void TestPlugin::resolveSymbols(ComputeCore*core){
// here, we resolve symbols owned by other m_plugins
// but needed by the current m_plugin
// obviously, this is not needed here because
// we only have one m_plugin
MY_TEST_SLAVE_MODE_STEP_A=core->getSlaveModeFromSymbol(m_plugin,"MY_TEST_SLAVE_MODE_STEP_A");
// this slave mode is registered somewhere in RayPlatform
RAY_SLAVE_MODE_DO_NOTHING=core->getSlaveModeFromSymbol(m_plugin,"RAY_SLAVE_MODE_DO_NOTHING");
bool*test=(bool*) core->getObjectFromSymbol(m_plugin,"BooleanState");
__BindPlugin(TestPlugin);
__BindAdapter(TestPlugin,MY_TEST_MASTER_MODE_STEP_A);
__BindAdapter(TestPlugin,MY_TEST_MASTER_MODE_STEP_B);
__BindAdapter(TestPlugin,MY_TEST_MASTER_MODE_STEP_C);
__BindAdapter(TestPlugin,MY_TEST_SLAVE_MODE_STEP_A);
__BindAdapter(TestPlugin,MY_TEST_SLAVE_MODE_STEP_B);
__BindAdapter(TestPlugin,MY_TEST_SLAVE_MODE_STEP_C);
__BindAdapter(TestPlugin,MY_TEST_MPI_TAG_STOP_AND_DIE);
__BindAdapter(TestPlugin,MY_TEST_MPI_TAG_TIME_BOMB);
}
void GeneOntology::resolveSymbols(ComputeCore*core){
RAY_MASTER_MODE_ONTOLOGY_MAIN=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_ONTOLOGY_MAIN");
RAY_MASTER_MODE_KILL_RANKS=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_KILL_RANKS");
RAY_MASTER_MODE_NEIGHBOURHOOD=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_NEIGHBOURHOOD");
RAY_MPI_TAG_ONTOLOGY_MAIN=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_ONTOLOGY_MAIN");
RAY_SLAVE_MODE_ONTOLOGY_MAIN=core->getSlaveModeFromSymbol(m_plugin,"RAY_SLAVE_MODE_ONTOLOGY_MAIN");
core->setMasterModeToMessageTagSwitch(m_plugin,RAY_MASTER_MODE_ONTOLOGY_MAIN,RAY_MPI_TAG_ONTOLOGY_MAIN);
core->setMessageTagToSlaveModeSwitch(m_plugin,RAY_MPI_TAG_ONTOLOGY_MAIN,RAY_SLAVE_MODE_ONTOLOGY_MAIN);
core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_ONTOLOGY_MAIN,RAY_MASTER_MODE_NEIGHBOURHOOD);
//core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_ONTOLOGY_MAIN,RAY_MASTER_MODE_KILL_RANKS);
m_parameters=(Parameters*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/Parameters.ray");
m_subgraph=(GridTable*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/deBruijnGraph_part.ray");
m_colorSet=(ColorSet*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/VirtualColorManagementUnit.ray");
m_timePrinter=(TimePrinter*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/Timer.ray");
m_searcher=(Searcher*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/plugin_Searcher.ray");
m_slaveStarted=false;
m_started=false;
__BindPlugin(GeneOntology);
__BindAdapter(GeneOntology,RAY_MASTER_MODE_ONTOLOGY_MAIN);
__BindAdapter(GeneOntology,RAY_SLAVE_MODE_ONTOLOGY_MAIN);
__BindAdapter(GeneOntology,RAY_MPI_TAG_SYNCHRONIZE_TERMS);
__BindAdapter(GeneOntology,RAY_MPI_TAG_SYNCHRONIZE_TERMS_REPLY);
__BindAdapter(GeneOntology,RAY_MPI_TAG_SYNCHRONIZATION_DONE);
}
void PhylogenyViewer::resolveSymbols(ComputeCore*core){
RAY_MASTER_MODE_PHYLOGENY_MAIN=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_PHYLOGENY_MAIN");
RAY_MASTER_MODE_KILL_RANKS=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_KILL_RANKS");
RAY_MASTER_MODE_NEIGHBOURHOOD=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_NEIGHBOURHOOD");
RAY_MASTER_MODE_ONTOLOGY_MAIN=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_ONTOLOGY_MAIN");
RAY_MPI_TAG_PHYLOGENY_MAIN=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_PHYLOGENY_MAIN");
RAY_MPI_TAG_TOUCH_TAXON=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_TOUCH_TAXON");
RAY_MPI_TAG_TOUCH_TAXON_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_TOUCH_TAXON_REPLY");
RAY_MPI_TAG_LOADED_TAXONS=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_LOADED_TAXONS");
RAY_MPI_TAG_SYNCED_TAXONS=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_SYNCED_TAXONS");
RAY_MPI_TAG_TAXON_OBSERVATIONS=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_TAXON_OBSERVATIONS");
RAY_MPI_TAG_TAXON_OBSERVATIONS_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_TAXON_OBSERVATIONS_REPLY");
RAY_SLAVE_MODE_PHYLOGENY_MAIN=core->getSlaveModeFromSymbol(m_plugin,"RAY_SLAVE_MODE_PHYLOGENY_MAIN");
core->setMasterModeToMessageTagSwitch(m_plugin,RAY_MASTER_MODE_PHYLOGENY_MAIN,RAY_MPI_TAG_PHYLOGENY_MAIN);
core->setMessageTagToSlaveModeSwitch(m_plugin,RAY_MPI_TAG_PHYLOGENY_MAIN,RAY_SLAVE_MODE_PHYLOGENY_MAIN);
core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_PHYLOGENY_MAIN,RAY_MASTER_MODE_ONTOLOGY_MAIN);
m_parameters=(Parameters*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/Parameters.ray");
m_subgraph=(GridTable*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/deBruijnGraph_part.ray");
m_colorSet=(ColorSet*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/VirtualColorManagementUnit.ray");
m_timePrinter=(TimePrinter*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/Timer.ray");
m_searcher=(Searcher*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/plugin_Searcher.ray");
m_started=false;
__BindPlugin(PhylogenyViewer);
}
/**
* resolve symbols
*/
void GenomeNeighbourhood::resolveSymbols(ComputeCore*core){
RAY_MASTER_MODE_KILL_RANKS=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_KILL_RANKS");
RAY_MASTER_MODE_NEIGHBOURHOOD=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_NEIGHBOURHOOD");
RAY_SLAVE_MODE_NEIGHBOURHOOD=core->getSlaveModeFromSymbol(m_plugin,"RAY_SLAVE_MODE_NEIGHBOURHOOD");
RAY_MPI_TAG_NEIGHBOURHOOD=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_NEIGHBOURHOOD");
RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT");
RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE");
RAY_MPI_TAG_ASK_VERTEX_PATH=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_ASK_VERTEX_PATH");
/* configure workflow */
core->setMasterModeToMessageTagSwitch(m_plugin,RAY_MASTER_MODE_NEIGHBOURHOOD,RAY_MPI_TAG_NEIGHBOURHOOD);
core->setMessageTagToSlaveModeSwitch(m_plugin,RAY_MPI_TAG_NEIGHBOURHOOD,RAY_SLAVE_MODE_NEIGHBOURHOOD);
/* this is done here because we need symbols */
core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_NEIGHBOURHOOD,RAY_MASTER_MODE_KILL_RANKS);
// fetch parallel shared objects
m_timePrinter=(TimePrinter*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/Timer.ray");
m_contigs=(vector<GraphPath>*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/ContigPaths.ray");
m_contigNames=(vector<PathHandle>*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/ContigNames.ray");
m_parameters=(Parameters*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/Parameters.ray");
m_contigLengths=(map<PathHandle,int>*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/ContigLengths.ray");
m_virtualCommunicator=core->getVirtualCommunicator();
m_core=core;
m_started=false;
m_rank=core->getRank();
m_outboxAllocator=core->getOutboxAllocator();
m_workerId=0;
m_slaveStarted=false;
/* this plugin is disabled because it is not ready yet */
m_pluginIsEnabled=false;
if(m_parameters->hasOption("-find-neighbourhoods"))
m_pluginIsEnabled=true;
if(m_parameters->hasOption("-enable-neighbourhoods"))
m_pluginIsEnabled=true;
__BindPlugin(GenomeNeighbourhood);
__BindAdapter(GenomeNeighbourhood,RAY_MASTER_MODE_NEIGHBOURHOOD);
__BindAdapter(GenomeNeighbourhood,RAY_SLAVE_MODE_NEIGHBOURHOOD);
__BindAdapter(GenomeNeighbourhood,RAY_MPI_TAG_NEIGHBOURHOOD_DATA);
}
void SeedingData::resolveSymbols(ComputeCore*core){
RAY_SLAVE_MODE_START_SEEDING=core->getSlaveModeFromSymbol(m_plugin,"RAY_SLAVE_MODE_START_SEEDING");
RAY_SLAVE_MODE_DO_NOTHING=core->getSlaveModeFromSymbol(m_plugin,"RAY_SLAVE_MODE_DO_NOTHING");
RAY_SLAVE_MODE_SEND_SEED_LENGTHS=core->getSlaveModeFromSymbol(m_plugin,"RAY_SLAVE_MODE_SEND_SEED_LENGTHS");
RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT");
RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE");
RAY_MPI_TAG_IS_DONE_SENDING_SEED_LENGTHS=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_IS_DONE_SENDING_SEED_LENGTHS");
RAY_MPI_TAG_SEEDING_IS_OVER=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_SEEDING_IS_OVER");
RAY_MPI_TAG_SEND_SEED_LENGTHS=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_SEND_SEED_LENGTHS");
RAY_MPI_TAG_SEND_SEED_LENGTHS_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_SEND_SEED_LENGTHS_REPLY");
__BindPlugin(SeedingData);
}
void SequencesIndexer::resolveSymbols(ComputeCore*core){
RAY_SLAVE_MODE_INDEX_SEQUENCES=core->getSlaveModeFromSymbol(m_plugin,"RAY_SLAVE_MODE_INDEX_SEQUENCES");
RAY_SLAVE_MODE_DO_NOTHING=core->getSlaveModeFromSymbol(m_plugin,"RAY_SLAVE_MODE_DO_NOTHING");
RAY_MPI_TAG_MASTER_IS_DONE_ATTACHING_READS_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_MASTER_IS_DONE_ATTACHING_READS_REPLY");
RAY_MPI_TAG_ATTACH_SEQUENCE=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_ATTACH_SEQUENCE");
RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE");
RAY_MPI_TAG_GET_READ_MARKERS_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_READ_MARKERS_REPLY");
RAY_MPI_TAG_GET_READ_MATE_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_READ_MATE_REPLY");
RAY_MPI_TAG_REQUEST_VERTEX_READS_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_REQUEST_VERTEX_READS_REPLY");
RAY_MPI_TAG_VERTEX_READS_FROM_LIST_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_VERTEX_READS_FROM_LIST_REPLY");
RAY_MPI_TAG_VERTEX_READS_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_VERTEX_READS_REPLY");
__BindPlugin(SequencesIndexer);
__BindAdapter(SequencesIndexer,RAY_SLAVE_MODE_INDEX_SEQUENCES);
}
void VerticesExtractor::resolveSymbols(ComputeCore*core){
RAY_SLAVE_MODE_ADD_EDGES=core->getSlaveModeFromSymbol(m_plugin,"RAY_SLAVE_MODE_ADD_EDGES");
RAY_SLAVE_MODE_WRITE_KMERS=core->getSlaveModeFromSymbol(m_plugin,"RAY_SLAVE_MODE_WRITE_KMERS");
RAY_MPI_TAG_IN_EDGES_DATA=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_IN_EDGES_DATA");
RAY_MPI_TAG_OUT_EDGES_DATA=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_OUT_EDGES_DATA");
RAY_MPI_TAG_VERTICES_DATA=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_VERTICES_DATA");
RAY_MPI_TAG_VERTICES_DISTRIBUTED=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_VERTICES_DISTRIBUTED");
RAY_MPI_TAG_WRITE_KMERS=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_WRITE_KMERS");
RAY_MPI_TAG_WRITE_KMERS_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_WRITE_KMERS_REPLY");
RAY_MPI_TAG_BUILD_GRAPH=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_BUILD_GRAPH");
RAY_MPI_TAG_VERTEX_INFO_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_VERTEX_INFO_REPLY");
core->setMessageTagToSlaveModeSwitch(m_plugin,RAY_MPI_TAG_BUILD_GRAPH, RAY_SLAVE_MODE_ADD_EDGES );
core->setMessageTagToSlaveModeSwitch(m_plugin,RAY_MPI_TAG_WRITE_KMERS, RAY_SLAVE_MODE_WRITE_KMERS);
__BindPlugin(VerticesExtractor);
}
void SeedingData::registerPlugin(ComputeCore*core){
m_core=core;
PluginHandle plugin=core->allocatePluginHandle();
m_plugin=plugin;
core->setPluginName(plugin,"SeedingData");
core->setPluginDescription(plugin,"Computes unique paths in the graph");
core->setPluginAuthors(plugin,"Sébastien Boisvert");
core->setPluginLicense(plugin,"GNU General Public License version 3");
__ConfigureSlaveModeHandler(SeedingData, RAY_SLAVE_MODE_START_SEEDING);
__ConfigureSlaveModeHandler(SeedingData, RAY_SLAVE_MODE_SEND_SEED_LENGTHS);
RAY_MPI_TAG_SEND_SEED_LENGTHS_REPLY=core->allocateMessageTagHandle(plugin);
core->setMessageTagSymbol(plugin,RAY_MPI_TAG_SEND_SEED_LENGTHS_REPLY,"RAY_MPI_TAG_SEND_SEED_LENGTHS_REPLY");
__BindPlugin(SeedingData);
m_core->setObjectSymbol(m_plugin, &m_SEEDING_seeds,"/RayAssembler/ObjectStore/Seeds.ray");
}
void Partitioner::resolveSymbols(ComputeCore*core){
RAY_SLAVE_MODE_DO_NOTHING=core->getSlaveModeFromSymbol(m_plugin,"RAY_SLAVE_MODE_DO_NOTHING");
RAY_SLAVE_MODE_COUNT_FILE_ENTRIES=core->getSlaveModeFromSymbol(m_plugin,"RAY_SLAVE_MODE_COUNT_FILE_ENTRIES");
RAY_MASTER_MODE_COUNT_FILE_ENTRIES=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_COUNT_FILE_ENTRIES");
RAY_MASTER_MODE_LOAD_SEQUENCES=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_LOAD_SEQUENCES");
RAY_MPI_TAG_COUNT_FILE_ENTRIES=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_COUNT_FILE_ENTRIES");
RAY_MPI_TAG_COUNT_FILE_ENTRIES_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_COUNT_FILE_ENTRIES_REPLY");
RAY_MPI_TAG_FILE_ENTRY_COUNT=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_FILE_ENTRY_COUNT");
RAY_MPI_TAG_FILE_ENTRY_COUNT_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_FILE_ENTRY_COUNT_REPLY");
RAY_MPI_TAG_REQUEST_FILE_ENTRY_COUNTS=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_REQUEST_FILE_ENTRY_COUNTS");
RAY_MPI_TAG_REQUEST_FILE_ENTRY_COUNTS_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_REQUEST_FILE_ENTRY_COUNTS_REPLY");
RAY_MPI_TAG_COUNT_FILE_ENTRIES=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_COUNT_FILE_ENTRIES");
RAY_MPI_TAG_COUNT_FILE_ENTRIES_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_COUNT_FILE_ENTRIES_REPLY");
core->setMessageTagToSlaveModeSwitch(m_plugin,RAY_MPI_TAG_COUNT_FILE_ENTRIES, RAY_SLAVE_MODE_COUNT_FILE_ENTRIES );
core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_COUNT_FILE_ENTRIES,RAY_MASTER_MODE_LOAD_SEQUENCES);
__BindPlugin(Partitioner);
}