[SCM] Yet Another Dynamic Engine. Platform for discrete element modeling. branch, master, updated. debian/0.60.1-1-13-ge358c3b
Anton Gladky
gladky.anton at gmail.com
Tue Mar 22 10:43:49 UTC 2011
The following commit has been merged in the master branch:
commit 3d93a61f7a533450f009764e87701a8780811719
Author: Anton Gladky <gladky.anton at gmail.com>
Date: Tue Mar 22 12:33:51 2011 +0100
Deleted patches, aplied by upstream in 0.60.2
diff --git a/debian/patches/fix-forcecontainer-crash-lp724396.patch b/debian/patches/fix-forcecontainer-crash-lp724396.patch
deleted file mode 100644
index daaa258..0000000
--- a/debian/patches/fix-forcecontainer-crash-lp724396.patch
+++ /dev/null
@@ -1,165 +0,0 @@
-Description: fixes crash in forceContainer after adding particles into the simulation
-Author: Sergei Dorofeenko <dorofeenko at icp.ac.ru>, Václav Šmilauer <eu at doxos.eu>, Anton Gladky <gladky.anton at gmail.com>
-Bug: https://bugs.launchpad.net/bugs/724396
-Applied-Upstream: http://bazaar.launchpad.net/~yade-dev/yade/0.60/revision/2567
-
---- a/core/ForceContainer.hpp
-+++ b/core/ForceContainer.hpp
-@@ -4,7 +4,6 @@
- #include<string.h>
- #include<vector>
- #include<yade/lib-base/Math.hpp>
--// for Body::id_t
- #include<yade/core/Body.hpp>
-
- #include<boost/static_assert.hpp>
-@@ -52,14 +51,17 @@
- std::vector<vvector> _moveData;
- std::vector<vvector> _rotData;
- vvector _force, _torque, _move, _rot;
-+ std::vector<size_t> sizeOfThreads;
- size_t size;
-+ bool syncedSizes;
- int nThreads;
- bool synced,moveRotUsed;
- boost::mutex globalMutex;
-+ Vector3r _zero;
-
-- inline void ensureSize(Body::id_t id){
-+ inline void ensureSize(Body::id_t id, int threadN){
- assert(nThreads>omp_get_thread_num());
-- if (size<=(size_t)id) resize(min((size_t)1.5*(id+100),(size_t)(id+2000)));
-+ if (sizeOfThreads[threadN]<=(size_t)id) resize(min((size_t)1.5*(id+100),(size_t)(id+2000)),threadN);
- }
-
- inline void ensureSynced(){ if(!synced) throw runtime_error("ForceContainer not thread-synchronized; call sync() first!"); }
-@@ -74,30 +76,43 @@
- // dummy function to avoid template resolution failure
- friend class boost::serialization::access; template<class ArchiveT> void serialize(ArchiveT & ar, unsigned int version){}
- public:
-- ForceContainer(): size(0), synced(true),moveRotUsed(false),syncCount(0), lastReset(0){
-+ ForceContainer(): size(0),syncedSizes(true),synced(true),moveRotUsed(false),_zero(Vector3r::Zero()),syncCount(0),lastReset(0){
- nThreads=omp_get_max_threads();
- for(int i=0; i<nThreads; i++){
- _forceData.push_back(vvector()); _torqueData.push_back(vvector());
-- _moveData.push_back(vvector()); _rotData.push_back(vvector());
-+ _moveData.push_back(vvector()); _rotData.push_back(vvector());
-+ sizeOfThreads.push_back(0);
- }
- }
-
-- const Vector3r& getForce(Body::id_t id) { ensureSize(id); ensureSynced(); return _force[id]; }
-- void addForce(Body::id_t id, const Vector3r& f){ ensureSize(id); synced=false; _forceData[omp_get_thread_num()][id]+=f;}
-- const Vector3r& getTorque(Body::id_t id) { ensureSize(id); ensureSynced(); return _torque[id]; }
-- void addTorque(Body::id_t id, const Vector3r& t){ ensureSize(id); synced=false; _torqueData[omp_get_thread_num()][id]+=t;}
-- const Vector3r& getMove(Body::id_t id) { ensureSize(id); ensureSynced(); return _move[id]; }
-- void addMove(Body::id_t id, const Vector3r& m) { ensureSize(id); synced=false; moveRotUsed=true; _moveData[omp_get_thread_num()][id]+=m;}
-- const Vector3r& getRot(Body::id_t id) { ensureSize(id); ensureSynced(); return _rot[id]; }
-- void addRot(Body::id_t id, const Vector3r& r) { ensureSize(id); synced=false; moveRotUsed=true; _rotData[omp_get_thread_num()][id]+=r;}
-+ const Vector3r& getForce(Body::id_t id) { ensureSynced(); return ((size_t)id<size)?_force[id]:_zero; }
-+ void addForce(Body::id_t id, const Vector3r& f){ ensureSize(id,omp_get_thread_num()); synced=false; _forceData[omp_get_thread_num()][id]+=f;}
-+ const Vector3r& getTorque(Body::id_t id) { ensureSynced(); return ((size_t)id<size)?_torque[id]:_zero; }
-+ void addTorque(Body::id_t id, const Vector3r& t){ ensureSize(id,omp_get_thread_num()); synced=false; _torqueData[omp_get_thread_num()][id]+=t;}
-+ const Vector3r& getMove(Body::id_t id) { ensureSynced(); return ((size_t)id<size)?_move[id]:_zero; }
-+ void addMove(Body::id_t id, const Vector3r& m) { ensureSize(id,omp_get_thread_num()); synced=false; moveRotUsed=true; _moveData[omp_get_thread_num()][id]+=m;}
-+ const Vector3r& getRot(Body::id_t id) { ensureSynced(); return ((size_t)id<size)?_rot[id]:_zero; }
-+ void addRot(Body::id_t id, const Vector3r& r) { ensureSize(id,omp_get_thread_num()); synced=false; moveRotUsed=true; _rotData[omp_get_thread_num()][id]+=r;}
- /* To be benchmarked: sum thread data in getForce/getTorque upon request for each body individually instead of by the sync() function globally */
- // this function is used from python so that running simulation is not slowed down by sync'ing on occasions
- // since Vector3r writes are not atomic, it might (rarely) return wrong value, if the computation is running meanwhile
-- Vector3r getForceSingle (Body::id_t id){ ensureSize(id); Vector3r ret(Vector3r::Zero()); for(int t=0; t<nThreads; t++){ ret+=_forceData [t][id]; } return ret; }
-- Vector3r getTorqueSingle(Body::id_t id){ ensureSize(id); Vector3r ret(Vector3r::Zero()); for(int t=0; t<nThreads; t++){ ret+=_torqueData[t][id]; } return ret; }
-- Vector3r getMoveSingle (Body::id_t id){ ensureSize(id); Vector3r ret(Vector3r::Zero()); for(int t=0; t<nThreads; t++){ ret+=_moveData [t][id]; } return ret; }
-- Vector3r getRotSingle (Body::id_t id){ ensureSize(id); Vector3r ret(Vector3r::Zero()); for(int t=0; t<nThreads; t++){ ret+=_rotData [t][id]; } return ret; }
--
-+ Vector3r getForceSingle (Body::id_t id){ Vector3r ret(Vector3r::Zero()); for(int t=0; t<nThreads; t++){ ret+=((size_t)id<sizeOfThreads[t])?_forceData [t][id]:_zero; } return ret; }
-+ Vector3r getTorqueSingle(Body::id_t id){ Vector3r ret(Vector3r::Zero()); for(int t=0; t<nThreads; t++){ ret+=((size_t)id<sizeOfThreads[t])?_torqueData[t][id]:_zero; } return ret; }
-+ Vector3r getMoveSingle (Body::id_t id){ Vector3r ret(Vector3r::Zero()); for(int t=0; t<nThreads; t++){ ret+=((size_t)id<sizeOfThreads[t])?_moveData [t][id]:_zero; } return ret; }
-+ Vector3r getRotSingle (Body::id_t id){ Vector3r ret(Vector3r::Zero()); for(int t=0; t<nThreads; t++){ ret+=((size_t)id<sizeOfThreads[t])?_rotData [t][id]:_zero; } return ret; }
-+
-+ inline void syncSizesOfContainers() {
-+ if (syncedSizes) return;
-+ //check whether all containers have equal length, and if not resize it
-+ for(int i=0; i<nThreads; i++){
-+ if (sizeOfThreads[i]<size) resize(size,i);
-+ }
-+ _force.resize(size,Vector3r::Zero());
-+ _torque.resize(size,Vector3r::Zero());
-+ _move.resize(size,Vector3r::Zero());
-+ _rot.resize(size,Vector3r::Zero());
-+ syncedSizes=true;
-+ }
- /* Sum contributions from all threads, save to _force&_torque.
- * Locks globalMutex, since one thread modifies common data (_force&_torque).
- * Must be called before get* methods are used. Exception is thrown otherwise, since data are not consistent. */
-@@ -105,7 +120,9 @@
- if(synced) return;
- boost::mutex::scoped_lock lock(globalMutex);
- if(synced) return; // if synced meanwhile
-- // #pragma omp parallel for schedule(static)
-+
-+ syncSizesOfContainers();
-+
- for(long id=0; id<(long)size; id++){
- Vector3r sumF(Vector3r::Zero()), sumT(Vector3r::Zero());
- for(int thread=0; thread<nThreads; thread++){ sumF+=_forceData[thread][id]; sumT+=_torqueData[thread][id];}
-@@ -123,31 +140,24 @@
- unsigned long syncCount;
- long lastReset;
-
-- /* Change size of containers (number of bodies).
-- * Locks globalMutex, since on threads modifies other threads' data.
-- * Called very rarely (a few times at the beginning of the simulation). */
-- void resize(size_t newSize){
-- boost::mutex::scoped_lock lock(globalMutex);
-- if(size>=newSize) return; // in case on thread was waiting for resize, but it was already satisfied by another one
-- for(int thread=0; thread<nThreads; thread++){
-- _forceData [thread].resize(newSize,Vector3r::Zero());
-- _torqueData[thread].resize(newSize,Vector3r::Zero());
-- _moveData[thread].resize(newSize,Vector3r::Zero());
-- _rotData[thread].resize(newSize,Vector3r::Zero());
-- }
-- _force.resize(newSize,Vector3r::Zero()); _torque.resize(newSize,Vector3r::Zero());
-- _move.resize(newSize,Vector3r::Zero()); _rot.resize(newSize,Vector3r::Zero());
-- size=newSize;
-+ void resize(size_t newSize, int threadN){
-+ _forceData [threadN].resize(newSize,Vector3r::Zero());
-+ _torqueData[threadN].resize(newSize,Vector3r::Zero());
-+ _moveData[threadN].resize(newSize,Vector3r::Zero());
-+ _rotData[threadN].resize(newSize,Vector3r::Zero());
-+ sizeOfThreads[threadN] = newSize;
-+ if (size<newSize) size=newSize;
-+ syncedSizes=false;
- }
- /*! Reset all data, also reset summary forces/torques and mark the container clean. */
- // perhaps should be private and friend Scene or whatever the only caller should be
- void reset(long iter){
- for(int thread=0; thread<nThreads; thread++){
-- memset(&_forceData [thread][0],0,sizeof(Vector3r)*size);
-- memset(&_torqueData[thread][0],0,sizeof(Vector3r)*size);
-+ memset(&_forceData [thread][0],0,sizeof(Vector3r)*sizeOfThreads[thread]);
-+ memset(&_torqueData[thread][0],0,sizeof(Vector3r)*sizeOfThreads[thread]);
- if(moveRotUsed){
-- memset(&_moveData [thread][0],0,sizeof(Vector3r)*size);
-- memset(&_rotData [thread][0],0,sizeof(Vector3r)*size);
-+ memset(&_moveData [thread][0],0,sizeof(Vector3r)*sizeOfThreads[thread]);
-+ memset(&_rotData [thread][0],0,sizeof(Vector3r)*sizeOfThreads[thread]);
- }
- }
- memset(&_force [0], 0,sizeof(Vector3r)*size);
-@@ -226,5 +236,4 @@
- const bool& getMoveRotUsed() const {return moveRotUsed;}
- };
-
--
- #endif
---- a/core/Scene.cpp
-+++ b/core/Scene.cpp
-@@ -70,7 +70,6 @@
- if(needsInitializers){
- checkStateTypes();
- FOREACH(shared_ptr<Engine> e, initializers){ e->scene=this; if(e->dead || !e->isActivated()) continue; e->action(); }
-- forces.resize(bodies->size());
- needsInitializers=false;
- }
- if(!subStepping && subStep<0){
diff --git a/debian/patches/fix-memory-leak-in-InsertionSortCollider-lp721107.patch b/debian/patches/fix-memory-leak-in-InsertionSortCollider-lp721107.patch
deleted file mode 100644
index cfe3078..0000000
--- a/debian/patches/fix-memory-leak-in-InsertionSortCollider-lp721107.patch
+++ /dev/null
@@ -1,53 +0,0 @@
-Description: fixes memory leak in insertionsortcollider
-Author: Sergei Dorofeenko <dorofeenko at icp.ac.ru>, Václav Šmilauer <eu at doxos.eu>
-Bug: https://bugs.launchpad.net/bugs/721107
-Applied-Upstream: http://bazaar.launchpad.net/~yade-dev/yade/0.60/revision/2565
-
---- a/pkg/common/InsertionSortCollider.cpp
-+++ b/pkg/common/InsertionSortCollider.cpp
-@@ -92,7 +92,7 @@
- // or the time of scheduled run already came, or we were never scheduled yet
- if(!strideActive) return true;
- if(!newton || (nBins>=1 && !newton->velocityBins)) return true;
-- if(nBins>=1 && newton->velocityBins->incrementDists_shouldCollide(scene->dt)) return true;
-+ if(nBins>=1 && newton->velocityBins->checkSize_incrementDists_shouldCollide(scene)) return true;
- if(nBins<=0){
- if(fastestBodyMaxDist<0){fastestBodyMaxDist=0; return true;}
- fastestBodyMaxDist+=sqrt(newton->maxVelocitySq)*scene->dt;
---- a/pkg/common/VelocityBins.cpp
-+++ b/pkg/common/VelocityBins.cpp
-@@ -9,8 +9,12 @@
- #endif
- CREATE_LOGGER(VelocityBins);
-
--bool VelocityBins::incrementDists_shouldCollide(Real dt){
-+bool VelocityBins::checkSize_incrementDists_shouldCollide(const Scene* scene){
-+ // number of particles increased, recollision necessary
-+ // smaller number of particles is handled in setBins
-+ if(bodyBins.size()<scene->bodies->size()) { bodyBins.resize(scene->bodies->size(),/* put new particles to the slowest bin*/ bins.size()-1); return true; }
- int i=0;
-+ const Real& dt=scene->dt;
- FOREACH(Bin& bin, bins){
- // NOTE: this mimics the integration scheme of NewtonIntegrator
- // if you use different integration method, it must be changed (or the infrastructure somehow modified to allow for that)
---- a/pkg/common/VelocityBins.hpp
-+++ b/pkg/common/VelocityBins.hpp
-@@ -23,7 +23,7 @@
- struct Bin{
- Bin(): binMinVelSq(-1), binMaxVelSq(-1), maxDist(0), currDist(0), currMaxVelSq(0), nBodies(0){
- #ifdef YADE_OPENMP
-- threadMaxVelSq.resize(omp_get_max_threads());
-+ threadMaxVelSq.resize(omp_get_max_threads(),0.);
- #endif
- };
- // limits for bin memebrship
-@@ -60,7 +60,8 @@
- void setBins(Scene*, Real currMaxVelSq, Real refSweepLength);
-
- // Increment maximum per-bin distances and tell whether some bodies may be already getting out of the swept bbox (in that case, we need to recompute bounding volumes and run the collider)
-- bool incrementDists_shouldCollide(Real dt);
-+ // Also returns true if number of particles changed, in which case it adjusts internal storage accordingly
-+ bool checkSize_incrementDists_shouldCollide(const Scene*);
-
- /* NOTE: following 3 functions are separated because of multi-threaded operation of NewtonIntegrator
- in that case, every thread must have its own per-bin maximum and binVelSqFinalize will assign the
diff --git a/debian/patches/series b/debian/patches/series
index 0618eb2..e69de29 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +0,0 @@
-fix-memory-leak-in-InsertionSortCollider-lp721107.patch
-vtkNetCDF-is-deleted-from-libs.patch
-fix-forcecontainer-crash-lp724396.patch
diff --git a/debian/patches/vtkNetCDF-is-deleted-from-libs.patch b/debian/patches/vtkNetCDF-is-deleted-from-libs.patch
deleted file mode 100644
index 43f41b3..0000000
--- a/debian/patches/vtkNetCDF-is-deleted-from-libs.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Description: vtkNetCDF was deleted from libs due to absence in libvtk5.6-dev. Seems, functionality is not corrupted.
-Author: Anton Gladky <gladky.anton at gmail.com>
-Applied-Upstream: http://bazaar.launchpad.net/~yade-dev/yade/0.60/revision/2566
-
---- a/SConstruct
-+++ b/SConstruct
-@@ -377,7 +377,7 @@
- else: featureNotOK('qt4','Building with Qt4 implies the QGLViewer library installed (package libqglviewer-qt4-dev package in debian/ubuntu, libQGLViewer in RPM-based distributions)')
- if 'vtk' in env['features']:
- ok=conf.CheckLibWithHeader(['vtkCommon'],'vtkInstantiator.h','c++','vtkInstantiator::New();',autoadd=1)
-- env.Append(LIBS=['vtkHybrid','vtkFiltering','vtkRendering','vtkIO','vtkexoIIc','vtkParallel','vtkGraphics','vtkverdict','vtkImaging','vtkftgl','vtkDICOMParser','vtkmetaio','vtksqlite','vtkNetCDF'])
-+ env.Append(LIBS=['vtkHybrid','vtkFiltering','vtkRendering','vtkIO','vtkexoIIc','vtkParallel','vtkGraphics','vtkverdict','vtkImaging','vtkftgl','vtkDICOMParser','vtkmetaio','vtksqlite'])
- if not ok: featureNotOK('vtk',note="Installer can`t find vtk-library. Be sure you have it installed (usually, libvtk5-dev package). Or you might have to add VTK header directory (e.g. /usr/include/vtk-5.4) to CPPPATH.")
- if 'gts' in env['features']:
- env.ParseConfig('pkg-config gts --cflags --libs');
--
Yet Another Dynamic Engine. Platform for discrete element modeling.
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