 |
Rosetta
2021.16
|
All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
|
Rosetta
2021.16
|
#include <MRSJobQueenChecker.hh>
Public Member Functions | |
| MRSJobQueenChecker () | |
| ~MRSJobQueenChecker () override | |
| core::Size | estimate_number_of_bytes_needed_for_archiving () |
| create serialized poses for every input job and use these to predict the amount of memory required for archiving results More... | |
| jd3::JobDigraphOP | create_initial_job_dag () override |
| The job dag encodes which job nodes are independent or dependant on each other. If you have a applicationwhere all inputs are independant and only a single run of a protocol is needed, Then do not override this method. More... | |
| std::list< jd3::LarvalJobOP > | determine_job_list (jd3::JobDAGNodeID job_dag_node_index, core::Size max_njobs) override |
| Create a list of LarvalJobs for each Node Index. Only can create max_njobs to save memory. More... | |
 Public Member Functions inherited from protocols::multistage_rosetta_scripts::MRSJobQueen | |
| MRSJobQueen () | |
| ~MRSJobQueen () override | |
| jd3::JobOP | complete_larval_job_maturation (jd3::LarvalJobCOP larval_job, utility::options::OptionCollectionCOP job_options, utility::vector1< jd3::JobResultCOP > const &input_job_results) override |
| The derived JobQueen must define the method that takes a larval job and the job-specific options and matures the larval job into a full job. More... | |
| void | note_job_completed (jd3::GlobalJobID job_id, jd3::JobStatus status, core::Size nresults, bool are_you_a_unit_test) |
| this was only created for the unit test. Please do not call this. More... | |
| void | note_job_completed (core::Size, jd3::JobStatus, core::Size) |
| void | note_job_completed (jd3::LarvalJobCOP job, jd3::JobStatus status, core::Size nresults) override |
| The JD calls this function on completion of a LarvalJob, after updating the JobTracker. More... | |
| void | completed_job_summary (jd3::GlobalJobID job_id, jd3::ResultIndex result_index, jd3::JobSummaryOP summary) |
| void | completed_job_summary (jd3::LarvalJobCOP job, jd3::ResultIndex result_index, jd3::JobSummaryOP summary) override |
| As each job completes, this function is called for each result coming from a LarvalJob. More... | |
| jd3::JobDAGNodeID | stage_for_global_job_id (jd3::GlobalJobID global_job_id) const |
| std::list< jd3::JobResultID > | job_results_that_should_be_discarded () override |
| The IDs of jobs that should be discarded, IE not kept in memory for the next set of job nodes. More... | |
| std::list < jd3::output::OutputSpecificationOP > | jobs_that_should_be_output () override |
| By default outputs all recently finished jobs for JD output (stored in recent_successes_). Override this method if you want to cull these lists. More... | |
| TagManager const & | tag_manager () const |
| void | determine_validity_of_stage_tags () |
| core::Size | num_input_structs () const |
| core::Size | num_stages () const |
| core::Size | num_results_to_keep_for_stage (core::Size stage) const |
| Public Member Functions inherited from protocols::jd3::standard::StandardJobQueen | |
| StandardJobQueen () | |
| The StandardJobQueen constructor asks the PoseInputterFactory for a PoseInputter and creates a ResourceManager. More... | |
| ~StandardJobQueen () override | |
| void | update_job_dag (JobDigraphUpdater &updater) override |
| Starting the Job ///. More... | |
| protocols::jd3::JobOP | mature_larval_job (protocols::jd3::LarvalJobCOP job, utility::vector1< JobResultCOP > const &input_job_results) override |
| Mature the LarvalJob into a full Job that will be run on a processor. Calls complete_larval_job_maturation, which you will need to override. More... | |
| output::ResultOutputterOP | result_outputter (output::OutputSpecification const &spec) override |
| Return the bag of of PoseOutputters (in the form of a MultipleOutputter) for the Pose that has been requested and specified by a particular OutputSpecification;. More... | |
| bool | has_job_previously_been_output (protocols::jd3::LarvalJobCOP job) override |
| Checks the outputter to see if the job already has been output. Used for JD override behavior. More... | |
| std::list < deallocation::DeallocationMessageOP > | deallocation_messages () override |
| Resource Management ///. More... | |
| void | process_deallocation_message (deallocation::DeallocationMessageOP message) override |
| A deallocation message first sent to the JobDistributor on this host originating from a remote JobQueen. If a derived JobQueen has deallocation messages she needs to recieve, she should override derived_process_deallocation_message. More... | |
| void | flush () override |
| Send all buffered output to disk – called by the JobDistributor right before it shuts down if it hits an error or catches an exception that it cannot ignore. More... | |
| std::string | job_definition_xsd () const override |
| XSD Functions ///. More... | |
| std::string | resource_definition_xsd () const override |
| JobQueens may optionally define an XSD for their resource definition file which is fed to their resource manager (if they control one). If the JobDistributor is awakened with the flag "jd3::output_resource_xsd <output file>" on the command line, and if the derived JobQueen defines an XSD for resources she uses, then the JobDistributor will write out the resource definition XSD to the output file. The derived queen may return an empty string to indicate that no resources are definable for the resource manager. More... | |
| void | determine_preliminary_job_list_from_xml_file (std::string const &job_def_string) |
| Read from an input string representing the contents of the job-definiton XML file and construct a set of PreliminaryLarvalJobs; this function is primarily useful for testing, but could be used to organize jobs by an enterprising job distributor or by another JobQueen. More... | |
| Public Member Functions inherited from protocols::jd3::JobQueen | |
| JobQueen () | |
| ~JobQueen () override | |
| JobDigraphOP | create_and_set_initial_job_dag () |
| Creates the initial job dag using create_initial_job_dag function and sets it to the JQ. More... | |
| void | note_job_completed_and_track (LarvalJobCOP job, JobStatus status, core::Size nresults) |
| Call note_job_completed in derived classes and track the job using the JobTracker. More... | |
| LarvalJobs | determine_job_list_and_track (JobDAGNodeID job_dag_node_index, core::Size max_njobs) |
| Call determine_job_list in derived classes and track the jobs using the JobTracker. More... | |
Static Public Member Functions | |
| static std::pair< core::Size, core::Size > | fa_and_cen_sizes_for_archives (core::pose::PoseOP pose) |
| Static Public Member Functions inherited from protocols::jd3::standard::StandardJobQueen | |
| static std::string | job_def_complex_type_name (std::string const &type) |
| Naming function for the complexTypes in the job-definition XSD. More... | |
Additional Inherited Members | |
| Protected Member Functions inherited from protocols::multistage_rosetta_scripts::MRSJobQueen | |
| core::pose::PoseOP | pose_for_job_derived (jd3::LarvalJobCOP job, utility::options::OptionCollection const &options) |
| core::pose::PoseOP | pose_for_inner_job_derived (jd3::InnerLarvalJobCOP inner_job, utility::options::OptionCollection const &options) |
| void | all_settings_to_defualt () |
| jd3::LarvalJobOP | get_nth_job_for_initial_stage (jd3::LocalJobID local_job_id) |
| jd3::LarvalJobOP | get_nth_job_for_noninitial_stage (jd3::JobDAGNodeID stage, jd3::LocalJobID local_job_id) |
| void | append_common_tag_subelements (utility::tag::XMLSchemaDefinition &xsd, utility::tag::XMLSchemaComplexTypeGenerator &ct_gen) const override |
| Here, you specify which tags that are defined in the <common> element. More... | |
| void | parse_job_definition_tags (utility::tag::TagCOP common_block_tags, utility::vector1< jd3::standard::PreliminaryLarvalJob > const &) override |
| This gives the derived JobQueen a chance to read any relevant information from the job-definition file. The second argument holds a PreliminaryLarvalJob for every job block and the PreliminaryLarvalJob itself has all of the information given in its corresponding block. More... | |
| void | parse_common_tag (utility::tag::TagCOP common_tag) |
| void | parse_single_stage_tag (utility::tag::TagCOP subprotocol_tag) |
| void | append_job_tag_subelements (utility::tag::XMLSchemaDefinition &job_definition_xsd, utility::tag::XMLSchemaComplexTypeGenerator &job_ct_gen) const override |
| XML Schema ///. More... | |
| void | parse_single_job_tag (jd3::standard::PreliminaryLarvalJob const &prelim_larval_job, jd3::PrelimJobNodeID input_pose_id) |
| jd3::PrelimJobNodeID | input_pose_id_for_jobid (jd3::GlobalJobID global_jobid) const |
| void | print_job_lineage () const |
| void | assign_output_index (jd3::LarvalJobCOP larval_job, jd3::ResultIndex result_index_for_job, core::Size n_results_for_job, jd3::JobOutputIndex &output_index) override |
| The derived job queen may assign her own numbering to output Poses if she chooses. More... | |
| void | assign_output_index (jd3::GlobalJobID global_job_id, jd3::ResultIndex result_id, jd3::JobOutputIndex &output_index) |
| void | cluster (jd3::JobDAGNodeID stage_about_to_start) |
| Protected Member Functions inherited from protocols::jd3::standard::StandardJobQueen | |
| virtual LarvalJobs | next_batch_of_larval_jobs_for_job_node (JobDAGNodeID job_dag_node_index, core::Size max_njobs) |
| Called during the SJQs determine_job_list function. Override this function to create LarvalJobs for nodes other than preliminary job nodes. More... | |
| GlobalJobID | current_job_index () const |
| Get the current larval job index from the JobTracker. More... | |
| virtual void | determine_preliminary_job_list () |
| Preliminary Larval Jobs ///. More... | |
| bool | get_preliminary_larval_jobs_determined () const |
| Has determine_preliminary_job_list been called? More... | |
| PreliminaryLarvalJobTracker & | get_prelim_larval_job_tracker () |
| Get write access to the PreliminaryLarvalJobTracker. More... | |
| PreliminaryLarvalJobTracker const & | get_prelim_larval_job_tracker () const |
| Get read access to the PreliminaryLarvalJobTracker. More... | |
| utility::vector1 < PreliminaryLarvalJob > const & | get_preliminary_larval_jobs () const |
| Read access to derived JobQueens to the preliminary job list. More... | |
| virtual void | note_preliminary_job_node_is_complete (PrelimJobNodeID pjn_index) |
| Respond to the completion of a preliminary job node in derived SJQs. More... | |
| virtual InnerLarvalJobs | refine_preliminary_job (PreliminaryLarvalJob const &prelim_job) |
| Optional Larval Job Creation ///. More... | |
| virtual LarvalJobs | expand_job_list (InnerLarvalJobOP inner_job, core::Size max_larval_jobs_to_create) |
| Expand an InnerLarvalJob into a full set of LarvalJobs, creating nstruct LarvalJob objects Increments larval_job_counter_. More... | |
| virtual StandardInnerLarvalJobOP | create_inner_larval_job (core::Size nstruct, JobDAGNodeID job_node, PrelimJobNodeID preliminary_job_node) const |
| Factory method for derived classes if they wish to rely on classes derived from StandardInnerLarvalJob. This is invoked by the StandardJobQueen in her determine_job_list method just as jobs are prepared. If the base StandardInnerLarvalJob class is desired, then do not override this method. More... | |
| virtual LarvalJobOP | create_larval_job (InnerLarvalJobOP job, NStructIndex nstruct_index, core::Size larval_job_index) |
| Factory method for derived classes if they wish to rely on classes derived from LarvalJob. This is invoked by the StandardJobQueen in the expand_job_list method. If the base LarvalJob class is desired, then do not override this method. More... | |
| InnerLarvalJobOP | create_and_init_inner_larval_job_from_preliminary (core::Size nstruct, PrelimJobNodeID prelim_job_node, JobDAGNodeID job_node) const |
| Adds information regarding the job definition (job tag, input source, jobdef tag, and outputter). Uses the PreliminaryInnerLarvalJob to do so. More... | |
| void | create_and_store_output_specification_for_job_result (LarvalJobCOP job, ResultIndex result_index, core::Size nresults) |
| Output Specifications and Ouputters ///. More... | |
| void | create_and_store_output_specification_for_job_result (LarvalJobCOP job, utility::options::OptionCollection const &job_options, ResultIndex result_index, core::Size nresults) |
| Create an output specification for a given job + result index and store it in the recent_successes_ list, which will be given to the JobDistributor upon request. More... | |
| virtual output::OutputSpecificationOP | create_output_specification_for_job_result (LarvalJobCOP job, utility::options::OptionCollection const &job_options, ResultIndex result_index, core::Size nresults) |
| Construct the OutputSpecification for a completed successful job. More... | |
| JobOutputIndex | build_output_index (protocols::jd3::LarvalJobCOP larval_job, ResultIndex result_index_for_job, core::Size n_results_for_job) |
| Construct a JobOutputIndex for a given job based on "the obvious", but giving derived classes the chance to assign their own indices via the assign_output_index function. More... | |
| virtual void | derived_process_deallocation_message (deallocation::DeallocationMessageOP message) |
| If the derived class has deallocation messages that it needs to broadcast to remote nodes and then to process on those remote nodes, then the StanardJobQueen will pass them along to the derived job queen using this function. More... | |
| pose_outputters::PoseOutputterOP | pose_outputter_for_job (InnerLarvalJob const &innerJob) |
| Create or get the PoseOutputter from the job. Cache the Outputter in the SJQ. More... | |
| pose_outputters::PoseOutputterOP | pose_outputter_for_job (InnerLarvalJob const &innerJob, utility::options::OptionCollection const &job_options) |
| Create or get the PoseOutputter from the job. Cache the Outputter in the SJQ. More... | |
| pose_outputters::PoseOutputterOP | pose_outputter_for_job (pose_outputters::PoseOutputSpecification const &spec) |
| Find the PoseOutputter for a job specification, respecting the Job-distributor provided output file suffix. More... | |
| utility::vector1 < pose_outputters::SecondaryPoseOutputterOP > | secondary_outputters_for_job (InnerLarvalJob const &innerJob, utility::options::OptionCollection const &job_options) |
| core::pose::PoseOP | pose_for_inner_job (InnerLarvalJobCOP inner_job) |
| core::pose::PoseOP | pose_for_inner_job (InnerLarvalJobCOP inner_job, utility::options::OptionCollection const &options) |
| Return a copy of the Pose to be used with the given inner job. More... | |
| core::pose::PoseOP | pose_for_job (LarvalJobCOP job, utility::options::OptionCollection const &options) |
| Return a copy of the Pose to be used with the given job. Wrapper for pose_for_inner_job() More... | |
| utility::options::OptionCollectionOP | options_for_job (InnerLarvalJob const &inner_job) const |
| Options Collection ///. More... | |
| utility::options::OptionCollectionOP | options_from_tag (utility::tag::TagCOP job_options_tags) const |
| Create an OptionCollection from tags and OptionKeys stored in the SJQ. More... | |
| pose_inputters::PoseInputterOP | pose_inputter_for_job (InnerLarvalJob const &inner_job) const |
| Access the pose inputter. More... | |
| void | add_options (utility::options::OptionKeyList const &opts) |
| void | add_option (utility::options::OptionKey const &key) |
| void | remove_default_input_element () |
| Override the basic specification of input elements as either PDBs, Silent Structures, or ResourceManager defined structures. This should be called during the derived class's constructor if it is to be used. More... | |
| utility::tag::TagCOP | common_block_tags () const |
| Return the set of subtags that are common to the whole set of jobs in the Job definition file, if any are given. This set of tags is read from disk at most once per execution. More... | |
| void | set_common_block_precedes_job_blocks (bool setting) |
| By default, the common block is given before the job blocks in the job definition file. Setting this value to false reverses the order and the common block goes at the end of the file. More... | |
| void | do_not_accept_all_pose_inputters_from_factory () |
| Expert Override Input/Output behavior ///. More... | |
| void | allow_pose_inputter (pose_inputters::PoseInputterCreatorOP creator) |
| void | do_not_accept_all_pose_outputters_from_factory () |
| void | allow_pose_outputter (pose_outputters::PoseOutputterCreatorOP creator) |
| void | set_default_outputter (pose_outputters::PoseOutputterCreatorOP creator) |
| Protected Member Functions inherited from protocols::jd3::JobQueen | |
| JobDigraph const & | get_job_graph () const |
| Get read access to the current job graph. More... | |
| JobTracker & | get_job_tracker () |
| Get write access to the current job tracker. More... | |
| JobTracker const & | get_job_tracker () const |
| Get read access to the current job tracker. More... | |
| Static Protected Member Functions inherited from protocols::multistage_rosetta_scripts::MRSJobQueen | |
| static std::string | protocols_subelement_mangler (std::string const &name) |
| static std::string | job_subelement_mangler (std::string const &name) |
| protocols::multistage_rosetta_scripts::MRSJobQueenChecker::MRSJobQueenChecker | ( | ) |
|
override |
|
overridevirtual |
The job dag encodes which job nodes are independent or dependant on each other. If you have a applicationwhere all inputs are independant and only a single run of a protocol is needed, Then do not override this method.
The StandardJobQueen provides an implementation of this function which returns the most straight-forward DAG representing a set of jobs that have no interdependencies: a DAG with a single node and no edges.
Override this method if you have a need for any more job nodes other than what is created from input structures and the Job Definition file.
The base class provides a digraph with a single node – that is, all the jobs are independent of each other. This is equivalent to the kind of jobs that could be run in JD2.
Reimplemented from protocols::multistage_rosetta_scripts::MRSJobQueen.
References protocols::multistage_rosetta_scripts::MRSJobQueen::create_initial_job_dag(), and protocols::multistage_rosetta_scripts::MRSJobQueen::determine_validity_of_stage_tags().
|
overridevirtual |
Create a list of LarvalJobs for each Node Index. Only can create max_njobs to save memory.
The StandardJobQueen manages the process of creating the list of LarvalJobs that will later be matured into actual jobs and run by the JobDistributor. It is not recommended that derived job queens override this method; doing so will mean that some of the data the SJQ relies on will not be initialized – see comments on the SJQs data members below to understand the consequences of overriding this method.
It is recommended to override next_batch_of_larval_jobs_for_job_node instead of this method However, if you do override this - especially for more complicated protocols - be sure to call similar functions here
The process begins by first constructing the job definition and resource definition XSDs. With these schemas, the StandardJobQueen validates the input XML files (if present). The StandardJobQueen then populates preliminary versions of LarvalJob objects./ If the XSD includes "command line options" (which may be specified either from the command line or in the <options> sections of the Job XML file), the StandardJobQueen loads the preliminary LarvalJob objects with the options. These preliminary LarvalJob objects will not have been nstruct expanded (i.e. if there are 100 nstruct for each of 5 different jobs, then there will only be 5 preliminary larval jobs created). It then passes the preliminary LarvalJob list and the TagOP objects for each preliminary LarvalJob to the derived class through the refine_job_list method.
Reimplemented from protocols::multistage_rosetta_scripts::MRSJobQueen.
| core::Size protocols::multistage_rosetta_scripts::MRSJobQueenChecker::estimate_number_of_bytes_needed_for_archiving | ( | ) |
create serialized poses for every input job and use these to predict the amount of memory required for archiving results
References fa_and_cen_sizes_for_archives(), protocols::jd3::standard::StandardJobQueen::get_preliminary_larval_jobs(), protocols::jd3::standard::PreliminaryLarvalJob::inner_job, protocols::multistage_rosetta_scripts::MRSJobQueen::num_input_structs(), protocols::multistage_rosetta_scripts::MRSJobQueen::num_results_to_keep_for_stage(), protocols::multistage_rosetta_scripts::MRSJobQueen::num_stages(), protocols::jd3::standard::StandardJobQueen::options_for_job(), protocols::jd3::standard::StandardJobQueen::pose_for_inner_job(), and protocols::TR().
|
static |
1.8.7