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protocols::jd2 Namespace Reference

Namespaces

 archive
 
 JobInputterInputSource
 
 parser
 

Classes

class  AtomTreeDiffJobInputter
 
class  AtomTreeDiffJobInputterCreator
 
class  AtomTreeDiffJobOutputter
 
class  AtomTreeDiffJobOutputterCreator
 
class  BatchJobInputter
 
class  BOINCJobDistributor
 
class  DockDesignParser
 Reading the xml file and generating the mover. More...
 
class  FileJobOutputter
 
class  FileSystemJobDistributor
 
class  InnerJob
 
class  InnerMultiThreadingJob
 
class  JD2ResourceManager
 
class  JD2ResourceManagerCreator
 
class  JD2ResourceManagerJobInputter
 
class  JD2ResourceManagerJobInputterCreator
 
class  Job
 
class  JobDistributor
 
class  JobDistributorFactory
 
class  JobInputter
 
class  JobInputterCreator
 Abstract base class for a JobInputter factory; the Creator class is responsible for creating a particular mover class. More...
 
class  JobInputterRegistrator
 This templated class will register an instance of an JobInputterCreator (class T) with the JobInputterFactory. It will ensure that no JobInputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
 
class  JobInputterFactory
 
class  JobOutputter
 
class  JobOutputterCreator
 Abstract base class for a JobOutputter factory; the Creator class is responsible for creating a particular mover class. More...
 
class  JobOutputterRegistrator
 This templated class will register an instance of an JobOutputterCreator (class T) with the JobOutputterFactory. It will ensure that no JobOutputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
 
class  JobOutputterFactory
 
class  LazySilentFileJobInputter
 
class  LazySilentFileJobInputterCreator
 
class  MpiFileBuffer
 
class  WriteOut_MpiFileBuffer
 
class  DebugOut_MpiFileBuffer
 
class  MPIFileBufJobDistributor
 
class  MPIMultiCommJobDistributor
 
class  MPIWorkPartitionJobDistributor
 
class  MPIWorkPoolJobDistributor
 
class  MultiThreadingJob
 
class  NoOutputJobOutputter
 
class  NoOutputJobOutputterCreator
 
class  Parser
 
class  PDBJobInputter
 
class  PDBJobInputterCreator
 
class  PDBJobOutputter
 
class  PDBJobOutputterCreator
 
class  PoseInputStreamJobInputter
 
class  PoseInputStreamJobInputterCreator
 
class  ScoreMap
 
class  ScoreOnlyJobOutputter
 
class  ScoreOnlyJobOutputterCreator
 
class  ShuffleFileSystemJobDistributor
 
class  SilentFileJobInputter
 
class  SilentFileJobInputterCreator
 
class  SilentFileJobOutputter
 
class  CompareTags
 
class  SilentFileJobOutputterCreator
 
class  SingleFileBuffer
 
class  WriteFileSFB
 

Typedefs

typedef
utility::pointer::owning_ptr
< GenericJobInputter > 
GenericJobInputterOP
 
typedef
utility::pointer::owning_ptr
< AtomTreeDiffJobInputter
AtomTreeDiffJobInputterOP
 
typedef
utility::pointer::owning_ptr
< AtomTreeDiffJobOutputter
AtomTreeDiffJobOutputterOP
 
typedef
utility::pointer::owning_ptr
< AtomTreeDiffJobOutputter
const > 
AtomTreeDiffJobOutputterCOP
 
typedef
utility::pointer::owning_ptr
< BatchJobInputter
BatchJobInputterOP
 
typedef utility::tag::TagPtr TagPtr
 
typedef utility::vector0< TagPtrTagPtrs
 
typedef
utility::pointer::owning_ptr
< FileJobOutputter
FileJobOutputterOP
 
typedef
utility::pointer::owning_ptr
< InnerJob
InnerJobOP
 
typedef
utility::pointer::owning_ptr
< InnerJob const > 
InnerJobCOP
 
typedef
utility::pointer::owning_ptr
< InnerMultiThreadingJob
InnerMultiThreadingJobOP
 
typedef
utility::pointer::owning_ptr
< InnerMultiThreadingJob const > 
InnerMultiThreadingJobCOP
 
typedef
utility::pointer::owning_ptr
< Job
JobOP
 
typedef
utility::pointer::owning_ptr
< Job const > 
JobCOP
 
typedef utility::vector1< JobOPJobs
 
typedef
utility::pointer::access_ptr
< JobInputter
JobInputterAP
 
typedef
utility::pointer::access_ptr
< JobInputter const > 
JobInputterCAP
 
typedef
utility::pointer::owning_ptr
< JobInputter
JobInputterOP
 
typedef
utility::pointer::owning_ptr
< JobInputter const > 
JobInputterCOP
 
typedef
utility::pointer::owning_ptr
< JobInputterCreator
JobInputterCreatorOP
 
typedef
utility::pointer::owning_ptr
< JobInputterCreator const > 
JobInputterCreatorCOP
 
typedef
utility::pointer::owning_ptr
< JobInputterFactory
JobInputterFactoryOP
 
typedef
utility::pointer::owning_ptr
< JobInputterFactory const > 
JobInputterFactoryCOP
 
typedef
utility::pointer::owning_ptr
< JobOutputter
JobOutputterOP
 
typedef
utility::pointer::owning_ptr
< JobOutputter const > 
JobOutputterCOP
 
typedef
utility::pointer::owning_ptr
< JobOutputterCreator
JobOutputterCreatorOP
 
typedef
utility::pointer::owning_ptr
< JobOutputterCreator const > 
JobOutputterCreatorCOP
 
typedef
utility::pointer::owning_ptr
< JobOutputterFactory
JobOutputterFactoryOP
 
typedef
utility::pointer::owning_ptr
< JobOutputterFactory const > 
JobOutputterFactoryCOP
 
typedef
utility::pointer::owning_ptr
< LazySilentFileJobInputter
LazySilentFileJobInputterOP
 
typedef
utility::pointer::owning_ptr
< MpiFileBuffer
MpiFileBufferOP
 
typedef
utility::pointer::owning_ptr
< MpiFileBuffer const > 
MpiFileBufferCOP
 
typedef
utility::pointer::owning_ptr
< MultiThreadingJob
MultiThreadingJobOP
 
typedef
utility::pointer::owning_ptr
< MultiThreadingJob const > 
MultiThreadingJobCOP
 
typedef
utility::pointer::owning_ptr
< Parser
ParserOP
 
typedef
utility::pointer::owning_ptr
< Parser const > 
ParserCOP
 
typedef
utility::pointer::owning_ptr
< PDBJobInputter
PDBJobInputterOP
 
typedef
utility::pointer::owning_ptr
< PDBJobOutputter
PDBJobOutputterOP
 
typedef
utility::pointer::owning_ptr
< PoseInputStreamJobInputter
PoseInputStreamJobInputterOP
 
typedef
utility::pointer::owning_ptr
< SilentFileJobInputter
SilentFileJobInputterOP
 
typedef
utility::pointer::owning_ptr
< SilentFileJobOutputter
SilentFileJobOutputterOP
 
typedef
utility::pointer::owning_ptr
< SingleFileBuffer
SingleFileBufferOP
 
typedef
utility::pointer::owning_ptr
< SingleFileBuffer const > 
SingleFileBufferCOP
 

Enumerations

enum  mpi_tags {
  NEW_JOB_ID_TAG = 10, BAD_INPUT_TAG = 20, JOB_SUCCESS_TAG = 30, REQUEST_MESSAGE_TAG = 40,
  RECEIVE_MESSAGE_TAG = 50
}
 Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input. More...
 

Functions

static basic::Tracer TR ("protocols.jd2.DockDesignParser")
 
bool operator== (InnerJob const &a, InnerJob const &b)
 
bool operator!= (InnerJob const &a, InnerJob const &b)
 
std::ostream & operator<< (std::ostream &out, const InnerJob &inner_job)
 
static Tracer TR ("protocols.resource_manager.planner.JD2ResourceManager")
 
static basic::Tracer tr ("protocols.jd2.JD2ResourceManagerJobInputter")
 
JobOP const JD2_BOGUS_JOB (new Job((new InnerJob("EMPTY_JOB_use_jd2", 0)), 0))
 
bool operator== (Job const &a, Job const &b)
 
bool operator!= (Job const &a, Job const &b)
 
std::ostream & operator<< (std::ostream &out, const Job &job)
 
static basic::Tracer tr ("protocols.jd2.JobDistributor")
 
static basic::Tracer TR ("protocols.jd2.JobInputterFactory")
 
static basic::Tracer TR ("protocols.jd2.JobOutputterFactory")
 
static basic::Tracer tr ("protocols.jd2.MpiFileBuffer")
 
Size const MPI_WIND_DOWN (1001)
 
Size const MPI_BLOCK_FILE (1002)
 
Size const MPI_RELEASE_FILE (1003)
 
Size const MPI_CLOSE_FILE (1004)
 
core::Size const MPI_JOB_DIST_TAG (1542)
 this tag is used for all communication with JobDistributor ( use this tag to be received in the main MSG-loop of jd2 cf. process_message() ) More...
 
static basic::Tracer tr ("protocols.jd2.MpiFileBuffer")
 
std::string const START_BLOCK ("MPI_FILE_BUFFER_BLOCK_START")
 
std::string const END_BLOCK ("MPI_FILE_BUFFER_BLOCK_END")
 
void register_options ()
 
static basic::Tracer TR ("protocols.jd2.JobDistributor")
 
void output_intermediate_pose (core::pose::Pose const &pose, std::string const &stage_tag, int copy_count, bool score_only)
 end parser interface, start Job Distributor interface///////////// More...
 
std::string current_output_name ()
 gets used output name of pose ask jd for current-job —> ask jobOutputter for name of this job More...
 
std::string current_batch ()
 
bool jd2_used ()
 is this application running with jd2 — used for some code that yields backward compatability with old JobDistributor More...
 
std::string current_output_filename ()
 call the 'filename' accessor of the current job-distributor with the current job More...
 
void write_score_tracer (core::pose::Pose const &pose_in, std::string tracer_point)
 
JobOP get_current_job ()
 
core::pose::PoseCOP get_current_jobs_starting_pose ()
 
void add_job_data_to_ss (core::io::silent::SilentStructOP ss, JobCOP job_op)
 
void set_native_in_mover (protocols::moves::Mover &mover)
 
core::Size current_replica ()
 returns 0 if no replicas (i.e., multiple processes per job ) otherwise it returns the sub-rank of the process within the job starting at 1 More...
 

Variables

JobOP const JD2_BOGUS_JOB
 
core::Size const NEW_JOB_ID = 1
 Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input. More...
 
core::Size const BAD_INPUT = 2
 
core::Size const JOB_SUCCESS = 3
 
core::Size const JOB_FAILED_NO_RETRY = 4
 

Typedef Documentation

typedef utility::tag::TagPtr protocols::jd2::TagPtr

Enumeration Type Documentation

Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.

Enumerator
NEW_JOB_ID_TAG 
BAD_INPUT_TAG 
JOB_SUCCESS_TAG 
REQUEST_MESSAGE_TAG 
RECEIVE_MESSAGE_TAG 

Function Documentation

void protocols::jd2::add_job_data_to_ss ( core::io::silent::SilentStructOP  ss,
JobCOP  job_op 
)
std::string protocols::jd2::current_batch ( )
std::string protocols::jd2::current_output_filename ( )
std::string protocols::jd2::current_output_name ( )
core::Size protocols::jd2::current_replica ( )
std::string const protocols::jd2::END_BLOCK ( "MPI_FILE_BUFFER_BLOCK_END"  )
JobOP protocols::jd2::get_current_job ( )
core::pose::PoseCOP protocols::jd2::get_current_jobs_starting_pose ( )
JobOP const protocols::jd2::JD2_BOGUS_JOB ( new   Job(new InnerJob("EMPTY_JOB_use_jd2", 0)), 0)
bool protocols::jd2::jd2_used ( )
Size const protocols::jd2::MPI_BLOCK_FILE ( 1002  )
Size const protocols::jd2::MPI_CLOSE_FILE ( 1004  )
core::Size const protocols::jd2::MPI_JOB_DIST_TAG ( 1542  )
Size const protocols::jd2::MPI_RELEASE_FILE ( 1003  )
Size const protocols::jd2::MPI_WIND_DOWN ( 1001  )
bool protocols::jd2::operator!= ( InnerJob const &  a,
InnerJob const &  b 
)
bool protocols::jd2::operator!= ( Job const &  a,
Job const &  b 
)
std::ostream& protocols::jd2::operator<< ( std::ostream &  out,
const InnerJob &  inner_job 
)
std::ostream& protocols::jd2::operator<< ( std::ostream &  out,
const Job &  job 
)
bool protocols::jd2::operator== ( InnerJob const &  a,
InnerJob const &  b 
)

Only compare the pointer value of the pose the inner job is referencing.

References protocols::jd2::InnerJob::bad_, protocols::jd2::InnerJob::input_tag_, protocols::jd2::InnerJob::nstruct_max_, and protocols::jd2::InnerJob::pose_.

bool protocols::jd2::operator== ( Job const &  a,
Job const &  b 
)
void protocols::jd2::output_intermediate_pose ( core::pose::Pose const &  pose,
std::string const &  stage_tag,
int  copy_count,
bool  score_only 
)

end parser interface, start Job Distributor interface/////////////

writes pose to intermediate-scorefile using current Job and JobOutputter .. copy count is used if multiple poses with same job-tag are written as for instance into a trajectory. -1 indicates no copy count >=0 copy_count will be attached as zerofilled postfix to job-tag

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), protocols::jd2::JobDistributor::job_outputter(), and TR().

Referenced by protocols::abinitio::AbrelaxMover::apply(), protocols::abinitio::FragmentSampler::apply(), protocols::abinitio::FragmentSampler::checkpointed_cycle_block(), protocols::abinitio::FragmentSampler::do_stage1_cycles(), and protocols::canonical_sampling::SilentTrajectoryRecorder::write_model().

void protocols::jd2::register_options ( )
void protocols::jd2::set_native_in_mover ( protocols::moves::Mover mover)
std::string const protocols::jd2::START_BLOCK ( "MPI_FILE_BUFFER_BLOCK_START"  )

this is a implementation of Buffer for silent-file-based output.

static basic::Tracer protocols::jd2::TR ( "protocols.jd2.JobInputterFactory"  )
static
static basic::Tracer protocols::jd2::TR ( "protocols.jd2.JobOutputterFactory"  )
static
static basic::Tracer protocols::jd2::tr ( "protocols.jd2.MpiFileBuffer"  )
static
static basic::Tracer protocols::jd2::tr ( "protocols.jd2.MpiFileBuffer"  )
static
static basic::Tracer protocols::jd2::tr ( "protocols.jd2.JobDistributor"  )
static
static basic::Tracer protocols::jd2::TR ( "protocols.jd2.JobDistributor"  )
static
static basic::Tracer protocols::jd2::tr ( "protocols.jd2.JD2ResourceManagerJobInputter"  )
static

Referenced by protocols::jd2::archive::MPIArchiveJobDistributor::_notify_archive(), protocols::jd2::archive::VarianceStatisticsArchive::add_evaluated_structure(), protocols::jd2::archive::NormalizedEvaluatedArchive::add_evaluated_structure(), protocols::jd2::archive::EvaluatedArchive::add_evaluated_structure(), protocols::jd2::archive::EvaluatedArchive::add_evaluation(), protocols::jd2::archive::EvaluatedArchive::add_structure(), protocols::jd2::AtomTreeDiffJobInputter::AtomTreeDiffJobInputter(), protocols::jd2::archive::MPIArchiveJobDistributor::batch_underflow(), protocols::jd2::BatchJobInputter::BatchJobInputter(), protocols::jd2::SingleFileBuffer::block(), protocols::jd2::WriteFileSFB::block(), protocols::jd2::MpiFileBuffer::block_file(), protocols::jd2::archive::ArchiveManager::cancel_batch(), protocols::jd2::JD2ResourceManagerJobInputter::cleanup_after_job_completion(), protocols::jd2::MpiFileBuffer::clear_channel_from_garbage_collector(), protocols::jd2::SingleFileBuffer::close(), protocols::jd2::MpiFileBuffer::close_channel(), protocols::jd2::MpiFileBuffer::close_file(), protocols::jd2::archive::NormalizedEvaluatedArchive::determine_score_variations(), protocols::jd2::SilentFileJobOutputter::dump_pose(), protocols::jd2::MPIFileBufJobDistributor::eat_signal(), protocols::jd2::archive::EvaluatedArchive::evaluate_pose(), protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(), protocols::jd2::LazySilentFileJobInputter::fill_jobs(), protocols::jd2::PoseInputStreamJobInputter::fill_jobs(), protocols::jd2::JD2ResourceManagerJobInputter::fill_jobs(), protocols::jd2::AtomTreeDiffJobInputter::fill_jobs(), protocols::jd2::SilentFileJobInputter::fill_jobs(), protocols::jd2::archive::ArchiveManager::finalize_batch(), protocols::jd2::MpiFileBuffer::flush_channel(), protocols::jd2::MpiFileBuffer::garbage_collection(), protocols::jd2::archive::DebugArchive::generate_batch(), protocols::jd2::MPIFileBufJobDistributor::go(), protocols::jd2::archive::MPIArchiveJobDistributor::go(), protocols::jd2::archive::ArchiveManager::go(), protocols::jd2::JobDistributor::go_main(), protocols::jd2::archive::ArchiveManager::idle(), protocols::jd2::archive::ArchiveBase::init_from_decoy_set(), protocols::jd2::JobDistributor::init_jd(), protocols::jd2::archive::ArchiveManager::jobs_completed(), protocols::jd2::LazySilentFileJobInputter::LazySilentFileJobInputter(), protocols::jd2::JobDistributor::load_new_batch(), protocols::jd2::archive::MPIArchiveJobDistributor::mark_job_as_completed(), protocols::jd2::JobDistributor::mark_job_as_completed(), protocols::jd2::MPIFileBufJobDistributor::master_get_new_job_id(), protocols::jd2::MPIFileBufJobDistributor::master_go(), protocols::jd2::MPIFileBufJobDistributor::master_job_succeeded(), protocols::jd2::MPIFileBufJobDistributor::master_mark_current_job_id_for_repetition(), protocols::jd2::MPIFileBufJobDistributor::master_remove_bad_inputs_from_job_list(), protocols::jd2::JobDistributor::next_batch(), protocols::jd2::archive::MPIArchiveJobDistributor::notify_archive(), protocols::jd2::JD2ResourceManagerJobInputter::parse_jobs_table_tag(), protocols::jd2::LazySilentFileJobInputter::pose_from_job(), protocols::jd2::PoseInputStreamJobInputter::pose_from_job(), protocols::jd2::JD2ResourceManagerJobInputter::pose_from_job(), protocols::jd2::AtomTreeDiffJobInputter::pose_from_job(), protocols::jd2::SilentFileJobInputter::pose_from_job(), protocols::jd2::PoseInputStreamJobInputter::PoseInputStreamJobInputter(), protocols::jd2::MPIFileBufJobDistributor::process_message(), protocols::jd2::archive::MPIArchiveJobDistributor::process_message(), protocols::jd2::archive::ArchiveManager::queue_batch(), protocols::jd2::JD2ResourceManagerJobInputter::read_Data_for_subtag(), protocols::jd2::archive::ArchiveManager::read_existing_batches(), protocols::jd2::archive::EvaluatedArchive::read_structures(), protocols::jd2::archive::ArchiveBase::read_structures(), protocols::jd2::archive::MPIArchiveJobDistributor::receive_batch(), protocols::jd2::MpiFileBuffer::release_file(), protocols::jd2::MpiFileBuffer::remote_close_file(), protocols::jd2::archive::EvaluatedArchive::remove_evaluation(), protocols::jd2::archive::EvaluatedArchive::rescore(), protocols::jd2::archive::ArchiveBase::restore_from_file(), protocols::jd2::MpiFileBuffer::run(), protocols::jd2::archive::ArchiveBase::save_to_file(), protocols::jd2::archive::NormalizedEvaluatedArchive::score_variation(), protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations(), protocols::jd2::archive::EvaluatedArchive::select_score(), protocols::jd2::MPIFileBufJobDistributor::send_job_to_slave(), protocols::jd2::archive::ArchiveManager::send_stop_to_jobdistributor(), protocols::jd2::JobDistributor::set_batch_id(), protocols::jd2::SilentFileJobOutputter::set_defaults(), protocols::jd2::archive::EvaluatedArchive::set_weight(), protocols::jd2::MPIMultiCommJobDistributor::setup_sub_communicators(), protocols::jd2::SilentFileJobInputter::SilentFileJobInputter(), protocols::jd2::MPIFileBufJobDistributor::slave_get_new_job_id(), protocols::jd2::MPIFileBufJobDistributor::slave_mark_current_job_id_for_repetition(), protocols::jd2::archive::EvaluatedArchive::start_evaluation_timer(), protocols::jd2::archive::ArchiveManager::start_new_batch(), protocols::jd2::MpiFileBuffer::store_to_channel(), protocols::jd2::archive::MPIArchiveJobDistributor::sync_batches(), protocols::jd2::SilentFileJobOutputter::write_all_structs(), protocols::jd2::archive::Batch::write_info_file(), protocols::jd2::WriteFileSFB::write_lines(), protocols::jd2::WriteFileSFB::WriteFileSFB(), and protocols::jd2::WriteFileSFB::~WriteFileSFB().

static Tracer protocols::jd2::TR ( "protocols.resource_manager.planner.JD2ResourceManager"  )
static
static basic::Tracer protocols::jd2::TR ( "protocols.jd2.DockDesignParser"  )
static

Referenced by protocols::jd2::AtomTreeDiffJobOutputter::dump_pose(), protocols::jd2::FileJobOutputter::file(), protocols::jd2::FileJobOutputter::FileJobOutputter(), protocols::jd2::PDBJobInputter::fill_jobs(), protocols::jd2::PDBJobOutputter::final_pose(), protocols::jd2::JobInputterFactory::get_JobInputter_from_string(), protocols::jd2::JobOutputterFactory::get_JobOutputter_from_string(), protocols::jd2::ShuffleFileSystemJobDistributor::get_new_job_id(), protocols::jd2::FileSystemJobDistributor::mark_current_job_id_for_repetition(), protocols::jd2::MPIWorkPoolJobDistributor::master_get_new_job_id(), protocols::jd2::MPIWorkPoolJobDistributor::master_go(), protocols::jd2::MPIWorkPoolJobDistributor::master_job_succeeded(), protocols::jd2::MPIWorkPoolJobDistributor::master_mark_current_job_id_for_repetition(), protocols::jd2::MPIWorkPoolJobDistributor::master_remove_bad_inputs_from_job_list(), protocols::jd2::MPIWorkPartitionJobDistributor::MPIWorkPartitionJobDistributor(), protocols::jd2::PDBJobOutputter::other_pose(), output_intermediate_pose(), protocols::jd2::PDBJobInputter::PDBJobInputter(), protocols::jd2::PDBJobOutputter::PDBJobOutputter(), protocols::jd2::PDBJobInputter::pose_from_job(), protocols::jd2::FileSystemJobDistributor::remove_bad_inputs_from_job_list(), protocols::jd2::MPIWorkPartitionJobDistributor::remove_bad_inputs_from_job_list(), protocols::jd2::FileJobOutputter::scorefile(), protocols::jd2::MPIWorkPoolJobDistributor::slave_get_new_job_id(), protocols::jd2::MPIWorkPoolJobDistributor::slave_job_succeeded(), and protocols::jd2::MPIWorkPoolJobDistributor::slave_mark_current_job_id_for_repetition().

void protocols::jd2::write_score_tracer ( core::pose::Pose const &  pose_in,
std::string  tracer_point 
)

Variable Documentation

core::Size const protocols::jd2::BAD_INPUT = 2
JobOP const protocols::jd2::JD2_BOGUS_JOB
core::Size const protocols::jd2::JOB_FAILED_NO_RETRY = 4
core::Size const protocols::jd2::JOB_SUCCESS = 3
core::Size const protocols::jd2::NEW_JOB_ID = 1

Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.

Referenced by protocols::jd2::MPIFileBufJobDistributor::process_message(), and protocols::jd2::MPIFileBufJobDistributor::slave_get_new_job_id().