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Commit 650ce0a8 authored by DE MOOR Florestan's avatar DE MOOR Florestan
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ITT calls to analyze some sections with VTune

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gatb-core/src/CMakeLists.txt
+ 11
− 0
View file @ 650ce0a8
......@@ -84,12 +84,23 @@ add_definitions (${gatb-core-flags})
include_directories (${gatb-core-includes})
# VTune
include_directories(/opt/intel/oneapi/vtune/latest/sdk/include)
link_directories (/opt/intel/oneapi/vtune/latest/sdk/lib64)
link_directories (/opt/intel/oneapi/vtune/latest/sdk/lib32)
find_package (Threads)
add_library (gatbcore-static STATIC ${ComponentFiles} )
#add_library (gatbcore-dynamic SHARED ${ComponentFiles} )
set_target_properties (gatbcore-static PROPERTIES OUTPUT_NAME gatbcore clean_direct_output 1)
#set_target_properties (gatbcore-dynamic PROPERTIES OUTPUT_NAME gatbcore clean_direct_output 1)
# VTune
target_link_libraries(gatbcore-static /opt/intel/oneapi/vtune/latest/sdk/lib64/libittnotify.a)
target_link_libraries(gatbcore-static /opt/intel/oneapi/vtune/latest/sdk/lib32/libittnotify.a)
target_link_libraries(gatbcore-static ${CMAKE_THREAD_LIBS_INIT})
################################################################################
# INSTALLATION
################################################################################
......
gatb-core/src/gatb/debruijn/impl/Graph.cpp
+ 23
− 0
View file @ 650ce0a8
......@@ -51,6 +51,8 @@
#include <gatb/debruijn/impl/Simplifications.hpp>
#include <ittnotify.h>
using namespace std;
using namespace gatb::core::system::impl;
......@@ -88,6 +90,11 @@ using namespace gatb::core::tools::misc::impl;
namespace gatb { namespace core { namespace debruijn { namespace impl {
/********************************************************************************/
const string ITT_SECTION_DSK = "dsk";
const string ITT_SECTION_BLOOM = "bloom";
const string ITT_SECTION_CFP = "cfp";
const string ITT_SECTION_BRANCHING = "branching";
template<size_t span, typename Node_in>
unsigned long getNodeIndex (const GraphData<span>& data, Node_in& node);
......@@ -296,6 +303,8 @@ void build_visitor_solid<Node,Edge,GraphDataVariant>::operator() (GraphData<span
size_t compressLevel = props->get(STR_COMPRESS_LEVEL) ? props->getInt(STR_COMPRESS_LEVEL) : 0;
bool configOnly = props->get(STR_CONFIG_ONLY) != 0;
string itt_section = props->get(STR_ITT_SECTION) ? props->getStr(STR_ITT_SECTION) : "";
string output = props->get(STR_URI_OUTPUT) ?
props->getStr(STR_URI_OUTPUT) :
(props->getStr(STR_URI_OUTPUT_DIR) + "/" + system::impl::System::file().getBaseName (bank->getId()));
......@@ -395,6 +404,8 @@ void build_visitor_solid<Node,Edge,GraphDataVariant>::operator() (GraphData<span
/************************************************************/
DEBUG ((cout << "build_visitor : SortingCountAlgorithm BEGIN\n"));
if (itt_section == ITT_SECTION_DSK) { __itt_resume(); }
/** We create a DSK instance and execute it. */
SortingCountAlgorithm<span> sortingCount (
bank,
......@@ -424,6 +435,8 @@ void build_visitor_solid<Node,Edge,GraphDataVariant>::operator() (GraphData<span
// also set _nbSolidKmers here, as for example, _kmerSize was set at startup since we knew it already
graph._nbSolidKmers = solidCounts->getNbItems();
if (itt_section == ITT_SECTION_DSK) { __itt_pause(); }
}
......@@ -448,6 +461,8 @@ void build_visitor_postsolid<Node,Edge,GraphDataVariant>::operator() (GraphData<
// todo: see remark in build_visitor_solid, we should be able to get that info from elsewhere
size_t minimizerSize = props->get(STR_MINIMIZER_SIZE) ? props->getInt(STR_MINIMIZER_SIZE) : 8;
string itt_section = props->get(STR_ITT_SECTION) ? props->getStr(STR_ITT_SECTION) : "";
/** We create the kmer model. */
data.setModel (new typename Kmer<span>::ModelCanonical (kmerSize));
......@@ -507,6 +522,7 @@ void build_visitor_postsolid<Node,Edge,GraphDataVariant>::operator() (GraphData<
/************************************************************/
/* Bloom */
/************************************************************/
if (itt_section == ITT_SECTION_BLOOM) { __itt_resume(); }
if (graph.checkState(GraphTemplate<Node, Edge, GraphDataVariant>::STATE_SORTING_COUNT_DONE) && !(graph.checkState(GraphTemplate<Node, Edge, GraphDataVariant>::STATE_BLOOM_DONE)))
{
DEBUG ((cout << "build_visitor : BloomAlgorithm BEGIN\n"));
......@@ -527,10 +543,12 @@ void build_visitor_postsolid<Node,Edge,GraphDataVariant>::operator() (GraphData<
DEBUG ((cout << "build_visitor : BloomAlgorithm END\n"));
}
if (itt_section == ITT_SECTION_BLOOM) { __itt_pause(); }
/************************************************************/
/* Debloom */
/************************************************************/
if (itt_section == ITT_SECTION_CFP) { __itt_resume(); }
if (graph.checkState(GraphTemplate<Node, Edge, GraphDataVariant>::STATE_BLOOM_DONE) && !(graph.checkState(GraphTemplate<Node, Edge, GraphDataVariant>::STATE_DEBLOOM_DONE)))
{
DEBUG ((cout << "build_visitor : DebloomAlgorithm BEGIN\n"));
......@@ -562,10 +580,12 @@ void build_visitor_postsolid<Node,Edge,GraphDataVariant>::operator() (GraphData<
DEBUG ((cout << "build_visitor : DebloomAlgorithm END\n"));
}
if (itt_section == ITT_SECTION_CFP) { __itt_pause(); }
/************************************************************/
/* Branching */
/************************************************************/
if (itt_section == ITT_SECTION_BRANCHING) { __itt_resume(); }
if (graph.checkState(GraphTemplate<Node, Edge, GraphDataVariant>::STATE_DEBLOOM_DONE) && !(graph.checkState(GraphTemplate<Node, Edge, GraphDataVariant>::STATE_BRANCHING_DONE)))
{
DEBUG ((cout << "build_visitor : BranchingAlgorithm BEGIN\n"));
......@@ -590,6 +610,7 @@ void build_visitor_postsolid<Node,Edge,GraphDataVariant>::operator() (GraphData<
DEBUG ((cout << "build_visitor : BranchingAlgorithm END\n"));
}
if (itt_section == ITT_SECTION_BRANCHING) { __itt_pause(); }
/************************************************************/
......@@ -661,6 +682,8 @@ IOptionsParser* GraphTemplate<Node, Edge, GraphDataVariant>::getOptionsParser (b
parserGeneral->push_front (new OptionNoParam (STR_ALL_ABUNDANCE_COUNTS, "output all k-mer abundance counts instead of mean" ));
parserGeneral->push_front (new OptionOneParam (STR_NB_CORES, "number of cores", false, "0" ));
parserGeneral->push_front (new OptionNoParam (STR_CONFIG_ONLY, "dump config only"));
parserGeneral->push_front (new OptionOneParam (STR_ITT_SECTION, "section to resume and pause VTune collection", false, "dsk"));
parser->push_back (parserGeneral);
......
gatb-core/src/gatb/tools/misc/api/StringsRepository.hpp
+ 3
− 0
View file @ 650ce0a8
......@@ -131,6 +131,8 @@ public:
const char* attr_kmer_abundance () { return "abundance"; }
const char* attr_bloom_type () { return "bloom_kind"; }
const char* attr_debloom_type () { return "debloom_kind"; }
const char* itt_section () { return "-itt-section"; }
};
/********************************************************************************/
......@@ -183,6 +185,7 @@ public:
#define STR_CONFIG_ONLY gatb::core::tools::misc::StringRepository::singleton().config_only()
#define STR_STORAGE_TYPE gatb::core::tools::misc::StringRepository::singleton().storage_type ()
#define STR_KFF gatb::core::tools::misc::StringRepository::singleton().kff()
#define STR_ITT_SECTION gatb::core::tools::misc::StringRepository::singleton().itt_section()
/********************************************************************************/
......
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