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Split out some tree traversal functions into separate file and added forest statistics function

release/4.3a0
Richard Roberts 2013-11-07 21:41:21 +00:00
parent c707059af1
commit 1a41b9f4a2
5 changed files with 309 additions and 159 deletions
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9
gtsam/CMakeLists.txt
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@ -50,11 +50,10 @@ install(FILES ${gtsam_core_headers} DESTINATION include/gtsam)
# assemble core libaries
foreach(subdir ${gtsam_subdirs})
# Build convenience libraries
file(GLOB subdir_cpp_srcs "${subdir}/*.cpp")
file(GLOB subdir_headers "${subdir}/*.h")
list(REMOVE_ITEM subdir_cpp_srcs ${excluded_sources})
list(REMOVE_ITEM subdir_headers ${excluded_headers})
set(subdir_srcs ${subdir_cpp_srcs} ${subdir_headers}) # Include header files so they show up in Visual Studio
file(GLOB_RECURSE subdir_srcs "${subdir}/*.cpp" "${subdir}/*.h") # Include header files so they show up in Visual Studio
list(REMOVE_ITEM subdir_srcs ${excluded_sources})
file(GLOB subdir_test_files "${subdir}/tests/*")
list(REMOVE_ITEM subdir_srcs ${subdir_test_files}) # Remove test files from sources compiled into library
gtsam_assign_source_folders("${subdir_srcs}") # Create MSVC structure
set(${subdir}_srcs ${subdir_srcs})

2
gtsam/base/CMakeLists.txt
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@ -1,5 +1,5 @@
# Install headers
file(GLOB base_headers "*.h")
file(GLOB base_headers "*.h" "treeTraversal/*.h")
install(FILES ${base_headers} DESTINATION include/gtsam/base)
# Files to exclude from compilation of tests and timing scripts

157
gtsam/base/treeTraversal-inst.h
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@ -16,6 +16,9 @@
*/
#pragma once
#include <gtsam/base/treeTraversal/parallelTraversalTasks.h>
#include <gtsam/base/treeTraversal/statistics.h>
#include <gtsam/base/FastList.h>
#include <gtsam/base/FastVector.h>
#include <gtsam/inference/Key.h>
@ -28,13 +31,6 @@
#include <boost/foreach.hpp>
#include <boost/bind.hpp>
#ifdef GTSAM_USE_TBB
# include <tbb/tbb.h>
# undef max // TBB seems to include windows.h and we don't want these macros
# undef min
# undef ERROR
#endif
namespace gtsam {
/** Internal functions used for traversing trees */
@ -59,151 +55,6 @@ namespace gtsam {
void operator()(const boost::shared_ptr<NODE>& node, const DATA& data) {}
};
#ifdef GTSAM_USE_TBB
/* ************************************************************************* */
template<typename NODE, typename DATA, typename VISITOR_POST>
class PostOrderTask : public tbb::task
{
public:
const boost::shared_ptr<NODE>& treeNode;
boost::shared_ptr<DATA> myData;
VISITOR_POST& visitorPost;
PostOrderTask(const boost::shared_ptr<NODE>& treeNode, const boost::shared_ptr<DATA>& myData, VISITOR_POST& visitorPost) :
treeNode(treeNode), myData(myData), visitorPost(visitorPost) {}
tbb::task* execute()
{
// Run the post-order visitor
(void) visitorPost(treeNode, *myData);
return NULL;
}
};
/* ************************************************************************* */
template<typename NODE, typename DATA, typename VISITOR_PRE, typename VISITOR_POST>
class PreOrderTask : public tbb::task
{
public:
const boost::shared_ptr<NODE>& treeNode;
boost::shared_ptr<DATA> myData;
VISITOR_PRE& visitorPre;
VISITOR_POST& visitorPost;
int problemSizeThreshold;
bool makeNewTasks;
PreOrderTask(const boost::shared_ptr<NODE>& treeNode, const boost::shared_ptr<DATA>& myData,
VISITOR_PRE& visitorPre, VISITOR_POST& visitorPost, int problemSizeThreshold,
bool makeNewTasks = true) :
treeNode(treeNode), myData(myData), visitorPre(visitorPre), visitorPost(visitorPost),
problemSizeThreshold(problemSizeThreshold), makeNewTasks(makeNewTasks) {}
tbb::task* execute()
{
if (makeNewTasks)
{
if(!treeNode->children.empty())
{
// Allocate post-order task as a continuation
PostOrderTask<NODE, DATA, VISITOR_POST>& postOrderTask =
*new(allocate_continuation()) PostOrderTask<NODE, DATA, VISITOR_POST>(treeNode, myData, visitorPost);
bool overThreshold = (treeNode->problemSize() >= problemSizeThreshold);
tbb::task_list childTasks;
BOOST_FOREACH(const boost::shared_ptr<NODE>& child, treeNode->children)
{
// Process child in a subtask. Important: Run visitorPre before calling
// allocate_child so that if visitorPre throws an exception, we will not have
// allocated an extra child, this causes a TBB error.
boost::shared_ptr<DATA> childData = boost::allocate_shared<DATA>(tbb::scalable_allocator<DATA>(), visitorPre(child, *myData));
childTasks.push_back(*new(postOrderTask.allocate_child())
PreOrderTask(child, childData, visitorPre, visitorPost,
problemSizeThreshold, overThreshold));
}
// If we have child tasks, start subtasks and wait for them to complete
postOrderTask.set_ref_count((int) treeNode->children.size());
spawn(childTasks);
}
else
{
// Run the post-order visitor in this task if we have no children
(void) visitorPost(treeNode, *myData);
}
}
else
{
// Process this node and its children in this task
processNodeRecursively(treeNode, *myData);
}
// Return NULL
return NULL;
}
void processNodeRecursively(const boost::shared_ptr<NODE>& node, DATA& myData)
{
BOOST_FOREACH(const boost::shared_ptr<NODE>& child, node->children)
{
DATA childData = visitorPre(child, myData);
processNodeRecursively(child, childData);
}
// Run the post-order visitor
(void) visitorPost(node, myData);
}
};
/* ************************************************************************* */
template<typename ROOTS, typename NODE, typename DATA, typename VISITOR_PRE, typename VISITOR_POST>
class RootTask : public tbb::task
{
public:
const ROOTS& roots;
DATA& myData;
VISITOR_PRE& visitorPre;
VISITOR_POST& visitorPost;
int problemSizeThreshold;
RootTask(const ROOTS& roots, DATA& myData, VISITOR_PRE& visitorPre, VISITOR_POST& visitorPost,
int problemSizeThreshold) :
roots(roots), myData(myData), visitorPre(visitorPre), visitorPost(visitorPost),
problemSizeThreshold(problemSizeThreshold) {}
tbb::task* execute()
{
typedef PreOrderTask<NODE, DATA, VISITOR_PRE, VISITOR_POST> PreOrderTask;
// Create data and tasks for our children
tbb::task_list tasks;
BOOST_FOREACH(const boost::shared_ptr<NODE>& root, roots)
{
boost::shared_ptr<DATA> rootData = boost::allocate_shared<DATA>(tbb::scalable_allocator<DATA>(), visitorPre(root, myData));
tasks.push_back(*new(allocate_child())
PreOrderTask(root, rootData, visitorPre, visitorPost, problemSizeThreshold));
}
// Set TBB ref count
set_ref_count(1 + (int)roots.size());
// Spawn tasks
spawn_and_wait_for_all(tasks);
// Return NULL
return NULL;
}
};
template<typename NODE, typename ROOTS, typename DATA, typename VISITOR_PRE, typename VISITOR_POST>
RootTask<ROOTS, NODE, DATA, VISITOR_PRE, VISITOR_POST>&
CreateRootTask(const ROOTS& roots, DATA& rootData, VISITOR_PRE& visitorPre, VISITOR_POST& visitorPost,
int problemSizeThreshold)
{
typedef RootTask<ROOTS, NODE, DATA, VISITOR_PRE, VISITOR_POST> RootTask;
return *new(tbb::task::allocate_root()) RootTask(roots, rootData, visitorPre, visitorPost, problemSizeThreshold);
}
#endif
}
/** Traverse a forest depth-first with pre-order and post-order visits.
@ -306,7 +157,7 @@ namespace gtsam {
typedef typename FOREST::Node Node;
typedef boost::shared_ptr<Node> sharedNode;
tbb::task::spawn_root_and_wait(CreateRootTask<Node>(
tbb::task::spawn_root_and_wait(internal::CreateRootTask<Node>(
forest.roots(), rootData, visitorPre, visitorPost, problemSizeThreshold));
#else
DepthFirstForest(forest, rootData, visitorPre, visitorPost);

205
gtsam/base/treeTraversal/parallelTraversalTasks.h Normal file
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@ -0,0 +1,205 @@
/* ----------------------------------------------------------------------------
* GTSAM Copyright 2010, Georgia Tech Research Corporation,
* Atlanta, Georgia 30332-0415
* All Rights Reserved
* Authors: Frank Dellaert, et al. (see THANKS for the full author list)
* See LICENSE for the license information
* -------------------------------------------------------------------------- */
/**
* @file parallelTraversalTasks.h
* @author Richard Roberts
* @date April 9, 2013
*/
#pragma once
#include <gtsam/global_includes.h>
#include <boost/shared_ptr.hpp>
#include <boost/make_shared.hpp>
#include <boost/foreach.hpp>
#ifdef GTSAM_USE_TBB
# include <tbb/tbb.h>
# undef max // TBB seems to include windows.h and we don't want these macros
# undef min
# undef ERROR
namespace gtsam {
/** Internal functions used for traversing trees */
namespace treeTraversal {
namespace internal {
/* ************************************************************************* */
template<typename NODE, typename DATA, typename VISITOR_POST>
class PostOrderTask : public tbb::task
{
public:
const boost::shared_ptr<NODE>& treeNode;
boost::shared_ptr<DATA> myData;
VISITOR_POST& visitorPost;
PostOrderTask(const boost::shared_ptr<NODE>& treeNode, const boost::shared_ptr<DATA>& myData, VISITOR_POST& visitorPost) :
treeNode(treeNode), myData(myData), visitorPost(visitorPost) {}
tbb::task* execute()
{
// Run the post-order visitor
(void) visitorPost(treeNode, *myData);
return NULL;
}
};
/* ************************************************************************* */
template<typename NODE, typename DATA, typename VISITOR_PRE, typename VISITOR_POST>
class PreOrderTask : public tbb::task
{
public:
const boost::shared_ptr<NODE>& treeNode;
boost::shared_ptr<DATA> myData;
VISITOR_PRE& visitorPre;
VISITOR_POST& visitorPost;
int problemSizeThreshold;
bool makeNewTasks;
bool isPostOrderPhase;
PreOrderTask(const boost::shared_ptr<NODE>& treeNode, const boost::shared_ptr<DATA>& myData,
VISITOR_PRE& visitorPre, VISITOR_POST& visitorPost, int problemSizeThreshold,
bool makeNewTasks = true) :
treeNode(treeNode), myData(myData), visitorPre(visitorPre), visitorPost(visitorPost),
problemSizeThreshold(problemSizeThreshold), makeNewTasks(makeNewTasks), isPostOrderPhase(false) {}
tbb::task* execute()
{
if(isPostOrderPhase)
{
// Run the post-order visitor since this task was recycled to run the post-order visitor
(void) visitorPost(treeNode, *myData);
return NULL;
}
else
{
if(makeNewTasks)
{
if(!treeNode->children.empty())
{
// Allocate post-order task as a continuation
isPostOrderPhase = true;
recycle_as_continuation();
//PostOrderTask<NODE, DATA, VISITOR_POST>& postOrderTask =
// *new(allocate_continuation()) PostOrderTask<NODE, DATA, VISITOR_POST>(treeNode, myData, visitorPost);
bool overThreshold = (treeNode->problemSize() >= problemSizeThreshold);
tbb::task* firstChild = 0;
tbb::task_list childTasks;
BOOST_FOREACH(const boost::shared_ptr<NODE>& child, treeNode->children)
{
// Process child in a subtask. Important: Run visitorPre before calling
// allocate_child so that if visitorPre throws an exception, we will not have
// allocated an extra child, this causes a TBB error.
boost::shared_ptr<DATA> childData = boost::allocate_shared<DATA>(tbb::scalable_allocator<DATA>(), visitorPre(child, *myData));
//childTasks.push_back(*new(postOrderTask.allocate_child())
// PreOrderTask(child, childData, visitorPre, visitorPost,
// problemSizeThreshold, overThreshold));
tbb::task* childTask = new(allocate_child())
PreOrderTask(child, childData, visitorPre, visitorPost,
problemSizeThreshold, overThreshold);
if(firstChild)
childTasks.push_back(*childTask);
else
firstChild = childTask;
}
// If we have child tasks, start subtasks and wait for them to complete
//postOrderTask.set_ref_count((int) treeNode->children.size());
set_ref_count(treeNode->children.size());
spawn(childTasks);
return firstChild;
}
else
{
// Run the post-order visitor in this task if we have no children
(void) visitorPost(treeNode, *myData);
return NULL;
}
}
else
{
// Process this node and its children in this task
processNodeRecursively(treeNode, *myData);
return NULL;
}
}
}
void processNodeRecursively(const boost::shared_ptr<NODE>& node, DATA& myData)
{
BOOST_FOREACH(const boost::shared_ptr<NODE>& child, node->children)
{
DATA childData = visitorPre(child, myData);
processNodeRecursively(child, childData);
}
// Run the post-order visitor
(void) visitorPost(node, myData);
}
};
/* ************************************************************************* */
template<typename ROOTS, typename NODE, typename DATA, typename VISITOR_PRE, typename VISITOR_POST>
class RootTask : public tbb::task
{
public:
const ROOTS& roots;
DATA& myData;
VISITOR_PRE& visitorPre;
VISITOR_POST& visitorPost;
int problemSizeThreshold;
RootTask(const ROOTS& roots, DATA& myData, VISITOR_PRE& visitorPre, VISITOR_POST& visitorPost,
int problemSizeThreshold) :
roots(roots), myData(myData), visitorPre(visitorPre), visitorPost(visitorPost),
problemSizeThreshold(problemSizeThreshold) {}
tbb::task* execute()
{
typedef PreOrderTask<NODE, DATA, VISITOR_PRE, VISITOR_POST> PreOrderTask;
// Create data and tasks for our children
tbb::task_list tasks;
BOOST_FOREACH(const boost::shared_ptr<NODE>& root, roots)
{
boost::shared_ptr<DATA> rootData = boost::allocate_shared<DATA>(tbb::scalable_allocator<DATA>(), visitorPre(root, myData));
tasks.push_back(*new(allocate_child())
PreOrderTask(root, rootData, visitorPre, visitorPost, problemSizeThreshold));
}
// Set TBB ref count
set_ref_count(1 + (int) roots.size());
// Spawn tasks
spawn_and_wait_for_all(tasks);
// Return NULL
return NULL;
}
};
template<typename NODE, typename ROOTS, typename DATA, typename VISITOR_PRE, typename VISITOR_POST>
RootTask<ROOTS, NODE, DATA, VISITOR_PRE, VISITOR_POST>&
CreateRootTask(const ROOTS& roots, DATA& rootData, VISITOR_PRE& visitorPre, VISITOR_POST& visitorPost, int problemSizeThreshold)
{
typedef RootTask<ROOTS, NODE, DATA, VISITOR_PRE, VISITOR_POST> RootTask;
return *new(tbb::task::allocate_root()) RootTask(roots, rootData, visitorPre, visitorPost, problemSizeThreshold);
}
}
}
}
#endif

95
gtsam/base/treeTraversal/statistics.h Normal file
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@ -0,0 +1,95 @@
/* ----------------------------------------------------------------------------
* GTSAM Copyright 2010, Georgia Tech Research Corporation,
* Atlanta, Georgia 30332-0415
* All Rights Reserved
* Authors: Frank Dellaert, et al. (see THANKS for the full author list)
* See LICENSE for the license information
* -------------------------------------------------------------------------- */
/**
* @file statistics.h
* @brief Tools for gathering statistics about a forest to aid tuning parallel traversal
* @author Richard Roberts
* @date April 9, 2013
*/
#pragma once
#include <gtsam/global_includes.h>
#include <gtsam/base/FastMap.h>
#include <ostream>
namespace gtsam {
namespace treeTraversal {
/* ************************************************************************* */
/// Struct to store gathered statistics about a forest
struct ForestStatistics
{
typedef FastMap<int, ValueWithDefault<int, 0> > Histogram;
Histogram problemSizeHistogram;
Histogram numberOfChildrenHistogram;
Histogram problemSizeOfSecondLargestChildHistogram;
static void Write(std::ostream& outStream, const Histogram& histogram)
{
if (!histogram.empty())
{
Histogram::const_iterator endIt = histogram.end();
-- endIt;
const int largest = endIt->first;
for (int bin = 0; bin <= largest; ++bin)
{
Histogram::const_iterator item = histogram.find(bin);
const int count = (item == histogram.end() ? 0 : *item->second);
outStream << bin << " " << count << "\n";
}
}
}
};
/* ************************************************************************* */
namespace internal {
template<class NODE>
ForestStatistics* statisticsVisitor(const boost::shared_ptr<NODE>& node, ForestStatistics* stats)
{
(*stats->problemSizeHistogram[node->problemSize()]) ++;
(*stats->numberOfChildrenHistogram[(int)node->children.size()]) ++;
if (node->children.size() > 1)
{
int largestProblemSize = 0;
int secondLargestProblemSize = 0;
BOOST_FOREACH(const boost::shared_ptr<NODE>& child, node->children)
{
if (child->problemSize() > largestProblemSize)
{
secondLargestProblemSize = largestProblemSize;
largestProblemSize = child->problemSize();
}
else if (child->problemSize() > secondLargestProblemSize)
{
secondLargestProblemSize = child->problemSize();
}
}
(*stats->problemSizeOfSecondLargestChildHistogram[secondLargestProblemSize]) ++;
}
return stats;
}
}
/* ************************************************************************* */
template<class FOREST>
ForestStatistics GatherStatistics(const FOREST& forest)
{
ForestStatistics stats;
ForestStatistics* statsPtr = &stats;
DepthFirstForest(forest, statsPtr, internal::statisticsVisitor<typename FOREST::Node>);
return stats;
}
}
}