0, 2., 3.));
btVector3 axis3 = AxisWorldToLocal(3, btVector3(1., 0., 0.));
btVector3 axis7 = AxisWorldToLocal(7, btVector3(1., 0., 0.));
CreateHinge(2, *body[3], *body[7], local3, local7, axis3, axis7);
joints[2]->setLimit(btScalar(0.), btScalar(M_PI_2+M_PI_4));
//znegative -- front
btVector3 local4 = PointWorldToLocal(4, btVector3(0, 2., -3.));
btVector3 local8 = PointWorldToLocal(8, btVector3(0, 2., -3.));
btVector3 axis4 = AxisWorldToLocal(4, btVector3(1., 0., 0.));
btVector3 axis8 = AxisWorldToLocal(8, btVector3(1., 0., 0.));
CreateHinge(3, *body[4], *body[8], local4, local8, axis4, axis8);
joints[3]->setLimit(btScalar(M_PI_4), btScalar(M_PI_4));
//hinge the legs to the body
//xright to main
btVector3 localHinge2 = PointWorldToLocal(2, btVector3(-1, 2., 0));
btVector3 mainHinge2 = PointWorldToLocal(0, btVector3(-1, 2., 0));
btVector3 localAxis2 = AxisWorldToLocal(2, btVector3(0., 0., 1.));
btVector3 mainAxis2 = AxisWorldToLocal(0, btVector3( 0., 0., 1.));
CreateHinge(4, *body[0], *body[2], mainHinge2, localHinge2, mainAxis2, localAxis2);
//joints[4]->setLimit(btScalar(-M_PI_2-M_PI_4), btScalar(M_PI_4));
//xleft to main
btVector3 localHinge1 = PointWorldToLocal(1, btVector3(1, 2., 0));
btVector3 mainHinge1 = PointWorldToLocal(0, btVector3(1, 2., 0));
btVector3 localAxis1 = AxisWorldToLocal(1, btVector3(0., 0., 1.));
btVector3 mainAxis1 = AxisWorldToLocal(0, btVector3( 0., 0., 1.));
CreateHinge(5, *body[0], *body[1], mainHinge1, localHinge1, mainAxis1, localAxis1);
//joints[5]->setLimit(btScalar(-M_PI_2), btScalar(M_PI_2));
//zpositive (back) to main
btVector3 localHinge3 = PointWorldToLocal(3, btVector3(0., 2., 1));
btVector3 mainHinge3 = PointWorldToLocal(0, btVector3(0., 2., 1));
btVector3 localAxis3 = AxisWorldToLocal(3, btVector3(1., 0., 0.));
btVector3 mainAxis3 = AxisWorldToLocal(0, btVector3( 1., 0., 0.));
CreateHinge(6, *body[0], *body[3], mainHinge3, localHinge3, mainAxis3, localAxis3);
//joints[6]->setLimit(btScalar(-M_PI_2-M_PI_4), btScalar(M_PI_4));
btVector3 localHinge4 = PointWorldToLocal(4, btVector3(0., 2., -1));
btVector3 mainHinge4= PointWorldToLocal(0, btVector3(0., 2., -1));
btVector3 localAxis4 = AxisWorldToLocal(4, btVector3(1., 0., 0. ));
btVector3 mainAxis4 = AxisWorldToLocal(0, btVector3( 1., 0., 0.));
CreateHinge(7, *body[0], *body[4], mainHinge4, localHinge4, mainAxis4, localAxis4);
//joints[7]->setLimit(btScalar(-M_PI_2), btScalar(M_PI_2));
clientResetScene();
}
void RagdollDemo::initPhysics()
{
// Setup the basic world
setTexturing(true);
setShadows(true);
setCameraDistance(btScalar(5.));
m_collisionConfiguration = new btDefaultCollisionConfiguration();
m_dispatcher = new btCollisionDispatcher(m_collisionConfiguration);
btVector3 worldAabbMin(-10000,-10000,-10000);
btVector3 worldAabbMax(10000,10000,10000);
m_broadphase = new btAxisSweep3 (worldAabbMin, worldAabbMax);
m_solver = new btSequentialImpulseConstraintSolver;
m_dynamicsWorld = new btDiscreteDynamicsWorld(m_dispatcher,m_broadphase,m_solver,m_collisionConfiguration);
//m_dynamicsWorld->getDispatchInfo().m_useConvexConservativeDistanceUtil = true;
//m_dynamicsWorld->getDispatchInfo().m_convexConservativeDistanceThreshold = 0.01f;
// Setup a big ground box
{
btCollisionShape* groundShape = new btBoxShape(btVector3(btScalar(200.),btScalar(10.),btScalar(200.)));
m_collisionShapes.push_back(groundShape);
btTransform groundTransform;
groundTransform.setIdentity();
groundTransform.setOrigin(btVector3(0,-10,0));
#define CREATE_GROUND_COLLISION_OBJECT 1
#ifdef CREATE_GROUND_COLLISION_OBJECT
btCollisionObject* fixedGround = new btCollisionObject();
fixedGround->setCollisionShape(groundShape);
fixedGround->setWorldTransform(groundTransform);
m_dynamicsWorld->addCollisionObject(fixedGround);
#else
localCreateRigidBody(btScalar(0.),groundTransform,groundShape);
#endif //CREATE_GROUND_COLLISION_OBJECT
}
// Spawn one ragdoll
btVector3 startOffset(1,0.5,0);
//spawnRagdoll(startOffset);
startOffset.setValue(-1,0.5,0);
//spawnRagdoll(startOffset);
CreateBox(0, 0., 0., 1., 1., 1., 0.2);
// fore limbs
CreateCylinder(1, 1., 0., 1., 0.1, 1., 1);
CreateCylinder(2, -1., 0., 1., 0.1, 1., 1);
CreateCylinder(3, 0., 1., 1., 0.1, 1., 2);
CreateCylinder(4, 0., -1., 1., 0.1, 1., 2);
CreateCylinder(5, 1.5, 0., .5, 0.1, 1., 3);
CreateCylinder(6, -1.5, 0., .5, 0.1, 1., 3);
CreateCylinder(7, 0., 1.5, .5, 0.1, 1., 3);
CreateCylinder(8, 0., -1.5, .5, 0.1, 1., 3);
btVector3 v = PointWorldToLocal(0, btVector3(0,1,0));
/* std::cerr << "v " << v[0] << " " << v[1] << " " << v[2] << std::endl; */
printf("(%f, %f, %f)\n", v[0], v[1], v[2]);
CreateHinge(0,
0, 1,
0.5, 0., 1.,
0., -1., 0.);
CreateHinge(1, 0, 2,
-.5, 0., 1.,
0., 1., 0.);
CreateHinge(2, 0, 3,
0., .5, 1.,
1., 0., 0.);
CreateHinge(3, 0, 4,
0., -.5, 1.,
-1., 0., 0.);
CreateHinge(4, 1, 5,
1.5, 0., 1.,
0., -1., 0.);
CreateHinge(5, 2, 6,
-1.5, 0., 1.,
0., 1., 0.);
CreateHinge(6, 3, 7,
0., 1.5, 1.,
1., 0., 0.);
CreateHinge(7, 4, 8,
0., -1.5, 1.,
-1., 0., 0.);
clientResetScene();
}
void VisItSimStripChart::paintEvent( QPaintEvent * )
{
int i =0;
float h = height();
float w = width();
QPen penLimits;
QPainter paint( this );
gridFont->setPointSize(pointSize);
paint.scale(1.0,zoom);
if ( center )
{
paint.translate( 0,points.back().y());
center = false;
}
// start drawing the data n times step away from the right
// hand edge of the window.
timeShift = int(w - ( (delta/2.0) * points.size()));
// do we have data to draw and are we enabled?
if ( points.empty()) return;
if ( !enabled ) return;
// display the grid
paintGrid( &paint);
VisItPointD startOffset(points.front().x(),0);
Points::iterator it;
// connect all points together to make the graph
for( it = points.begin(); it != points.end(); )
{
// Set the pen width and color
penLimits.setWidth(2);
// set pen color to normal
penLimits.setColor(Qt::darkGreen);
VisItPointD startPoint(0,0);
startPoint.setX( (*it).x() - startOffset.x());
startPoint.setY( (*it).y() - startOffset.y());
it++;
if ( it == points.end()) break;
VisItPointD endPoint(0,0);
endPoint.setX((*it).x() - startOffset.x());;
endPoint.setY((*it).y() - startOffset.y());;
// check to see if it is out of limit
if ( outOfBandLimitsEnabled )
{
if ( startPoint.y() > maxYLimit || startPoint.y() < minYLimit ||
endPoint.y() > maxYLimit || endPoint.y() < minYLimit )
{
// set pen color to out of limits
penLimits.setColor(Qt::red);
}
}
paint.setPen( penLimits );
QPoint startPoint_int;
QPoint endPoint_int;
// convert to screen space
startPoint_int.setX ( int(startPoint.x()*delta +timeShift));
startPoint_int.setY ( int ((h-((startPoint.y()-minPoint)*vdelta))));
endPoint_int.setX ( int(endPoint.x()*delta + timeShift));
endPoint_int.setY ( int((h-((endPoint.y()-minPoint)*vdelta)) ));
currentScaledY = ((h-((endPoint.y()-minPoint)*vdelta)) );
paint.drawLine( startPoint_int, endPoint_int ); // draw line
i++;
if ( i%10 == 0 )
{
paint.drawText( startPoint_int.x(),int(h-10), QString::number((*it).x()));
paint.drawText( startPoint_int.x(),int(middle*vdelta), QString::number((*it).x()));
paint.drawText( startPoint_int.x(),int(10), QString::number((*it).x()));
}
// draw limit extents
if ( outOfBandLimitsEnabled )
{
penLimits.setColor(Qt::red);
penLimits.setWidth(3);
paint.setPen( penLimits );
paint.drawLine( QPoint(int(0),int(h-((maxYLimit)-minPoint)*vdelta)), QPoint(int(w),int(h-((maxYLimit-minPoint)*vdelta)))); // draw line
paint.drawLine( QPoint(int(0),int(h-((minYLimit)-minPoint)*vdelta)), QPoint(int(w),int(h-((minYLimit)-minPoint)*vdelta))); // draw line
}
}
}
bool SVGTextPathElement::selfHasRelativeLengths() const
{
return startOffset().isRelative()
|| SVGTextContentElement::selfHasRelativeLengths();
}
int main (int argc, char *argv[]){
char *x, *y, *z, *xbuf, *hbuf, *chrNames[MAXNBCHR];
int fd;
off_t hsiz;
struct stat st;
MPI_File mpi_filed;
MPI_File mpi_file_split_comm;
MPI_Offset fileSize, unmapped_start, discordant_start;
int num_proc, rank;
int res, nbchr, i, paired, write_sam;
int ierr, errorcode = MPI_ERR_OTHER;
char *file_name, *output_dir;
char *header;
unsigned int headerSize;
unsigned char threshold;
size_t input_file_size;
size_t unmappedSize = 0;
size_t discordantSize = 0;
size_t *readNumberByChr = NULL, *localReadNumberByChr = NULL;
Read **reads;
double time_count;
double time_count1;
int g_rank, g_size;
MPI_Comm split_comm; //used to split communication when jobs have no reads to sort
int split_rank, split_size; //after split communication we update the rank and the size
double tic, toc;
int compression_level;
size_t fsiz, lsiz, loff;
const char *sort_name;
MPI_Info finfo;
/* Set default values */
compression_level = 3;
parse_mode = MODE_OFFSET;
sort_name = "coordinate";
paired = 0;
threshold = 0;
write_sam = 0;
/* Check command line */
while ((i = getopt(argc, argv, "c:hnpq:")) != -1) {
switch(i) {
case 'c': /* Compression level */
compression_level = atoi(optarg);
break;
case 'h': /* Usage display */
usage(basename(*argv));
return 0;
case 'n':
parse_mode = MODE_NAME;
sort_name = "queryname";
break;
case 'p': /* Paired reads */
paired = 1;
break;
case 'q': /* Quality threshold */
threshold = atoi(optarg);
break;
default:
usage(basename(*argv));
return 1;
}
}
if (argc - optind != 2) {
usage(basename(*argv));
return 1;
}
file_name = argv[optind];
output_dir = argv[optind+1];
/* Check arguments */
res = access(file_name, F_OK|R_OK);
if (res == -1)
err(1, "%s", file_name);
res = access(output_dir, F_OK|W_OK);
if (res == -1)
err(1, "%s", output_dir);
/* MPI inits */
res = MPI_Init(&argc, &argv);
assert(res == MPI_SUCCESS);
res = MPI_Comm_rank(MPI_COMM_WORLD, &rank);
assert(res == MPI_SUCCESS);
res = MPI_Comm_size(MPI_COMM_WORLD, &num_proc);
assert(res == MPI_SUCCESS);
g_rank = rank;
g_size = num_proc;
/* Small summary */
if (rank == 0) {
fprintf(stderr, "Number of processes : %d\n", num_proc);
fprintf(stderr, "Reads' quality threshold : %d\n", threshold);
fprintf(stderr, "Compression Level is : %d\n", compression_level);
fprintf(stderr, "SAM file to read : %s\n", file_name);
fprintf(stderr, "Output directory : %s\n", output_dir);
}
/* Process input file */
fd = open(file_name, O_RDONLY, 0666);
assert(fd != -1);
assert(fstat(fd, &st) != -1);
xbuf = mmap(NULL, (size_t)st.st_size, PROT_READ, MAP_FILE|MAP_PRIVATE, fd, 0);
assert(xbuf != MAP_FAILED);
/* Parse SAM header */
memset(chrNames, 0, sizeof(chrNames));
x = xbuf; nbchr = 0;
while (*x == '@') {
y = strchr(x, '\n');
z = x; x = y + 1;
if (strncmp(z, "@SQ", 3) != 0) continue;
/* Save reference names */
y = strstr(z, "SN:");
assert(y != NULL);
z = y + 3;
while (*z && !isspace((unsigned char)*z)) z++;
chrNames[nbchr++] = strndup(y + 3, z - y - 3);
assert(nbchr < MAXNBCHR - 2);
}
chrNames[nbchr++] = strdup(UNMAPPED);
chrNames[nbchr++] = strdup(DISCORDANT);
hsiz = x - xbuf;
hbuf = strndup(xbuf, hsiz);
if (rank == 0) {
fprintf(stderr, "The size of the file is %zu bytes\n", (size_t)st.st_size);
fprintf(stderr, "Header has %d+2 references\n", nbchr - 2);
}
asprintf(&header, "@HD\tVN:1.0\tSO:%s\n%s", sort_name, hbuf);
free(hbuf);
assert(munmap(xbuf, (size_t)st.st_size) != -1);
assert(close(fd) != -1);
//task FIRST FINE TUNING FINFO FOR READING OPERATIONS
MPI_Info_create(&finfo);
/*
* In this part you shall adjust the striping factor and unit according
* to the underlying filesystem.
* Harmless for other file system.
*
*/
MPI_Info_set(finfo,"striping_factor", STRIPING_FACTOR);
MPI_Info_set(finfo,"striping_unit", STRIPING_UNIT); //2G striping
MPI_Info_set(finfo,"ind_rd_buffer_size", STRIPING_UNIT); //2gb buffer
MPI_Info_set(finfo,"romio_ds_read",DATA_SIEVING_READ);
/*
* for collective reading and writing
* should be adapted too and tested according to the file system
* Harmless for other file system.
*/
MPI_Info_set(finfo,"nb_proc", NB_PROC);
MPI_Info_set(finfo,"cb_nodes", CB_NODES);
MPI_Info_set(finfo,"cb_block_size", CB_BLOCK_SIZE);
MPI_Info_set(finfo,"cb_buffer_size", CB_BUFFER_SIZE);
//we open the input file
ierr = MPI_File_open(MPI_COMM_WORLD, file_name, MPI_MODE_RDONLY , finfo, &mpi_filed);
//assert(in != -1);
if (ierr){
if (rank == 0) fprintf(stderr, "%s: Failed to open file in process 0 %s\n", argv[0], argv[1]);
MPI_Abort(MPI_COMM_WORLD, errorcode);
exit(2);
}
ierr = MPI_File_get_size(mpi_filed, &fileSize);
assert(ierr == MPI_SUCCESS);
input_file_size = (long long)fileSize;
/* Get chunk offset and size */
fsiz = input_file_size;
lsiz = fsiz / num_proc;
loff = rank * lsiz;
tic = MPI_Wtime();
headerSize = unmappedSize = discordantSize = strlen(header);
//We place file offset of each process to the begining of one read's line
size_t *goff =(size_t*)calloc((size_t)(num_proc+1), sizeof(size_t));
init_goff(mpi_filed,hsiz,input_file_size,num_proc,rank,goff);
//We calculate the size to read for each process
lsiz = goff[rank+1]-goff[rank];
//NOW WE WILL PARSE
size_t j=0;
size_t poffset = goff[rank]; //Current offset in file sam
//nbchr because we add the discordant reads in the structure
reads = (Read**)malloc((nbchr)*sizeof(Read));//We allocate a linked list of struct for each Chromosome (last chr = unmapped reads)
readNumberByChr = (size_t*)malloc((nbchr)*sizeof(size_t));//Array with the number of reads found in each chromosome
localReadNumberByChr = (size_t*)malloc((nbchr)*sizeof(size_t));//Array with the number of reads found in each chromosome
Read ** anchor = (Read**)malloc((nbchr)*sizeof(Read));//Pointer on the first read of each chromosome
//Init first read
for(i = 0; i < (nbchr); i++){
reads[i] = malloc(sizeof(Read));
reads[i]->coord = 0;
anchor[i] = reads[i];
readNumberByChr[i]=0;
}
toc = MPI_Wtime();
char *local_data_tmp = malloc(1024*1024);
char *local_data =(char*)malloc(((goff[rank+1]-poffset)+1)*sizeof(char));
size_t size_tmp= goff[rank+1]-poffset;
local_data[goff[rank+1]-poffset] = 0;
char *q=local_data;
//We read the file sam and parse
while(poffset < goff[rank+1]){
size_t size_to_read = 0;
if( (goff[rank+1]-poffset) < DEFAULT_INBUF_SIZE ){
size_to_read = goff[rank+1]-poffset;
}
else{
size_to_read = DEFAULT_INBUF_SIZE;
}
// we load the buffer
//hold temporary size of SAM
//due to limitation in MPI_File_read_at
local_data_tmp =(char*)realloc(local_data_tmp, (size_to_read+1)*sizeof(char));
local_data_tmp[size_to_read]=0;
// Original reading part is before 18/09/2015
MPI_File_read_at(mpi_filed, (MPI_Offset)poffset, local_data_tmp, size_to_read, MPI_CHAR, MPI_STATUS_IGNORE);
size_t local_offset=0;
assert(strlen(local_data_tmp) == size_to_read);
//we look where is the last line read for updating next poffset
size_t offset_last_line = size_to_read-1;
size_t extra_char=0;
while(local_data_tmp[offset_last_line] != '\n'){
offset_last_line -- ;
extra_char++;
}
local_data_tmp[size_to_read - extra_char]=0;
size_t local_data_tmp_sz = strlen(local_data_tmp);
//If it s the last line of file, we place a last '\n' for the function tokenizer
if(rank == num_proc-1 && ((poffset+size_to_read) == goff[num_proc])){
local_data_tmp[offset_last_line]='\n';
}
//Now we parse Read in local_data
parser_paired(local_data_tmp, rank, poffset, threshold, nbchr, &readNumberByChr, chrNames, &reads);
//now we copy local_data_tmp in local_data
char *p = local_data_tmp;
int pos =0;
while (*p && (pos < local_data_tmp_sz)) {*q=*p;p++;q++;pos++;}
//we go to the next line
poffset+=(offset_last_line+1);
local_offset+=(offset_last_line+1);
}
assert(size_tmp == strlen(local_data));
fprintf(stderr, "%d (%.2lf)::::: *** FINISH PARSING FILE ***\n", rank, MPI_Wtime()-toc);
if (local_data_tmp) free(local_data_tmp);
malloc_trim(0);
MPI_Barrier(MPI_COMM_WORLD);
//We set attribute next of the last read and go back to first read of each chromosome
for(i = 0; i < nbchr; i++){
reads[i]->next = NULL;
reads[i] = anchor[i];
}
free(anchor);
//We count how many reads we found
size_t nb_reads_total =0,nb_reads_global =0;
for(j=0;j<nbchr;j++){
nb_reads_total+=readNumberByChr[j];
}
MPI_Allreduce(&nb_reads_total, &nb_reads_global, 1, MPI_UNSIGNED_LONG, MPI_SUM, MPI_COMM_WORLD);
/*
* We care for unmapped and discordants reads
*/
int s = 0;
for (s = 1; s < 3; s++){
MPI_File mpi_file_split_comm2;
double time_count;
size_t total_reads = 0;
MPI_Allreduce(&readNumberByChr[nbchr-s], &total_reads , 1, MPI_LONG_LONG_INT, MPI_SUM, MPI_COMM_WORLD);
if ((rank == 0) && (s == 1))
fprintf(stderr, "rank %d :::: total read to sort for unmapped = %zu \n", rank, total_reads);
if ((rank == 0) && (s == 2))
fprintf(stderr, "rank %d :::: total read to sort for discordant = %zu \n", rank, total_reads);
MPI_Barrier(MPI_COMM_WORLD);
if (total_reads == 0){
// nothing to sort for unmapped
// maybe write an empty bam file
}
else{
int i1,i2;
size_t *localReadsNum_rank0 = (size_t *)malloc(num_proc*sizeof(size_t));
localReadsNum_rank0[0] = 0;
int file_pointer_to_free = 0;
int split_comm_to_free = 0;
//we build a vector with rank job
int val_tmp1 = 0;
int val_tmp2 = 0;
int chosen_rank = 0;
// the color tells in what communicator the rank pertain
// color = 0 will be the new communicator color
// otherwise the color is 1
int *color_vec_to_send = (int *)malloc(num_proc*sizeof(int));
// the key value tell the order in the new communicator
int *key_vec_to_send = (int *)malloc(num_proc*sizeof(int));
//rank 0 gather the vector
MPI_Allgather(&readNumberByChr[nbchr-s] , 1, MPI_LONG_LONG_INT, localReadsNum_rank0 , 1, MPI_LONG_LONG_INT, MPI_COMM_WORLD);
MPI_Barrier(MPI_COMM_WORLD);
if (rank == 0){
//we must chose the first rank with reads to sort
i1=0;
while (localReadsNum_rank0[i1] == 0){
chosen_rank++;
i1++;
}
}
//we broadcast the chosen rank
//task: replace the broadcast with a sendrecieve
MPI_Bcast( &chosen_rank, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Barrier(MPI_COMM_WORLD);
//we must chose which rank is going to split the communication
if (((rank == chosen_rank) || rank == 0) && (chosen_rank != 0)){
//the rank 0 will recieve the key_vec_to_send and colorvec_to_send
//first we exchange the size o
if (rank == chosen_rank){
header=(char *)malloc((headerSize + 1)*sizeof(char));
MPI_Recv(header, headerSize + 1, MPI_CHAR, 0, 0, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
}
if (rank == 0){
MPI_Send(header, headerSize + 1, MPI_CHAR, chosen_rank, 0, MPI_COMM_WORLD);
}
}
else {
//we do nothing here
}
if (rank == chosen_rank) {
int counter = 0;
//we compute the number of 0 in the localReadsNum_vec
for(i1 = 0; i1 < num_proc; i1++){
if (localReadsNum_rank0[i1] == 0) {
counter++;
}
}
// if no jobs without reads we do nothing
if ( counter == 0 ){
// nothing to do we associate split_comm with
split_comm = MPI_COMM_WORLD;
for (i2 = 0; i2 < num_proc; i2++) {
if (localReadsNum_rank0[i2] == 0) {
color_vec_to_send[i2] = 1;
key_vec_to_send[i2] = val_tmp2;
val_tmp2++;
} else {
color_vec_to_send[i2] = 0;
key_vec_to_send[i2] = val_tmp1;
val_tmp1++;
}
}
}
else{
// now we compute the color according to
// the number of reads to sort
for(i2 = 0; i2 < num_proc; i2++){
if (localReadsNum_rank0[i2] == 0){
color_vec_to_send[i2] = 1;
key_vec_to_send[i2] = val_tmp2;
val_tmp2++;
} else{
color_vec_to_send[i2] = 0;
key_vec_to_send[i2] = val_tmp1;
val_tmp1++;
}
} // end for loop
}// end if
}// end if (rank == chosen_rank)
MPI_Barrier(MPI_COMM_WORLD);
// we scatter the key and color vector
// we create key and color variable for each job
int local_color = 0;
int local_key = 0;
// we scatter the color and key
MPI_Scatter( color_vec_to_send, 1, MPI_INT, &local_color, 1, MPI_INT, chosen_rank, MPI_COMM_WORLD);
MPI_Scatter( key_vec_to_send, 1, MPI_INT, &local_key, 1, MPI_INT, chosen_rank, MPI_COMM_WORLD);
// we create a communicator
// we group all communicator
// with color of zero
if (local_color == 0){
MPI_Comm_split( MPI_COMM_WORLD, local_color, local_key, &split_comm);
ierr = MPI_File_open(split_comm, file_name, MPI_MODE_RDONLY , finfo, &mpi_file_split_comm2);
//we ask to liberate file pointer
file_pointer_to_free = 1;
//we ask to liberate the split_comm
split_comm_to_free = 1;
}
else{
MPI_Comm_split( MPI_COMM_WORLD, MPI_UNDEFINED, local_key, &split_comm);
mpi_file_split_comm2 = mpi_filed;
}
//now we change the rank in the reads structure
if (local_color == 0){
MPI_Comm_rank(split_comm, &split_rank);
MPI_Comm_size(split_comm, &split_size);
g_rank = split_rank;
g_size = split_size;
reads[nbchr-s] = reads[nbchr-s]->next;
localReadNumberByChr[nbchr-s] = readNumberByChr[nbchr-s];
if (s == 2){
unmapped_start = startOffset(g_rank,
g_size,
unmappedSize,
headerSize,
nbchr-s,
localReadNumberByChr[nbchr-s],
split_comm
);
if(!unmapped_start){
fprintf(stderr, "No header was defined for unmapped. \n Shutting down.\n");
MPI_Finalize();
return 0;
}
time_count = MPI_Wtime();
writeSam_discordant_and_unmapped(
split_rank,
output_dir,
header,
localReadNumberByChr[nbchr-s],
chrNames[nbchr-s],
reads[nbchr-s],
split_size,
split_comm,
file_name,
mpi_file_split_comm2,
finfo,
compression_level,
local_data,
goff[rank],
write_sam);
if (split_rank == chosen_rank){
fprintf(stderr, "rank %d :::::[MPISORT] Time to write chromosom %s , %f seconds \n\n\n", split_rank,
chrNames[nbchr-s], MPI_Wtime() - time_count);
}
}
else{
discordant_start = startOffset(g_rank,
g_size,
discordantSize,
headerSize,
nbchr-s,
localReadNumberByChr[nbchr-s],
split_comm);
if(!discordant_start){
fprintf(stderr, "No header was defined for discordant.\n Shutting down.\n");
MPI_Finalize();
return 0;
}
time_count = MPI_Wtime();
writeSam_discordant_and_unmapped(
g_rank,
output_dir,
header,
localReadNumberByChr[nbchr-s],
chrNames[nbchr-s],
reads[nbchr-s],
g_size,
split_comm,
file_name,
mpi_file_split_comm2,
finfo,
compression_level,
local_data,
goff[rank],
write_sam
);
if (split_rank == chosen_rank){
fprintf(stderr, "rank %d :::::[MPISORT] Time to write chromosom %s , %f seconds \n\n\n", split_rank,
chrNames[nbchr-s], MPI_Wtime() - time_count);
}
}
while( reads[nbchr-s]->next != NULL){
Read *tmp_chr = reads[nbchr-s];
reads[nbchr-s] = reads[nbchr-s]->next;
free(tmp_chr);
}
free(localReadsNum_rank0);
}
else{
// we do nothing
}
//we put a barrier before freeing pointers
MPI_Barrier(MPI_COMM_WORLD);
//we free the file pointer
if (file_pointer_to_free)
MPI_File_close(&mpi_file_split_comm2);
//we free the split_comm
if (split_comm_to_free)
MPI_Comm_free(&split_comm);
split_comm_to_free = 0;
file_pointer_to_free = 0;
free(color_vec_to_send);
free(key_vec_to_send);
}
} //end for (s=1; s < 3; s++){
/*
* We write the mapped reads in a file named chrX.bam
* We loop by chromosoms.
*/
MPI_Barrier(MPI_COMM_WORLD);
for(i = 0; i < (nbchr-2); i++){
/*
* First Part of the algorithm
*
* In this part we elected a rank which is the first rank
* to have reads to sort.
*
* Once elected a rank, we plit the communicator according to
* wether the rank has reads to sort for this chromosom.
*
* The new communicator is COMM_WORLD.
*
* If all jobs have reads to sort no need to split the communicator and then
* COMM_WORLD = MPI_COMM_WORLD
*
*/
int i1,i2;
size_t localReadsNum_rank0[num_proc];
localReadsNum_rank0[0]=0;
int file_pointer_to_free = 0;
int split_comm_to_free = 0;
//we build a vector with rank job
int val_tmp1 = 0;
int val_tmp2 = 0;
int chosen_rank = 0; //needed to tell what rank is going to compute the color and key
int chosen_split_rank= 0; //the rank that collect data once the communication splitted normally this rank is 0
// the color tells in what communicator the rank pertain
// color = 0 will be the new communicator color
// otherwise the color is 1
// the key value tell the order in the new communicator
int *color_vec_to_send = malloc(num_proc * sizeof(int));
int *key_vec_to_send = malloc(num_proc * sizeof(int));
// first we test if the there's reads to sort
// rank 0 recieve the sum of all the reads count
size_t total_reads_by_chr = 0;
MPI_Allreduce(&readNumberByChr[i], &total_reads_by_chr, 1, MPI_LONG_LONG_INT, MPI_SUM, MPI_COMM_WORLD);
//fprintf(stderr, "rank %d :::: readNumberByChr[i] = %zu \n", rank, readNumberByChr[i]);
//fprintf(stderr, "rank %d :::: total_reads_by_chr = %zu \n", rank, total_reads_by_chr);
if (total_reads_by_chr == 0)
continue; //pass to next chromosome
//rank 0 gather the vector
MPI_Allgather(&readNumberByChr[i] , 1, MPI_LONG_LONG_INT, localReadsNum_rank0 , 1, MPI_LONG_LONG_INT, MPI_COMM_WORLD);
if (rank == 0){
//the rank 0 chose the first rank with reads to sort
i1=0;
while ((localReadsNum_rank0[i1] == 0) && (i1 < num_proc)){
chosen_rank++;
i1++;
}
fprintf(stderr, "rank %d :::: Elected rank = %d \n", rank, chosen_rank);
}
//we broadcast the chosen rank
//task: replace the broadcast with a sendrecieve
MPI_Bcast( &chosen_rank, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Barrier(MPI_COMM_WORLD);
if (((rank == chosen_rank) || rank == 0) && (chosen_rank != 0)){
//first we exchange the size o
if (rank == chosen_rank){
header = malloc((headerSize + 1)*sizeof(char));
header[headerSize] = '\0';
MPI_Recv(header, headerSize + 1, MPI_CHAR, 0, 0, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
}
if (rank == 0){
MPI_Send(header, headerSize + 1, MPI_CHAR, chosen_rank, 0, MPI_COMM_WORLD);
}
}
else {
//we do nothing here
}
MPI_Barrier(MPI_COMM_WORLD);
if (rank == chosen_rank) {
int counter = 0;
//we compute the number of 0 in the localReadsNum_vec
for(i1 = 0; i1 < num_proc; i1++){
if (localReadsNum_rank0[i1] == 0) {
counter++;
}
}
// if no jobs without reads we do nothing
if ( counter == 0 ){
// nothing to do we associate split_comm with
fprintf(stderr, "rank %d ::::[MPISORT] we don't split the rank \n", rank);
split_comm = MPI_COMM_WORLD;
for (i2 = 0; i2 < num_proc; i2++) {
if (localReadsNum_rank0[i2] == 0) {
color_vec_to_send[i2] = 1;
key_vec_to_send[i2] = val_tmp2;
val_tmp2++;
} else {
color_vec_to_send[i2] = 0;
key_vec_to_send[i2] = val_tmp1;
val_tmp1++;
}
}
}
else{
// now we compute the color according to
// the number of reads to sort
fprintf(stderr, "rank %d ::::[MPISORT] we split the rank \n", rank);
for(i2 = 0; i2 < num_proc; i2++){
if (localReadsNum_rank0[i2] == 0){
color_vec_to_send[i2] = 1;
key_vec_to_send[i2] = val_tmp2;
val_tmp2++;
} else{
color_vec_to_send[i2] = 0;
key_vec_to_send[i2] = val_tmp1;
val_tmp1++;
}
} // end for loop
}// end if
}// end if (rank == plit_rank)
MPI_Barrier(MPI_COMM_WORLD);
//we create key and color variable for each job
int local_color = 0;
int local_key = 0;
// rank 0 scatter the color and the key vector
MPI_Scatter( color_vec_to_send, 1, MPI_INT, &local_color, 1, MPI_INT, chosen_rank, MPI_COMM_WORLD);
MPI_Scatter( key_vec_to_send, 1, MPI_INT, &local_key, 1, MPI_INT, chosen_rank, MPI_COMM_WORLD);
MPI_Barrier(MPI_COMM_WORLD);
// now we create a communicator
// we group all communicator
// with color of zero
if (local_color == 0){
MPI_Comm_split( MPI_COMM_WORLD, local_color, local_key, &split_comm);
ierr = MPI_File_open(split_comm, file_name, MPI_MODE_RDONLY, finfo, &mpi_file_split_comm);
//we ask to liberate file pointer
file_pointer_to_free = 1;
//we ask to liberate the split_comm
split_comm_to_free = 1;
}
else{
MPI_Comm_split( MPI_COMM_WORLD, MPI_UNDEFINED, local_key, &split_comm);
mpi_file_split_comm = mpi_filed;
}
//now we change the rank in the reads structure
if (local_color == 0){
MPI_Comm_rank(split_comm, &split_rank);
MPI_Comm_size(split_comm, &split_size);
//we update g_rank
g_rank = split_rank;
g_size = split_size;
}
else{
g_rank = split_rank;
g_size = split_size = num_proc;
}
localReadNumberByChr[i] = readNumberByChr[i];
MPI_Barrier(MPI_COMM_WORLD);
if ((local_color == 0) && (i < (nbchr - 2))) {
/*
* Second part of the algorithm
*
* First we load coordinates, offset sources, and read size in vector
*
* Then we sort the coordinates of the reads
* with a bitonic sorter
*
* Then according to the reads coordinates we reoder the offset sources, and size
* this is done thanks to the index of the sorting.
*
* Afterward we compute the offsets of the reads in
* the destination file.
*
* Finally we dispatch the information to all ranks
* in the communicator for the next step.
*/
//we do a local merge sort
if(reads[i] && reads[i]->next && reads[i]->next->next){
mergeSort(reads[i], readNumberByChr[i]);
}
size_t local_readNum = localReadNumberByChr[i];
reads[i] = reads[i]->next;
//first we compute the dimension of the parabitonic sort
// dimension is the number of processors where we
// perform the bitonic sort
// int dimensions = (int)(log2(num_processes));
// find next ( must be greater) power, and go one back
int dimensions = 1;
while (dimensions <= split_size)
dimensions <<= 1;
dimensions >>= 1;
// we get the maximum number of reads among
// all the workers
/*
* Here we split the programm in 2 cases
*
* 1) The first case de split_size is a power of 2 (the best case)
* this case is the simpliest we don't have extra communication to dispatch the read
* envenly between the jobs
*
* 2) The split_size is not a power of 2 (the worst case)
* well in this case we shall dispatch the jobs between jobs evenly.
*
*/
if (split_rank == chosen_split_rank){
fprintf(stderr, "Rank %d :::::[MPISORT] Dimensions for bitonic = %d \n", split_rank, dimensions);
fprintf(stderr, "Rank %d :::::[MPISORT] Split size = %d \n", split_rank, split_size);
}
//we test the computed dimension
if (dimensions == split_size ){
size_t max_num_read = 0;
MPI_Allreduce(&localReadNumberByChr[i], &max_num_read, 1, MPI_LONG_LONG_INT, MPI_MAX, split_comm);
// if the dimension == split_size
MPI_Barrier(split_comm);
size_t first_local_readNum = local_readNum;
/*
* Vector creation and allocation
fprintf(stderr, "split rank %d :::::[MPISORT] max_num_read = %zu \n", split_rank, max_num_read);
*/
local_readNum = max_num_read;
time_count = MPI_Wtime();
size_t *local_reads_coordinates_unsorted = calloc(local_readNum, sizeof(size_t));
size_t *local_reads_coordinates_sorted = calloc(local_readNum, sizeof(size_t));
size_t *local_offset_source_unsorted = calloc(local_readNum, sizeof(size_t));
size_t *local_offset_source_sorted = calloc(local_readNum, sizeof(size_t));
int *local_dest_rank_sorted = calloc(local_readNum, sizeof(int));
int *local_reads_sizes_unsorted = calloc(local_readNum, sizeof(int));
int *local_reads_sizes_sorted = calloc(local_readNum, sizeof(int));
int *local_source_rank_unsorted = calloc(local_readNum, sizeof(int));
int *local_source_rank_sorted = calloc(local_readNum, sizeof(int));
if (split_rank == chosen_split_rank)
fprintf(stderr, "rank %d :::::[MPISORT][MALLOC 1] time spent = %f s\n", split_rank, MPI_Wtime() - time_count);
local_reads_coordinates_unsorted[0] = 0;
local_reads_coordinates_sorted[0] = 0;
local_dest_rank_sorted[0] = 0;
local_reads_sizes_unsorted[0] = 0;
local_reads_sizes_sorted[0] = 0;
local_source_rank_unsorted[0] = 0;
local_source_rank_sorted[0] = 0;
local_offset_source_unsorted[0] = 0;
local_offset_source_sorted[0] = 0;
//those vectors are the same that local_..._sorted but without zero padding
size_t *local_reads_coordinates_sorted_trimmed = NULL;
int *local_dest_rank_sorted_trimmed = NULL;
int *local_reads_sizes_sorted_trimmed = NULL;
size_t *local_offset_source_sorted_trimmed = NULL;
size_t *local_offset_dest_sorted_trimmed = NULL;
int *local_source_rank_sorted_trimmed = NULL;
//vectors used in the bruck just after the parabitonic sort
size_t *local_reads_coordinates_sorted_trimmed_for_bruck = NULL;
int *local_dest_rank_sorted_trimmed_for_bruck = NULL;
int *local_reads_sizes_sorted_trimmed_for_bruck = NULL;
size_t *local_offset_source_sorted_trimmed_for_bruck = NULL;
size_t *local_offset_dest_sorted_trimmed_for_bruck = NULL;
int *local_source_rank_sorted_trimmed_for_bruck = NULL;
//task Init offset and size for source - free chr
// from mpiSort_utils.c
get_coordinates_and_offset_source_and_size_and_free_reads(
split_rank,
local_source_rank_unsorted,
local_reads_coordinates_unsorted,
local_offset_source_unsorted,
local_reads_sizes_unsorted,
reads[i],
first_local_readNum
);
//init indices for qksort
size_t *coord_index = (size_t*)malloc(local_readNum*sizeof(size_t));
for(j = 0; j < local_readNum; j++){
coord_index[j] = j;
}
//To start we sort locally the reads coordinates.
//this is to facilitate the bitonic sorting
//if the local coordinates to sort are to big we could get rid of
//this step.
time_count = MPI_Wtime();
base_arr2 = local_reads_coordinates_unsorted;
qksort(coord_index, local_readNum, sizeof(size_t), 0, local_readNum - 1, compare_size_t);
if (split_rank == chosen_split_rank)
fprintf(stderr, "rank %d :::::[MPISORT][LOCAL SORT] time spent = %f s\n", split_rank, MPI_Wtime() - time_count);
//We index data
for(j = 0; j < local_readNum; j++){
local_reads_coordinates_sorted[j] = local_reads_coordinates_unsorted[coord_index[j]];
local_source_rank_sorted[j] = local_source_rank_unsorted[coord_index[j]];
local_reads_sizes_sorted[j] = local_reads_sizes_unsorted[coord_index[j]];
local_offset_source_sorted[j] = local_offset_source_unsorted[coord_index[j]];
local_dest_rank_sorted[j] = rank; //will be updated after sorting the coordinates
}
/*
* FOR DEBUG
*
for(j = 0; j < local_readNum - 1; j++){
assert( local_reads_coordinates_sorted[j] < local_reads_coordinates_sorted[j+1]);
}
*/
free(coord_index); //ok
free(local_source_rank_unsorted); //ok
free(local_reads_coordinates_unsorted); //ok
free(local_reads_sizes_unsorted); //ok
free(local_offset_source_unsorted); //ok
// we need the total number of reads.
size_t total_num_read = 0;
MPI_Allreduce(&localReadNumberByChr[i], &total_num_read, 1, MPI_LONG_LONG_INT, MPI_SUM, split_comm);
/*
*
* In this section the number of bitonic dimension
* is equal to the split size.
*
* In this case there are less communication in preparation
* of the sorting.
*
* We use the parabitonic version 2.
*/
//we calll the bitonic
time_count = MPI_Wtime();
ParallelBitonicSort2(
split_comm,
split_rank,
dimensions,
local_reads_coordinates_sorted,
local_reads_sizes_sorted,
local_source_rank_sorted,
local_offset_source_sorted,
local_dest_rank_sorted,
max_num_read
);
if (split_rank == chosen_split_rank)
fprintf(stderr, "rank %d :::::[MPISORT][BITONIC 2] time spent = %f s\n",
split_rank, MPI_Wtime() - time_count);
size_t k1;
size_t tmp2 = 0;
for (k1 = 1; k1 < max_num_read; k1++){
assert(local_reads_coordinates_sorted[k1-1] <= local_reads_coordinates_sorted[k1]);
local_dest_rank_sorted[k1]= split_rank;
}
/*
for (k1 = 0; k1 < max_num_read; k1++){
fprintf(stderr, "rank %d :::::[MPISORT][BITONIC 2] local_reads_coordinates_sorted[%zu]= %zu s\n",
split_rank, k1, local_reads_coordinates_sorted[k1]);
fprintf(stderr, "rank %d :::::[MPISORT][BITONIC 2] local_source_rank_sorted[%zu]= %d s\n",
split_rank, k1, local_source_rank_sorted[k1]);
}
*/
size_t *local_offset_dest_sorted = malloc(max_num_read*sizeof(size_t));
size_t last_local_offset = 0;
// We compute the local_dest_offsets_sorted
size_t local_total_offset = 0;
for (k1 = 0; k1 < max_num_read; k1++){
local_offset_dest_sorted[k1] = local_reads_sizes_sorted[k1];
local_total_offset += local_reads_sizes_sorted[k1];
}
//we make the cumulative sum of all offsets
for (k1 = 1; k1 < max_num_read; k1++){
local_offset_dest_sorted[k1] = local_offset_dest_sorted[k1 - 1] + local_offset_dest_sorted[k1];
}
//we exchange the last destination offset
last_local_offset = local_offset_dest_sorted[max_num_read-1];
//number of block to send
int blocksize = 1;
MPI_Offset *y = calloc(split_size, sizeof(MPI_Offset));
MPI_Offset *y2 = calloc(split_size + 1, sizeof(MPI_Offset));
//we wait all processors
MPI_Gather(&last_local_offset, 1, MPI_LONG_LONG_INT, y, 1, MPI_LONG_LONG_INT, 0, split_comm);
if (split_rank ==0){
for (k1 = 1; k1 < (split_size + 1); k1++) {
y2[k1] = y[k1-1];
}
}
if (split_rank ==0){
for (k1 = 1; k1 < (split_size +1); k1++) {
y2[k1] = y2[k1-1] + y2[k1];
}
}
size_t offset_to_add = 0;
MPI_Scatter(y2, 1, MPI_LONG_LONG_INT, &offset_to_add, 1, MPI_LONG_LONG_INT, 0, split_comm);
free(y);
free(y2);
//we add offset of the previous rank
for (k1 = 0; k1 < max_num_read; k1++){
if (local_reads_sizes_sorted[k1] != 0)
local_offset_dest_sorted[k1] += offset_to_add;
else
local_offset_dest_sorted[k1] = 0;
}
/*
for (k1 = 0; k1 < max_num_read; k1++){
fprintf(stderr, "\n");
fprintf(stderr, "rank %d :::::[MPISORT][BITONIC 2] local_reads_coordinates_sorted[%zu]= %zu s\n",
split_rank, k1, local_reads_coordinates_sorted[k1]);
fprintf(stderr, "rank %d :::::[MPISORT][BITONIC 2] local_source_rank_sorted[%zu]= %d s\n",
split_rank, k1, local_source_rank_sorted[k1]);
fprintf(stderr, "rank %d :::::[MPISORT][BITONIC 2] local_offset_dest_sorted[%zu]= %d s\n",
split_rank, k1, local_offset_dest_sorted[k1]);
fprintf(stderr, "\n");
}
*/
/*
* we update destination rank according to
* original number of reads read.
*
*/
//we compute the new rank dest according to max_num_read
size_t previous_num_reads_per_job[dimensions];
//we create a vector of size split_size with previous reads per job
MPI_Allgather(&first_local_readNum , 1, MPI_LONG_LONG_INT, previous_num_reads_per_job , 1, MPI_LONG_LONG_INT, split_comm);
// we compute the position of of the read in the first
// reference without the zero padding of bitonic
size_t pos_ref0 = 0;
//we need the number of zeros we add for the padding
size_t N0 = max_num_read*dimensions - total_num_read;
int new_rank = 0;
int previous_rank = 0;
// we compute the new rank for
// the reads sorted by offset destination
size_t h = 0;
pos_ref0 = max_num_read*split_rank - N0;
for(j = 0; j < max_num_read; j++) {
if ( local_reads_sizes_sorted[j] != 0){
int new_rank = chosen_split_rank;
pos_ref0 = (max_num_read*split_rank +j) - N0;
if (pos_ref0 >= 0) {
size_t tmp2 = 0;
for (h = 0; h < dimensions; h++){
tmp2 += previous_num_reads_per_job[h];
if ( pos_ref0 < tmp2) {
new_rank = h;
break;
}
}
previous_rank = local_dest_rank_sorted[j];
local_dest_rank_sorted[j] = new_rank;
}
}
}
MPI_Barrier(split_comm);
size_t offset = 0;
size_t numItems = 0;
size_t num_read_for_bruck = 0;
int *p = local_reads_sizes_sorted;
if (p[0] != 0) {offset = 0;};
if (p[max_num_read -1] == 0){offset = max_num_read;}
else {while ((*p == 0) && (offset < max_num_read )){ offset++; p++;}}
/*
* REMOVE ZERO PADDING BEFORE BRUCK
*
*/
time_count = MPI_Wtime();
if (offset > 0){
// we remove zeros in the vector we have 2 cases
// the first offset < max_num_read
// and the entire vector is null
if ( offset < max_num_read ){
numItems = max_num_read - offset;
local_reads_coordinates_sorted_trimmed_for_bruck = malloc(numItems * sizeof(size_t));
local_offset_source_sorted_trimmed_for_bruck = malloc(numItems * sizeof(size_t));
local_offset_dest_sorted_trimmed_for_bruck = malloc(numItems * sizeof(size_t));
local_reads_sizes_sorted_trimmed_for_bruck = malloc(numItems * sizeof(int));
local_dest_rank_sorted_trimmed_for_bruck = malloc(numItems * sizeof(int));
local_source_rank_sorted_trimmed_for_bruck = malloc(numItems * sizeof(int));
size_t y=0;
for (y = 0; y < numItems; y++){
local_reads_coordinates_sorted_trimmed_for_bruck[y] = local_reads_coordinates_sorted[y+offset];
local_offset_source_sorted_trimmed_for_bruck[y] = local_offset_source_sorted[y+offset];
local_offset_dest_sorted_trimmed_for_bruck[y] = local_offset_dest_sorted[y+offset];
local_reads_sizes_sorted_trimmed_for_bruck[y] = local_reads_sizes_sorted[y+offset];
local_dest_rank_sorted_trimmed_for_bruck[y] = local_dest_rank_sorted[y+offset];
local_source_rank_sorted_trimmed_for_bruck[y] = local_source_rank_sorted[y+offset];
}
num_read_for_bruck = numItems;
/*
*
* FOR DEBUG
*
for(y = 0; y < num_read_for_bruck; y++){
assert( local_reads_sizes_sorted_trimmed_for_bruck[y] != 0 );
assert( local_source_rank_sorted_trimmed_for_bruck[y] < dimensions);
assert( local_dest_rank_sorted_trimmed_for_bruck[y] < dimensions);
assert( local_offset_source_sorted_trimmed_for_bruck[y] != 0);
assert( local_offset_dest_sorted_trimmed_for_bruck[y] != 0);
assert( local_reads_coordinates_sorted_trimmed_for_bruck[y] != 0);
}
*/
}
else{
numItems = 0;
local_reads_coordinates_sorted_trimmed_for_bruck = malloc(numItems * sizeof(size_t));
local_offset_source_sorted_trimmed_for_bruck = malloc(numItems * sizeof(size_t));
local_offset_dest_sorted_trimmed_for_bruck = malloc(numItems * sizeof(size_t));
local_reads_sizes_sorted_trimmed_for_bruck = malloc(numItems * sizeof(int));
local_dest_rank_sorted_trimmed_for_bruck = malloc(numItems * sizeof(int));
local_source_rank_sorted_trimmed_for_bruck = malloc(numItems * sizeof(int));
num_read_for_bruck = 0;
}
}
else {
numItems = local_readNum;
local_reads_coordinates_sorted_trimmed_for_bruck = malloc(local_readNum * sizeof(size_t));
local_offset_source_sorted_trimmed_for_bruck = malloc(local_readNum * sizeof(size_t));
local_offset_dest_sorted_trimmed_for_bruck = malloc(local_readNum * sizeof(size_t));
local_reads_sizes_sorted_trimmed_for_bruck = malloc(local_readNum * sizeof(int));
local_dest_rank_sorted_trimmed_for_bruck = malloc(local_readNum * sizeof(int));
local_source_rank_sorted_trimmed_for_bruck = malloc(local_readNum * sizeof(int));
size_t y=0;
for (y = 0; y < local_readNum; y++){
local_reads_coordinates_sorted_trimmed_for_bruck[y] = local_reads_coordinates_sorted[y];
local_offset_source_sorted_trimmed_for_bruck[y] = local_offset_source_sorted[y];
local_offset_dest_sorted_trimmed_for_bruck[y] = local_offset_dest_sorted[y];
local_reads_sizes_sorted_trimmed_for_bruck[y] = local_reads_sizes_sorted[y];
local_dest_rank_sorted_trimmed_for_bruck[y] = local_dest_rank_sorted[y];
local_source_rank_sorted_trimmed_for_bruck[y] = local_source_rank_sorted[y];
}
num_read_for_bruck = numItems;
/*
*
* FOR DEBUG
*
for(y = 0; y < num_read_for_bruck; y++){
assert( local_reads_sizes_sorted_trimmed_for_bruck[y] != 0 );
assert( local_source_rank_sorted_trimmed_for_bruck[y] < dimensions);
assert( local_dest_rank_sorted_trimmed_for_bruck[y] < dimensions);
assert( local_offset_source_sorted_trimmed_for_bruck[y] != 0);
assert( local_offset_dest_sorted_trimmed_for_bruck[y] != 0);
assert( local_reads_coordinates_sorted_trimmed_for_bruck[y] != 0);
}
*/
}
free(local_reads_coordinates_sorted);
free(local_offset_source_sorted);
free(local_offset_dest_sorted);
free(local_reads_sizes_sorted);
free(local_dest_rank_sorted);
free(local_source_rank_sorted);
if (split_rank == chosen_split_rank)
fprintf(stderr, "rank %d :::::[MPISORT][TRIMMING] time spent = %f s\n", split_rank, MPI_Wtime() - time_count);
/*
* We do a Bruck on rank of origin reading
*/
size_t m=0;
int num_proc = dimensions;
size_t *number_of_reads_by_procs = calloc( dimensions, sizeof(size_t));
//fprintf(stderr, "rank %d :::::[MPISORT] num_read_for_bruck = %zu \n", split_rank, num_read_for_bruck);
for(m = 0; m < num_read_for_bruck; m++){
//assert(new_pbs_orig_rank_off_phase1[m] < dimensions);
//assert(new_pbs_dest_rank_phase1[m] < dimensions);
number_of_reads_by_procs[local_source_rank_sorted_trimmed_for_bruck[m]]++;
}
int *local_source_rank_sorted_trimmed_for_bruckv2 = malloc( num_read_for_bruck * sizeof(int));
for(m = 0; m < num_read_for_bruck; m++){
local_source_rank_sorted_trimmed_for_bruckv2[m] = local_source_rank_sorted_trimmed_for_bruck[m];
}
size_t count6 = 0;
for(m = 0; m < dimensions; m++){
count6 += number_of_reads_by_procs[m];
}
assert( count6 == num_read_for_bruck );
MPI_Barrier(split_comm);
size_t **reads_coordinates = malloc(sizeof(size_t *) * dimensions);
size_t **local_source_offsets = malloc(sizeof(size_t *) * dimensions);
size_t **dest_offsets = malloc(sizeof(size_t *) * dimensions);
int **read_size = malloc(sizeof(int *) * dimensions);
int **dest_rank = malloc(sizeof(int *) * dimensions);
int **source_rank = malloc(sizeof(int *) * dimensions);
/*
* We send in order
*
* local_offset_source_sorted_trimmed_for_bruck
* local_dest_rank_sorted_trimmed_for_bruck
* local_reads_coordinates_sorted_trimmed_for_bruck
* local_reads_sizes_sorted_trimmed_for_bruck
*
*/
COMM_WORLD = split_comm;
time_count = MPI_Wtime();
bruckWrite3(split_rank,
dimensions,
count6,
number_of_reads_by_procs,
local_source_rank_sorted_trimmed_for_bruckv2,
local_offset_source_sorted_trimmed_for_bruck, //offset sources
&local_source_offsets,
local_dest_rank_sorted_trimmed_for_bruck, //destination rank
&dest_rank,
local_reads_coordinates_sorted_trimmed_for_bruck, //reads coordinates
&reads_coordinates,
local_reads_sizes_sorted_trimmed_for_bruck, //read size
&read_size,
local_source_rank_sorted_trimmed_for_bruck, //source rank
&source_rank,
local_offset_dest_sorted_trimmed_for_bruck,
&dest_offsets
);
if (split_rank == chosen_split_rank)
fprintf(stderr, "rank %d :::::[MPISORT][BRUCK 3] time spent = %f s\n",
split_rank, MPI_Wtime() - time_count);
time_count = MPI_Wtime();
free(local_reads_coordinates_sorted_trimmed_for_bruck);
free(local_dest_rank_sorted_trimmed_for_bruck);
free(local_reads_sizes_sorted_trimmed_for_bruck);
free(local_offset_source_sorted_trimmed_for_bruck);
free(local_offset_dest_sorted_trimmed_for_bruck);
free(local_source_rank_sorted_trimmed_for_bruck);
free(local_source_rank_sorted_trimmed_for_bruckv2);
local_reads_coordinates_sorted_trimmed = malloc(first_local_readNum * sizeof(size_t));
local_offset_source_sorted_trimmed = malloc(first_local_readNum * sizeof(size_t));
local_offset_dest_sorted_trimmed = malloc(first_local_readNum * sizeof(size_t));
local_dest_rank_sorted_trimmed = malloc(first_local_readNum * sizeof(int));
local_source_rank_sorted_trimmed = malloc(first_local_readNum * sizeof(int));
local_reads_sizes_sorted_trimmed = malloc(first_local_readNum * sizeof(int));
if (split_rank == chosen_split_rank)
fprintf(stderr, "rank %d :::::[MPISORT][FREE + MALLOC] time spent = %f s\n",
split_rank, MPI_Wtime() - time_count);
/*
* GET DATA AFTER BRUCK
*
*/
j=0;
size_t k = 0;
for(m = 0; m < num_proc; m++)
{
for(k = 0; k < number_of_reads_by_procs[m]; k++)
{
local_offset_dest_sorted_trimmed[k + j] = dest_offsets[m][k];
local_dest_rank_sorted_trimmed[k + j] = dest_rank[m][k];
local_reads_sizes_sorted_trimmed[k + j] = read_size[m][k];
local_offset_source_sorted_trimmed[k + j] = local_source_offsets[m][k];
local_reads_coordinates_sorted_trimmed[k + j] = reads_coordinates[m][k];
local_source_rank_sorted_trimmed[k + j] = source_rank[m][k];
}
free(dest_offsets[m]);
free(dest_rank[m]);
free(read_size[m]);
free(local_source_offsets[m]);
free(reads_coordinates[m]);
free(source_rank[m]);
j += number_of_reads_by_procs[m];
}
free(number_of_reads_by_procs);
if (dest_rank != NULL)
free(dest_rank);
if (read_size != NULL)
free(read_size);
if (local_source_offsets != NULL)
free(local_source_offsets);
if (reads_coordinates != NULL)
free(reads_coordinates);
if (source_rank != NULL)
free(source_rank);
if (dest_offsets != NULL)
free(dest_offsets);
local_readNum = first_local_readNum;
/*
*
* FOR DEBUG
*
for ( j = 0; j < local_readNum; j++){
assert ( local_reads_coordinates_sorted_trimmed[j] != 0 );
assert ( local_offset_source_sorted_trimmed[j] != 0 );
assert ( local_offset_dest_sorted_trimmed[j] != 0 );
assert ( local_reads_sizes_sorted_trimmed != 0 );
assert ( local_dest_rank_sorted_trimmed[j] < split_size );
assert ( local_source_rank_sorted_trimmed[j] < split_size );
}
*/
free(local_reads_coordinates_sorted_trimmed);
if (split_rank == chosen_split_rank)
fprintf(stderr, "rank %d :::::[MPISORT] we call write SAM \n", split_rank);
malloc_trim(0);
time_count = MPI_Wtime();
writeSam(
split_rank,
output_dir,
header,
local_readNum,
total_reads_by_chr,
chrNames[i],
reads[i],
split_size,
split_comm,
chosen_split_rank,
file_name,
mpi_file_split_comm,
finfo,
compression_level,
local_offset_dest_sorted_trimmed,
local_offset_source_sorted_trimmed,
local_reads_sizes_sorted_trimmed,
local_dest_rank_sorted_trimmed,
local_source_rank_sorted_trimmed,
local_data,
goff[rank],
first_local_readNum
);
if (split_rank == chosen_split_rank){
fprintf(stderr, "rank %d :::::[MPISORT][WRITESAM] chromosom %s ::: %f seconds\n\n\n",
split_rank, chrNames[i], MPI_Wtime() - time_count);
}
}
else{
/*
* We are in the case the number of cpu is
* not a power of 2
*
*
*/
parallel_sort_any_dim(
dimensions, //dimension for parabitonic
local_readNum,
split_rank,
split_size,
reads,
i, //chromosom number
chosen_split_rank,
split_comm,
localReadNumberByChr,
local_data,
file_name,
output_dir,
finfo,
compression_level,
total_reads_by_chr,
goff[rank],
headerSize,
header,
chrNames[i],
mpi_file_split_comm
);
} //end if dimensions < split_rank
} //if ((local_color == 0) && (i < (nbchr - 2))) //in the splitted dimension
else{
//we do nothing here
}
//we put a barrier before freeing pointers
MPI_Barrier(MPI_COMM_WORLD);
//we free the file pointer
if (file_pointer_to_free)
MPI_File_close(&mpi_file_split_comm);
//we free the split_comm
if (split_comm_to_free){
MPI_Comm_free(&split_comm);
}
free(color_vec_to_send);
free(key_vec_to_send);
}// end loop upon chromosoms (line 665)
bool EFX::saveXML(QXmlStreamWriter *doc)
{
Q_ASSERT(doc != NULL);
/* Function tag */
doc->writeStartElement(KXMLQLCFunction);
/* Common attributes */
saveXMLCommon(doc);
/* Fixtures */
QListIterator <EFXFixture*> it(m_fixtures);
while (it.hasNext() == true)
it.next()->saveXML(doc);
/* Propagation mode */
doc->writeTextElement(KXMLQLCEFXPropagationMode, propagationModeToString(m_propagationMode));
/* Speeds */
saveXMLSpeed(doc);
/* Direction */
saveXMLDirection(doc);
/* Run order */
saveXMLRunOrder(doc);
/* Algorithm */
doc->writeTextElement(KXMLQLCEFXAlgorithm, algorithmToString(algorithm()));
/* Width */
doc->writeTextElement(KXMLQLCEFXWidth, QString::number(width()));
/* Height */
doc->writeTextElement(KXMLQLCEFXHeight, QString::number(height()));
/* Rotation */
doc->writeTextElement(KXMLQLCEFXRotation, QString::number(rotation()));
/* StartOffset */
doc->writeTextElement(KXMLQLCEFXStartOffset, QString::number(startOffset()));
/* IsRelative */
doc->writeTextElement(KXMLQLCEFXIsRelative, QString::number(isRelative() ? 1 : 0));
/********************************************
* X-Axis
********************************************/
doc->writeStartElement(KXMLQLCEFXAxis);
doc->writeAttribute(KXMLQLCFunctionName, KXMLQLCEFXX);
/* Offset */
doc->writeTextElement(KXMLQLCEFXOffset, QString::number(xOffset()));
/* Frequency */
doc->writeTextElement(KXMLQLCEFXFrequency, QString::number(xFrequency()));
/* Phase */
doc->writeTextElement(KXMLQLCEFXPhase, QString::number(xPhase()));
/* End the (X) <Axis> tag */
doc->writeEndElement();
/********************************************
* Y-Axis
********************************************/
doc->writeStartElement(KXMLQLCEFXAxis);
doc->writeAttribute(KXMLQLCFunctionName, KXMLQLCEFXY);
/* Offset */
doc->writeTextElement(KXMLQLCEFXOffset, QString::number(yOffset()));
/* Frequency */
doc->writeTextElement(KXMLQLCEFXFrequency, QString::number(yFrequency()));
/* Phase */
doc->writeTextElement(KXMLQLCEFXPhase, QString::number(yPhase()));
/* End the (Y) <Axis> tag */
doc->writeEndElement();
/* End the <Function> tag */
doc->writeEndElement();
return true;
}
