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Message #07303
[SCM] Yet Another Dynamic Engine. Platform for discrete element modeling. branch, master, updated. debian/0.60.1-1-9-gf49f563
The following commit has been merged in the master branch:
commit f49f563fe88a39cf295361cd27d0ad7a690e4ad8
Author: Anton Gladky <gladky.anton@xxxxxxxxx>
Date: Fri Mar 18 10:05:47 2011 +0100
Added fix for lp:724396
diff --git a/debian/changelog b/debian/changelog
index eb0d218..c9e28a5 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,10 @@
yade (0.60.1-2) experimental; urgency=low
* Fixed https://bugs.launchpad.net/bugs/721107
- * vtk-feature is disabled temporarily due to
- incompatibility with libvtk5.6-dev, used
- by default in Debian unstable
+ * Fixed https://bugs.launchpad.net/bugs/724396
+ * vtkNetCDF was deleted from libs due to absence in libvtk5.6-dev
- -- Anton Gladky <gladky.anton@xxxxxxxxx> Sun, 20 Feb 2011 16:50:26 +0100
+ -- Anton Gladky <gladky.anton@xxxxxxxxx> Fri, 18 Mar 2011 06:57:21 +0100
yade (0.60.1-1) experimental; urgency=low
diff --git a/debian/patches/fix-forcecontainer-crash-lp724396.patch b/debian/patches/fix-forcecontainer-crash-lp724396.patch
new file mode 100644
index 0000000..daaa258
--- /dev/null
+++ b/debian/patches/fix-forcecontainer-crash-lp724396.patch
@@ -0,0 +1,165 @@
+Description: fixes crash in forceContainer after adding particles into the simulation
+Author: Sergei Dorofeenko <dorofeenko@xxxxxxxxx>, Václav Šmilauer <eu@xxxxxxxx>, Anton Gladky <gladky.anton@xxxxxxxxx>
+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.patch b/debian/patches/fix-memory-leak-in-InsertionSortCollider-lp721107.patch
similarity index 99%
rename from debian/patches/fix-memory-leak-in-InsertionSortCollider.patch
rename to debian/patches/fix-memory-leak-in-InsertionSortCollider-lp721107.patch
index 07faf04..cfe3078 100644
--- a/debian/patches/fix-memory-leak-in-InsertionSortCollider.patch
+++ b/debian/patches/fix-memory-leak-in-InsertionSortCollider-lp721107.patch
@@ -3,7 +3,6 @@ Author: Sergei Dorofeenko <dorofeenko@xxxxxxxxx>, Václav Šmilauer <eu@xxxxxxxx
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 @@
diff --git a/debian/patches/series b/debian/patches/series
index 7f85512..0618eb2 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
-fix-memory-leak-in-InsertionSortCollider.patch
+fix-memory-leak-in-InsertionSortCollider-lp721107.patch
vtkNetCDF-is-deleted-from-libs.patch
+fix-forcecontainer-crash-lp724396.patch
--
Yet Another Dynamic Engine. Platform for discrete element modeling.
