Author: Jack Maguire
We have already created larval jobs and created our TutorialJob class, so now we can write the method that matures larval jobs into TutorialJobs.
To get the jobs, the job distributor will call mature_larval_job().
This is a virtual function so we can override it if we want;
however, the StandardJobQueen does a lot of the work for us in its override of mature_larval_job().
Instead, we want to override complete_larval_job_maturation().
This method is called at the end of StandardJobQueen::mature_larval_job()
and allows our derived queen to make the finishing touches to the job.
Also, this will be the first time the job queen will be called on the worker nodes!
This means we need to do all of the initialization we did on the head node in Step 2.
I recommend starting a call to complete_larval_job_maturation() with a check to see if the queen has been initialized yet.
If the check fails, call initial_job_dag().
Let's declare the override of complete_larval_job_maturation() in the protected section of the header.
jd3::JobOP
complete_larval_job_maturation(
jd3::LarvalJobCOP larval_job,
utility::options::OptionCollectionCOP job_options,
utility::vector1< jd3::JobResultCOP > const & input_job_results
) override ; #include <protocols/tutorial/TutorialJob.hh>
#include <protocols/jd3/standard/StandardInnerLarvalJob.hh>
#include <protocols/jd3/standard/MoverAndPoseJob.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/relax/FastRelax.hh>
#include <protocols/minimization_packing/MinPackMover.hh>
#include <protocols/minimization_packing/MinMover.hh>We should be initializing all of our data to 0 in the constructor anyways, but now we have more incentive to do so.
We can check to see if num_input_structs_ is 0 at the beginning of complete_larval_job_maturation().
If it is 0, then we know we need to initialize().
//Constructor
TutorialQueen::TutorialQueen() :
StandardJobQueen(),
num_input_structs_( 0 ),
node_managers_( 0 ),
job_genealogist_( 0 )
{}This method is more-or-less unique to your specific protocol. This is where you create a Job that can be run based off of the limited information the head queen gives you.
JobOP
TutorialQueen::complete_larval_job_maturation(
LarvalJobCOP job,
utility::options::OptionCollectionCOP job_options,
utility::vector1< JobResultCOP > const & input_job_results
) {
if ( num_input_structs_ == 0 ) {
initial_job_dag();
}
standard::StandardInnerLarvalJobCOP standard_inner_larval_job
= utility::pointer::static_pointer_cast< const standard::StandardInnerLarvalJob >( job->inner_job() );
core::Size const global_job_id = job->job_index();
moves::MoverOP mover = 0;
core::scoring::ScoreFunctionOP sfxn = core::scoring::ScoreFunctionFactory::create_score_function( "ref2015.wts" );
core::pose::PoseOP pose = 0;
if( global_job_id <= node_managers_[ 1 ]->num_jobs() ){
//This job belongs to node 1
//local_job_id = global_job_id;
mover = utility::pointer::make_shared< relax::FastRelax >();
pose = pose_for_inner_job( standard_inner_larval_job );
} else if( global_job_id <= node_managers_[ 1 ]->num_jobs() + node_managers_[ 2 ]->num_jobs() ) {
//alternatively you could have used:
//else if( global_job_id <= node_managers_[ 3 ]->job_offset() )
//This job belongs to node 2
//local_job_id = global_job_id - node_managers_[ 2 ]->job_offset();
mover = utility::pointer::make_shared< minimization_packing::MinPackMover >();
pose = pose_for_inner_job( standard_inner_larval_job );
} else {
//This job belongs to node 3
//local_job_id = global_job_id - node_managers_[ 3 ]->job_offset();
mover = utility::pointer::make_shared< minimization_packing::MinMover >();
//We created this larval job and pose result so we know that there should be exactly 1 result and that result is a standard::PoseJobResult
runtime_assert( input_job_results.size() == 1 );
standard::PoseJobResult const & result1 = static_cast< standard::PoseJobResult const & >( * input_job_results[ 1 ] );
pose = result1.pose()->clone();
runtime_assert( pose );
}
TutorialJobOP tjob = utility::pointer::make_shared< TutorialJob >();
tjob->set_pose( pose );
tjob->set_sfxn( sfxn );
tjob->set_mover( mover );
return tjob;
} // -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington CoMotion, email: license@uw.edu.
/// @file protocols/tutorial/TutorialQueen.hh
/// @author Jack Maguire, jackmaguire1444@gmail.com
#ifndef INCLUDED_protocols_tutorial_TutorialQueen_HH
#define INCLUDED_protocols_tutorial_TutorialQueen_HH
#include <protocols/tutorial/TutorialQueen.fwd.hh>
#include <protocols/jd3/standard/StandardJobQueen.hh>
#include <protocols/jd3/JobDigraph.fwd.hh>
#include <protocols/jd3/dag_node_managers/NodeManager.fwd.hh>
#include <protocols/jd3/LarvalJob.fwd.hh>
#include <protocols/jd3/JobGenealogist.fwd.hh>
#include <utility/tag/Tag.fwd.hh>
namespace protocols {
namespace tutorial {
class TutorialQueen: public jd3::standard::StandardJobQueen {
public:
//constructor
TutorialQueen();
//destructor
~TutorialQueen() override;
jd3::JobDigraphOP
initial_job_dag()
override;
void
parse_job_definition_tags(
utility::tag::TagCOP common_block_tags,
utility::vector1< jd3::standard::PreliminaryLarvalJob > const &
) override;
std::list< jd3::LarvalJobOP > determine_job_list(
Size job_dag_node_index,
Size max_njobs
) override;
protected:
void init_node_managers();
void count_num_jobs_for_nodes_1_and_2 (
core::Size & num_jobs_for_node_1,
core::Size & num_jobs_for_node_2
);
jd3::LarvalJobOP get_next_larval_job_for_node_1_or_2( core::Size node );
jd3::LarvalJobOP get_next_larval_job_for_node_3();
jd3::JobOP
complete_larval_job_maturation(
jd3::LarvalJobCOP larval_job,
utility::options::OptionCollectionCOP job_options,
utility::vector1< jd3::JobResultCOP > const & input_job_results
) override ;
private:
core::Size num_input_structs_;
utility::vector1< jd3::dag_node_managers::NodeManagerOP > node_managers_;
jd3::JobGenealogistOP job_genealogist_;
};
} //tutorial
} //protocols
#endif // -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington CoMotion, email: license@uw.edu.
/// @file protocols/tutorial/TutorialQueen.cc
/// @author Jack Maguire, jackmaguire1444@gmail.com
#include <protocols/tutorial/TutorialQueen.hh>
#include <protocols/tutorial/TutorialJob.hh>
#include <protocols/jd3/JobDigraph.hh>
#include <protocols/jd3/dag_node_managers/NodeManager.hh>
#include <protocols/jd3/dag_node_managers/SimpleNodeManager.hh>
#include <protocols/jd3/LarvalJob.hh>
#include <protocols/jd3/JobGenealogist.hh>
#include <protocols/jd3/standard/StandardInnerLarvalJob.hh>
#include <protocols/jd3/standard/MoverAndPoseJob.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/relax/FastRelax.hh>
#include <protocols/minimization_packing/MinPackMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <utility/pointer/memory.hh>
#include <basic/Tracer.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
static basic::Tracer TR( "protocols.tutorial.TutorialQueen" );
using namespace protocols::jd3;
using namespace protocols::jd3::standard;
namespace protocols {
namespace tutorial {
//Constructor
TutorialQueen::TutorialQueen() :
StandardJobQueen(),
num_input_structs_( 0 ),
node_managers_( 0 ),
job_genealogist_( 0 )
{}
//Destructor
TutorialQueen::~TutorialQueen()
{}
JobDigraphOP
TutorialQueen::initial_job_dag() {
//you need to call this for the standard job queen to initialize
determine_preliminary_job_list();
init_node_managers();
job_genealogist_ = utility::pointer::make_shared< JobGenealogist >( 3, num_input_structs_ );
JobDigraphOP dag = utility::pointer::make_shared< JobDigraph >( 3 );
dag->add_edge( 1, 3 );
dag->add_edge( 2, 3 );
return dag;
}
std::list< jd3::LarvalJobOP >
TutorialQueen::determine_job_list (
core::Size job_dag_node_index,
core::Size max_njobs
) {
std::list< jd3::LarvalJobOP > job_list;
for( core::Size ii = 1; ii <= max_njobs; ++ii ){
jd3::LarvalJobOP next_job;
if( job_dag_node_index == 3 ){
next_job = get_next_larval_job_for_node_3();
} else {
next_job = get_next_larval_job_for_node_1_or_2( job_dag_node_index );
}
if( next_job == 0 ) {
return job_list;
} else {
job_list.push_back( next_job );
}
}
return job_list;
}
void
TutorialQueen::parse_job_definition_tags(
utility::tag::TagCOP common_block_tags,
utility::vector1< standard::PreliminaryLarvalJob > const & prelim_larval_jobs
){
num_input_structs_ = prelim_larval_jobs.size();
}
void
TutorialQueen::init_node_managers(){
using namespace jd3::dag_node_managers;
core::Size num_jobs_for_node1( 0 ), num_jobs_for_node2( 0 );
count_num_jobs_for_nodes_1_and_2( num_jobs_for_node1, num_jobs_for_node2 );
core::Size const num_results_to_keep_for_node1 = num_jobs_for_node1 / 2; //Let's keep half of the results
SimpleNodeManagerOP node1 = utility::pointer::make_shared< SimpleNodeManager >(
0, //Job offset
num_jobs_for_node1,
num_results_to_keep_for_node1
);
core::Size const num_results_to_keep_for_node2 = num_jobs_for_node2 / 3; //Let's keep half of the results
SimpleNodeManagerOP node2 = utility::pointer::make_shared< SimpleNodeManager >(
num_jobs_for_node1, //Job offset
num_jobs_for_node2,
num_results_to_keep_for_node2
);
core::Size const num_jobs_for_node3 = num_results_to_keep_for_node1 + num_results_to_keep_for_node2;
core::Size const num_results_to_keep_for_node3 = num_jobs_for_node3; //Let's keep/dump all of the results
SimpleNodeManagerOP node3 = utility::pointer::make_shared< SimpleNodeManager >(
num_jobs_for_node1 + num_jobs_for_node2, //Job offset
num_jobs_for_node3,
num_results_to_keep_for_node3
);
node_managers_.reserve( 3 );
node_managers_.push_back( node1 );
node_managers_.push_back( node2 );
node_managers_.push_back( node3 );
}
void
TutorialQueen::count_num_jobs_for_nodes_1_and_2(
core::Size & num_jobs_for_node_1,
core::Size & num_jobs_for_node_2
) {
num_jobs_for_node_1 = 0;
num_jobs_for_node_2 = 0;
//vector has 1 element for each <Job> tag
utility::vector1< standard::PreliminaryLarvalJob > const & all_preliminary_larval_jobs = preliminary_larval_jobs();
for( standard::PreliminaryLarvalJob const & pl_job : all_preliminary_larval_jobs ){
core::pose::PoseOP pose = pose_for_inner_job( pl_job.inner_job );
num_jobs_for_node_1 += pose->chain_sequence( 1 ).length();
num_jobs_for_node_2 += pose->chain_sequence( 2 ).length();
}
}
jd3::LarvalJobOP
TutorialQueen::get_next_larval_job_for_node_1_or_2( core::Size node ) {
//This is written very ineffeciently, but it will do for the scope of the tutorial
runtime_assert( node == 1 || node == 2 );
if( node_managers_[ node ]->done_submitting() ) {
return 0;
}
//each job has 2 indices:
//a local one, which tracks its index within its dag node
//a global one, which is unique accross the entire program
core::Size const local_job_id = node_managers_[ node ]->get_next_local_jobid();
core::Size const global_job_id = node_managers_[ node ]->job_offset() + local_job_id;
core::Size counter = local_job_id;
utility::vector1< standard::PreliminaryLarvalJob > const & all_preliminary_larval_jobs = preliminary_larval_jobs();
core::Size pose_input_source_id = 0;
//This part is not directly JD3-related, it's just a matter of finding the pose that we need for this specific job
for( standard::PreliminaryLarvalJob const & pl_job : all_preliminary_larval_jobs ){
core::pose::PoseOP pose = pose_for_inner_job( pl_job.inner_job );
++pose_input_source_id;
core::Size const nres_in_chain = pose->chain_sequence( node ).length();
if( nres_in_chain > counter ){
counter -= nres_in_chain;
} else {
break;
}
}
debug_assert( pose_input_source_id <= all_preliminary_larval_jobs.size() );
//These can be recycled between larval jobs
//So in reality, you will probably choose to store this somewhere and use it again the next time this method is called
//(you will have to change the arguments accordingly)
//jd3::InnerLarvalJobOP inner_ljob =
jd3::standard::StandardInnerLarvalJobOP inner_ljob =
create_and_init_inner_larval_job( 1, pose_input_source_id );
LarvalJobOP ljob = utility::pointer::make_shared< LarvalJob >(
inner_ljob, 1, global_job_id );
job_genealogist_->register_new_job (
node,
global_job_id,
pose_input_source_id
);
return ljob;
}
jd3::LarvalJobOP
TutorialQueen::get_next_larval_job_for_node_3(){
using namespace protocols::jd3;
if( node_managers_[ 3 ]->done_submitting() ) {
return 0;
}
core::Size const local_job_id = node_managers_[ 3 ]->get_next_local_jobid();
core::Size const global_job_id = node_managers_[ 3 ]->job_offset() + local_job_id;
core::Size const num_results_for_node1 = node_managers_[ 1 ]->results_to_keep().size();
core::Size const node_of_parent = ( local_job_id > num_results_for_node1 ? 2 : 1 );
jd3::JobResultID parent_result;
if( node_of_parent == 1 ){
parent_result = node_managers_[ 1 ]->get_nth_job_result_id( local_job_id );
} else {
core::Size const num_results_for_node2 = node_managers_[ 2 ]->results_to_keep().size();
core::Size const result_index = local_job_id - num_results_for_node1;
if( result_index > num_results_for_node2 ){
return 0;
}
parent_result = node_managers_[ 2 ]->get_nth_job_result_id( result_index );
}
job_genealogist_->register_new_job(
3,
global_job_id,
node_of_parent,
parent_result
);
core::Size const pose_input_source_id = job_genealogist_->input_source_for_job( 3, global_job_id );
jd3::standard::StandardInnerLarvalJobOP inner_ljob =
create_and_init_inner_larval_job( 1, pose_input_source_id );
LarvalJobOP ljob = utility::pointer::make_shared< LarvalJob >(
inner_ljob, 1, global_job_id );
return ljob;
}
JobOP
TutorialQueen::complete_larval_job_maturation(
LarvalJobCOP job,
utility::options::OptionCollectionCOP job_options,
utility::vector1< JobResultCOP > const & input_job_results
) {
if ( num_input_structs_ == 0 ) {
initial_job_dag();
}
standard::StandardInnerLarvalJobCOP standard_inner_larval_job
= utility::pointer::static_pointer_cast< const standard::StandardInnerLarvalJob >( job->inner_job() );
core::Size const global_job_id = job->job_index();
moves::MoverOP mover = 0;
core::scoring::ScoreFunctionOP sfxn = core::scoring::ScoreFunctionFactory::create_score_function( "ref2015.wts" );
core::pose::PoseOP pose = 0;
if( global_job_id <= node_managers_[ 1 ]->num_jobs() ){
//This job belongs to node 1
//local_job_id = global_job_id;
mover = utility::pointer::make_shared< relax::FastRelax >();
pose = pose_for_inner_job( standard_inner_larval_job );
} else if( global_job_id <= node_managers_[ 1 ]->num_jobs() + node_managers_[ 2 ]->num_jobs() ) {
//alternatively you could have used:
//else if( global_job_id <= node_managers_[ 3 ]->job_offset() )
//This job belongs to node 2
//local_job_id = global_job_id - node_managers_[ 2 ]->job_offset();
mover = utility::pointer::make_shared< minimization_packing::MinPackMover >();
pose = pose_for_inner_job( standard_inner_larval_job );
} else {
//This job belongs to node 3
//local_job_id = global_job_id - node_managers_[ 3 ]->job_offset();
mover = utility::pointer::make_shared< minimization_packing::MinMover >();
//We created this larval job and pose result so we know that there should be exactly 1 result and that result is a standard::PoseJobResult
runtime_assert( input_job_results.size() == 1 );
standard::PoseJobResult const & result1 = static_cast< standard::PoseJobResult const & >( * input_job_results[ 1 ] );
pose = result1.pose()->clone();
runtime_assert( pose );
}
TutorialJobOP tjob = utility::pointer::make_shared< TutorialJob >();
tjob->set_pose( pose );
tjob->set_sfxn( sfxn );
tjob->set_mover( mover );
return tjob;
}
} //tutorial
} //protocols