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Maj terminée. Pour consulter la release notes associée voici le lien :
https://about.gitlab.com/releases/2021/07/07/critical-security-release-gitlab-14-0-4-released/

Commit 3b54fc6c authored by COULAUD Olivier's avatar COULAUD Olivier
Browse files

Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/scalfmm/scalfmm

parents 5e687ea5 0cdd0b08
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Showing with 228 additions and 24 deletions
CMakeModules/morse/find/FindPTSCOTCH.cmake
View file @ 3b54fc6c
......@@ -264,10 +264,21 @@ if(PTSCOTCH_LIBRARIES)
if(CMAKE_THREAD_LIBS_INIT)
list(APPEND REQUIRED_LIBS "${CMAKE_THREAD_LIBS_INIT}")
endif()
if(UNIX OR WIN32)
set(Z_LIBRARY "Z_LIBRARY-NOTFOUND")
find_library(Z_LIBRARY NAMES z)
if(Z_LIBRARY)
list(APPEND REQUIRED_LIBS "-lz")
endif()
set(M_LIBRARY "M_LIBRARY-NOTFOUND")
find_library(M_LIBRARY NAMES m)
if(M_LIBRARY)
list(APPEND REQUIRED_LIBS "-lm")
endif()
list(APPEND REQUIRED_LIBS "-lz -lrt")
set(RT_LIBRARY "RT_LIBRARY-NOTFOUND")
find_library(RT_LIBRARY NAMES rt)
if(RT_LIBRARY)
list(APPEND REQUIRED_LIBS "-lrt")
endif()
# set required libraries for link
set(CMAKE_REQUIRED_INCLUDES "${REQUIRED_INCDIRS}")
......
CMakeModules/morse/find/FindSCOTCH.cmake
View file @ 3b54fc6c
......@@ -233,10 +233,21 @@ if(SCOTCH_LIBRARIES)
if(CMAKE_THREAD_LIBS_INIT)
list(APPEND REQUIRED_LIBS "${CMAKE_THREAD_LIBS_INIT}")
endif()
if(UNIX OR WIN32)
set(Z_LIBRARY "Z_LIBRARY-NOTFOUND")
find_library(Z_LIBRARY NAMES z)
if(Z_LIBRARY)
list(APPEND REQUIRED_LIBS "-lz")
endif()
set(M_LIBRARY "M_LIBRARY-NOTFOUND")
find_library(M_LIBRARY NAMES m)
if(M_LIBRARY)
list(APPEND REQUIRED_LIBS "-lm")
endif()
list(APPEND REQUIRED_LIBS "-lz -lrt")
set(RT_LIBRARY "RT_LIBRARY-NOTFOUND")
find_library(RT_LIBRARY NAMES rt)
if(RT_LIBRARY)
list(APPEND REQUIRED_LIBS "-lrt")
endif()
# set required libraries for link
set(CMAKE_REQUIRED_INCLUDES "${REQUIRED_INCDIRS}")
......
Src/Core/FFmmAlgorithmSectionTask.hpp
View file @ 3b54fc6c
......@@ -27,6 +27,7 @@
#include "../Containers/FVector.hpp"
#include "FCoreCommon.hpp"
#include "FP2PExclusion.hpp"
/**
* @author Berenger Bramas (berenger.bramas@inria.fr)
......@@ -45,7 +46,7 @@
*
* Upon destruction, this class does not deallocate pointers given to its constructor.
*/
template<class OctreeClass, class CellClass, class ContainerClass, class KernelClass, class LeafClass>
template<class OctreeClass, class CellClass, class ContainerClass, class KernelClass, class LeafClass, class P2PExclusionClass = FP2PMiddleExclusion>
class FFmmAlgorithmSectionTask : public FAbstractAlgorithm, public FAlgorithmTimers {
OctreeClass* const tree; ///< The octree to work on
......@@ -328,7 +329,7 @@ protected:
// There is a maximum of 26 neighbors
ContainerClass* neighbors[27];
const int SizeShape = 3*3*3;
const int SizeShape = P2PExclusionClass::SizeShape;
FVector<typename OctreeClass::Iterator> shapes[SizeShape];
typename OctreeClass::Iterator octreeIterator(tree);
......@@ -338,7 +339,7 @@ protected:
// Coloring all the cells
do{
const FTreeCoordinate& coord = octreeIterator.getCurrentGlobalCoordinate();
const int shapePosition = (coord.getX()%3)*9 + (coord.getY()%3)*3 + (coord.getZ()%3);
const int shapePosition = P2PExclusionClass::GetShapeIdx(coord);
shapes[shapePosition].push(octreeIterator);
......
Src/Core/FFmmAlgorithmTask.hpp
View file @ 3b54fc6c
......@@ -27,6 +27,7 @@
#include "../Containers/FVector.hpp"
#include "FCoreCommon.hpp"
#include "FP2PExclusion.hpp"
/**
* @author Berenger Bramas (berenger.bramas@inria.fr)
......@@ -39,7 +40,7 @@
*
* Of course this class does not deallocate pointer given in arguements.
*/
template<class OctreeClass, class CellClass, class ContainerClass, class KernelClass, class LeafClass>
template<class OctreeClass, class CellClass, class ContainerClass, class KernelClass, class LeafClass, class P2PExclusionClass = FP2PMiddleExclusion>
class FFmmAlgorithmTask : public FAbstractAlgorithm, public FAlgorithmTimers {
OctreeClass* const tree; //< The octree to work on
......@@ -389,7 +390,7 @@ protected:
// There is a maximum of 26 neighbors
ContainerClass* neighbors[27];
const int SizeShape = 3*3*3;
const int SizeShape = P2PExclusionClass::SizeShape;
FVector<typename OctreeClass::Iterator> shapes[SizeShape];
typename OctreeClass::Iterator octreeIterator(tree);
......@@ -398,7 +399,7 @@ protected:
// for each leafs
do{
const FTreeCoordinate& coord = octreeIterator.getCurrentGlobalCoordinate();
const int shapePosition = (coord.getX()%3)*9 + (coord.getY()%3)*3 + (coord.getZ()%3);
const int shapePosition = P2PExclusionClass::GetShapeIdx(coord);
shapes[shapePosition].push(octreeIterator);
......
Src/Core/FFmmAlgorithmThread.hpp
View file @ 3b54fc6c
......@@ -27,6 +27,7 @@
#include "../Containers/FOctree.hpp"
#include "FCoreCommon.hpp"
#include "FP2PExclusion.hpp"
#include <omp.h>
......@@ -45,7 +46,7 @@
*
* This class does not deallocate pointers given to its constructor.
*/
template<class OctreeClass, class CellClass, class ContainerClass, class KernelClass, class LeafClass>
template<class OctreeClass, class CellClass, class ContainerClass, class KernelClass, class LeafClass, class P2PExclusionClass = FP2PMiddleExclusion>
class FFmmAlgorithmThread : public FAbstractAlgorithm, public FAlgorithmTimers{
OctreeClass* const tree; ///< The octree to work on.
KernelClass** kernels; ///< The kernels.
......@@ -53,7 +54,7 @@ class FFmmAlgorithmThread : public FAbstractAlgorithm, public FAlgorithmTimers{
typename OctreeClass::Iterator* iterArray;
int leafsNumber;
static const int SizeShape = 3*3*3;
static const int SizeShape = P2PExclusionClass::SizeShape;
int shapeLeaf[SizeShape];
const int MaxThreads; ///< The maximum number of threads.
......@@ -140,7 +141,7 @@ protected:
do{
++leafsNumber;
const FTreeCoordinate& coord = octreeIterator.getCurrentCell()->getCoordinate();
++this->shapeLeaf[(coord.getX()%3)*9 + (coord.getY()%3)*3 + (coord.getZ()%3)];
++this->shapeLeaf[P2PExclusionClass::GetShapeIdx(coord)];
} while(octreeIterator.moveRight());
iterArray = new typename OctreeClass::Iterator[leafsNumber];
......@@ -441,7 +442,7 @@ protected:
//iterArray[leafs] = octreeIterator;
//++leafs;
const FTreeCoordinate& coord = octreeIterator.getCurrentGlobalCoordinate();
const int shapePosition = (coord.getX()%3)*9 + (coord.getY()%3)*3 + (coord.getZ()%3);
const int shapePosition = P2PExclusionClass::GetShapeIdx(coord);
omp_set_lock(&lockShape[shapePosition]);
const int positionToWork = startPosAtShape[shapePosition]++;
......
Src/Core/FFmmAlgorithmThreadBalance.hpp
View file @ 3b54fc6c
......@@ -11,6 +11,7 @@
#include "../Containers/FOctree.hpp"
#include "FCoreCommon.hpp"
#include "FP2PExclusion.hpp"
#include <omp.h>
#include <vector>
......@@ -29,12 +30,12 @@
*
* This class does not deallocate pointers given to its constructor.
*/
template<class OctreeClass, class CellClass, class ContainerClass, class KernelClass, class LeafClass>
template<class OctreeClass, class CellClass, class ContainerClass, class KernelClass, class LeafClass, class P2PExclusionClass = FP2PMiddleExclusion>
class FFmmAlgorithmThreadBalance : public FAbstractAlgorithm, public FAlgorithmTimers{
OctreeClass* const tree; ///< The octree to work on.
KernelClass** kernels; ///< The kernels.
static const int SizeShape = 3*3*3;
static const int SizeShape = P2PExclusionClass::SizeShape;
const int MaxThreads; ///< The maximum number of threads.
......@@ -206,7 +207,7 @@ protected:
do{
++leafsNumber;
const FTreeCoordinate& coord = octreeIterator.getCurrentCell()->getCoordinate();
++shapeLeaves[(coord.getX()%3)*9 + (coord.getY()%3)*3 + (coord.getZ()%3)];
++shapeLeaves[P2PExclusionClass::GetShapeIdx(coord)];
} while(octreeIterator.moveRight());
}
......@@ -367,7 +368,7 @@ protected:
// for each leafs
for(int idxLeaf = 0 ; idxLeaf < leafsNumber ; ++idxLeaf){
const FTreeCoordinate& coord = octreeIterator.getCurrentGlobalCoordinate();
const int shapePosition = (coord.getX()%3)*9 + (coord.getY()%3)*3 + (coord.getZ()%3);
const int shapePosition = P2PExclusionClass::GetShapeIdx(coord);
const int positionToWork = startPosAtShape[shapePosition]++;
......
Src/Core/FFmmAlgorithmThreadProc.hpp
View file @ 3b54fc6c
......@@ -40,6 +40,7 @@
#include <sys/time.h>
#include "FCoreCommon.hpp"
#include "FP2PExclusion.hpp"
#include <memory>
......@@ -63,7 +64,7 @@
* --tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=20
* --track-fds=yes ./Tests/testFmmAlgorithmProc ../Data/testLoaderSmall.fma.tmp
*/
template<class OctreeClass, class CellClass, class ContainerClass, class KernelClass, class LeafClass>
template<class OctreeClass, class CellClass, class ContainerClass, class KernelClass, class LeafClass, class P2PExclusionClass = FP2PMiddleExclusion>
class FFmmAlgorithmThreadProc : public FAbstractAlgorithm, public FAlgorithmTimers {
private:
OctreeClass* const tree; ///< The octree to work on
......@@ -1233,7 +1234,7 @@ protected:
// init
const int LeafIndex = OctreeHeight - 1;
const int SizeShape = 3*3*3;
const int SizeShape = P2PExclusionClass::SizeShape;
int shapeLeaf[SizeShape];
memset(shapeLeaf,0,SizeShape*sizeof(int));
......@@ -1394,7 +1395,7 @@ protected:
myLeafs[idxLeaf] = octreeIterator;
const FTreeCoordinate& coord = octreeIterator.getCurrentCell()->getCoordinate();
const int shape = (coord.getX()%3)*9 + (coord.getY()%3)*3 + (coord.getZ()%3);
const int shape = P2PExclusionClass::GetShapeIdx(coord);
shapeType[idxLeaf] = shape;
++shapeLeaf[shape];
......
Src/Core/FFmmAlgorithmThreadProcPeriodic.hpp
View file @ 3b54fc6c
......@@ -38,6 +38,7 @@
#include <omp.h>
#include "FCoreCommon.hpp"
#include "FP2PExclusion.hpp"
#include <memory>
......@@ -61,7 +62,7 @@
* --tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=20 --track-fds=yes
* ./Tests/testFmmAlgorithmProc ../Data/testLoaderSmall.fma.tmp
*/
template<class FReal, class OctreeClass, class CellClass, class ContainerClass, class KernelClass, class LeafClass>
template<class FReal, class OctreeClass, class CellClass, class ContainerClass, class KernelClass, class LeafClass, class P2PExclusionClass = FP2PMiddleExclusion>
class FFmmAlgorithmThreadProcPeriodic : public FAbstractAlgorithm {
OctreeClass* const tree; //< The octree to work on
KernelClass** kernels; //< The kernels
......@@ -1348,7 +1349,7 @@ protected:
// init
const int LeafIndex = OctreeHeight - 1;
const int SizeShape = 3*3*3;
const int SizeShape = P2PExclusionClass::SizeShape;
int shapeLeaf[SizeShape];
memset(shapeLeaf,0,SizeShape*sizeof(int));
......@@ -1511,7 +1512,7 @@ protected:
myLeafs[idxLeaf] = octreeIterator;
const FTreeCoordinate& coord = octreeIterator.getCurrentCell()->getCoordinate();
const int shape = (coord.getX()%3)*9 + (coord.getY()%3)*3 + (coord.getZ()%3);
const int shape = P2PExclusionClass::GetShapeIdx(coord);
shapeType[idxLeaf] = shape;
++shapeLeaf[shape];
......
Src/Core/FP2PExclusion.hpp 0 → 100644
View file @ 3b54fc6c
#ifndef FP2PEXCLUSION_HPP
#define FP2PEXCLUSION_HPP
#include "../Containers/FTreeCoordinate.hpp"
/**
* This class gives is responsible of the separation of the leaves
* using the coloring algorithm.
* In case of classic P2P and mutual interaction the BoxSeparations = 2 should be used.
* For our current mutual P2P is is a little more complicated because we need
* 2 boxes of separation but only in some directions.
*/
template <int BoxSeparations = 2>
class FP2PExclusion{
public:
static const int BoxesPerDim = (BoxSeparations+1);
static const int SizeShape = BoxesPerDim*BoxesPerDim*BoxesPerDim;
static int GetShapeIdx(const int inX, const int inY, const int inZ){
return (inX%BoxesPerDim)*(BoxesPerDim*BoxesPerDim) + (inY%BoxesPerDim)*BoxesPerDim + (inZ%BoxesPerDim);
}
static int GetShapeIdx(const FTreeCoordinate& coord){
return GetShapeIdx(coord.getX(), coord.getY(), coord.getZ());
}
};
/**
* Here the formula is related to the octree construction of neighbors list:
* const int index = (((idxX + 1) * 3) + (idxY +1)) * 3 + idxZ + 1;
* If go from 0 to 27,
* if we loop from 0 to 14, then we need "x" in [0;2[
* "y" "z" in [0;3[
*/
class FP2PMiddleExclusion{
public:
static const int SizeShape = 3*3*2;
static int GetShapeIdx(const int inX, const int inY, const int inZ){
return (inX%2)*9 + (inY%3)*3 + (inZ%3);
}
static int GetShapeIdx(const FTreeCoordinate& coord){
return GetShapeIdx(coord.getX(), coord.getY(), coord.getZ());
}
};
#endif // FP2PEXCLUSION_HPP
UTests/utestP2PExclusion.cpp 0 → 100644
View file @ 3b54fc6c
// ===================================================================================
// Copyright ScalFmm 2011 INRIA, Olivier Coulaud, Bérenger Bramas, Matthias Messner
// olivier.coulaud@inria.fr, berenger.bramas@inria.fr
// This software is a computer program whose purpose is to compute the FMM.
//
// This software is governed by the CeCILL-C and LGPL licenses and
// abiding by the rules of distribution of free software.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public and CeCILL-C Licenses for more details.
// "http://www.cecill.info".
// "http://www.gnu.org/licenses".
// ===================================================================================
#include "FUTester.hpp"
#include "Core/FP2PExclusion.hpp"
#include "Utils/FMath.hpp"
#include <memory>
/**
* This file is a unit test for the FNeigborIndexes classes
*/
/** this class test the list container */
class TestExclusion : public FUTester<TestExclusion> {
const int Size = 100;
void Exclusion2(){
const int Width = 2;
std::unique_ptr<int[]> grid(new int[Size*Size*Size]);
for(int idxShape = 0 ; idxShape < FP2PExclusion<Width>::SizeShape ; ++idxShape){
memset(grid.get(), 0, sizeof(int)*Size*Size*Size);
for(int idxX = 0 ; idxX < Size ; ++idxX){
for(int idxY = 0 ; idxY < Size ; ++idxY){
for(int idxZ = 0 ; idxZ < Size ; ++idxZ){
if(FP2PExclusion<Width>::GetShapeIdx(idxX,idxY,idxZ) == idxShape){
for(int idxX_neig = FMath::Max(0,idxX-1) ; idxX_neig < FMath::Min(Size,idxX+1) ; ++idxX_neig){
for(int idxY_neig = FMath::Max(0,idxY-1) ; idxY_neig < FMath::Min(Size,idxY+1) ; ++idxY_neig){
for(int idxZ_neig = FMath::Max(0,idxZ-1) ; idxZ_neig < FMath::Min(Size,idxZ+1) ; ++idxZ_neig){
uassert(grid[(idxX_neig*Size + idxY_neig)*Size + idxZ_neig] == 0);
grid[grid[(idxX_neig*Size + idxY_neig)*Size + idxZ_neig]] = 1;
}
}
}
}
}
}
}
}
}
void Exclusion1(){
const int Width = 1;
std::unique_ptr<int[]> grid(new int[Size*Size*Size]);
for(int idxShape = 0 ; idxShape < FP2PExclusion<Width>::SizeShape ; ++idxShape){
memset(grid.get(), 0, sizeof(int)*Size*Size*Size);
for(int idxX = 0 ; idxX < Size ; ++idxX){
for(int idxY = 0 ; idxY < Size ; ++idxY){
for(int idxZ = 0 ; idxZ < Size ; ++idxZ){
if(FP2PExclusion<Width>::GetShapeIdx(idxX,idxY,idxZ) == idxShape){
for(int idxX_neig = FMath::Max(0,idxX-1) ; idxX_neig < idxX ; ++idxX_neig){
for(int idxY_neig = FMath::Max(0,idxY-1) ; idxY_neig < idxY ; ++idxY_neig){
for(int idxZ_neig = FMath::Max(0,idxZ-1) ; idxZ_neig < idxZ ; ++idxZ_neig){
uassert(grid[(idxX_neig*Size + idxY_neig)*Size + idxZ_neig] == 0);
grid[grid[(idxX_neig*Size + idxY_neig)*Size + idxZ_neig]] = 1;
}
}
}
}
}
}
}
}
}
void Middle(){
std::unique_ptr<int[]> grid(new int[Size*Size*Size]);
for(int idxShape = 0 ; idxShape < FP2PMiddleExclusion::SizeShape ; ++idxShape){
memset(grid.get(), 0, sizeof(int)*Size*Size*Size);
for(int idxX = 0 ; idxX < Size ; ++idxX){
for(int idxY = 0 ; idxY < Size ; ++idxY){
for(int idxZ = 0 ; idxZ < Size ; ++idxZ){
if(FP2PMiddleExclusion::GetShapeIdx(idxX,idxY,idxZ) == idxShape){
for(int idxX_neig = FMath::Max(0,idxX-1) ; idxX_neig < FMath::Min(Size,idxX+1) ; ++idxX_neig){
for(int idxY_neig = FMath::Max(0,idxY-1) ; idxY_neig < FMath::Min(Size,idxY+1) ; ++idxY_neig){
for(int idxZ_neig = FMath::Max(0,idxZ-1) ; idxZ_neig < FMath::Min(Size,idxZ+1) ; ++idxZ_neig){
const int diffx = idxX_neig-idxX;
const int diffy = idxY_neig-idxY;
const int diffz = idxZ_neig-idxZ;
const int idx = (diffx+1)*9 + (diffy+1)*3 + (diffz+1);
if(idx < 14){
uassert(grid[(idxX_neig*Size + idxY_neig)*Size + idxZ_neig] == 0);
grid[grid[(idxX_neig*Size + idxY_neig)*Size + idxZ_neig]] = 1;
}
}
}
}
}
}
}
}
}
}
// set test
void SetTests(){
AddTest(&TestExclusion::Exclusion2,"Test 2 exclustion");
AddTest(&TestExclusion::Exclusion1,"Test 1 exclustion");
AddTest(&TestExclusion::Middle,"Test middle exclustion");
}
};
// You must do this
TestClass(TestExclusion)
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