BundlePairRmsdCalculatorGPU.cc File Reference

#include <protocols/sewing/BundlePairRmsdWorkUnit.hh>
#include <basic/gpu/GPU.hh>
#include <basic/gpu/Timer.hh>
#include <core/pose/util.hh>
#include <devel/init.hh>
#include <protocols/wum/WorkUnitList.hh>
#include <protocols/wum/WorkUnitManager.hh>
#include <protocols/wum/MPI_WorkUnitManager_Slave.hh>
#include <basic/database/schema_generator/PrimaryKey.hh>
#include <basic/database/schema_generator/ForeignKey.hh>
#include <basic/database/schema_generator/Column.hh>
#include <basic/database/schema_generator/Schema.hh>
#include <basic/database/sql_utils.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/wum.OptionKeys.gen.hh>
#include <basic/options/keys/inout.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <utility/mpi_util.hh>
#include <cstdio>
#include <numeric/xyzVector.hh>
#include <numeric/model_quality/rms.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <core/import_pose/import_pose.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <utility/sql_database/DatabaseSessionManager.hh>
#include <utility/string_util.hh>

Classes
struct	gpu_node_block_ptrs
struct	node_data
struct	calculation_data_for_one_block_pair

Namespaces
	BundlePairRmsdCalculator

Typedefs
typedef std::map< core::Size, utility::vector1< numeric::xyzVector< core::Real > > >	helix_coord_map
typedef std::map< core::Size, utility::vector1< core::Size > >	bundle_helices_map
typedef std::map< core::Size, bool >	helix_flipped_map

Functions
std::vector< std::string >	gpu_rmsd_programs ()
void	create_node_comparison_table (utility::sql_database::sessionOP db_session)
void	load_coordinates_from_database (utility::sql_database::sessionOP db_session, helix_coord_map &helix_coords, bundle_helices_map &bundle_helices, helix_flipped_map &helix_flipped)
void	ship_coordinates_to_gpu (basic::gpu::GPU &gpu, helix_coord_map const &helix_coords, bundle_helices_map const &bundle_helices, utility::vector1< node_data > &ndat, core::Size blockid, gpu_node_block_ptrs &block_ptrs)
void	compute_rms_and_clash_score_for_block_pair (basic::gpu::GPU &gpu, utility::vector1< node_data > const &ndat, core::Size const block1, core::Size const block2, gpu_node_block_ptrs const &block1ptrs, gpu_node_block_ptrs const &block2ptrs, float maximum_rmsd_tolerance, float minimum_square_distance_tolerance, calculation_data_for_one_block_pair &bpd)
void	retrieve_rms_and_clash_scores_from_gpu (basic::gpu::GPU &gpu, calculation_data_for_one_block_pair &bpd)
void	compare_gpu_result_against_cpu (helix_coord_map &helix_coords, bundle_helices_map &bundle_helices, helix_flipped_map &helix_flipped, utility::vector1< node_data > const &ndat, core::Size block1, core::Size block2, float maximum_rmsd_tolerance, float minimum_square_distance_tolerance, calculation_data_for_one_block_pair const &bpd)
void	feed_rms_and_clash_scores_to_database (utility::sql_database::sessionOP db_session, utility::vector1< node_data > const &ndat, core::Size block1, core::Size block2, calculation_data_for_one_block_pair const &bpd)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("BundlePairRmsdCalculator")
static int	BLOCK_SIZE = 512
basic::options::RealOptionKey const	BundlePairRmsdCalculator::max_rmsd ("max_rmsd")

Typedef Documentation

bundle_helices_map

typedef std::map<core::Size, utility::vector1< core::Size > > bundle_helices_map

helix_coord_map

typedef std::map<core::Size, utility::vector1< numeric::xyzVector<core::Real> > > helix_coord_map

helix_flipped_map

typedef std::map<core::Size, bool > helix_flipped_map

Function Documentation

compare_gpu_result_against_cpu()

void compare_gpu_result_against_cpu	(	helix_coord_map &	helix_coords,
		bundle_helices_map &	bundle_helices,
		helix_flipped_map &	helix_flipped,
		utility::vector1< node_data > const &	ndat,
		core::Size	block1,
		core::Size	block2,
		float	maximum_rmsd_tolerance,
		float	minimum_square_distance_tolerance,
		calculation_data_for_one_block_pair const &	bpd
	)

References ObjexxFCL::abs(), BLOCK_SIZE, numeric::model_quality::calc_rms_fast(), calculation_data_for_one_block_pair::clash_data, count, utility::io::oc::cout, numeric::xyzVector< T >::distance_squared(), test.T009_Exceptions::e, numeric::model_quality::findUU(), calculation_data_for_one_block_pair::good_node_pairs, create_a3b_hbs::i, create_a3b_hbs::ii, enumerate_junctions::int, create_a3b_hbs::j, beta_nonlocal::jj, create_a3b_hbs::k, kk, beta_nonlocal::mm, calculation_data_for_one_block_pair::n_good_node_pairs, ObjexxFCL::pow(), reverse(), calculation_data_for_one_block_pair::rms_data, runtime_assert, and erraser_analysis::temp.

compute_rms_and_clash_score_for_block_pair()

void compute_rms_and_clash_score_for_block_pair	(	basic::gpu::GPU &	gpu,
		utility::vector1< node_data > const &	ndat,
		core::Size const	block1,
		core::Size const	block2,
		gpu_node_block_ptrs const &	block1ptrs,
		gpu_node_block_ptrs const &	block2ptrs,
		float	maximum_rmsd_tolerance,
		float	minimum_square_distance_tolerance,
		calculation_data_for_one_block_pair &	bpd
	)

References BLOCK_SIZE, gpu_node_block_ptrs::comparison_coord_ind_list, gpu_node_block_ptrs::comparison_coord_ind_offset, gpu_node_block_ptrs::coords_for_col_calc, gpu_node_block_ptrs::coords_for_col_calc_offset, gpu_node_block_ptrs::coords_for_rms_calc, gpu_node_block_ptrs::d_bundle_ids, calculation_data_for_one_block_pair::d_calculate_pair_table, calculation_data_for_one_block_pair::d_clash_table, calculation_data_for_one_block_pair::d_good_node_pairs, calculation_data_for_one_block_pair::d_n_good_node_pairs, calculation_data_for_one_block_pair::d_rmsd_table, gpu_node_block_ptrs::n_comparison_coords, gpu_node_block_ptrs::n_coords_for_col_calc, calculation_data_for_one_block_pair::n_good_node_pairs, calculation_data_for_one_block_pair::read_n_good_node_pairs_event, gpu_node_block_ptrs::rms_coords_moment_of_inertia, and utility_exit_with_message.

Referenced by main().

create_node_comparison_table()

void create_node_comparison_table

(

utility::sql_database::sessionOP

db_session

)

References basic::database::schema_generator::Schema::add_column(), clash_score(), average_rmsds::rmsd, and basic::database::schema_generator::Schema::write().

Referenced by main().

feed_rms_and_clash_scores_to_database()

void feed_rms_and_clash_scores_to_database	(	utility::sql_database::sessionOP	db_session,
		utility::vector1< node_data > const &	ndat,
		core::Size	block1,
		core::Size	block2,
		calculation_data_for_one_block_pair const &	bpd
	)

References BLOCK_SIZE, calculation_data_for_one_block_pair::clash_data, utility::io::oc::cout, calculation_data_for_one_block_pair::good_node_pairs, create_a3b_hbs::ii, calculation_data_for_one_block_pair::n_good_node_pairs, calculation_data_for_one_block_pair::rms_data, basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), and utility_exit_with_message.

Referenced by main().

gpu_rmsd_programs()

std::vector< std::string > gpu_rmsd_programs

(

)

Referenced by main().

load_coordinates_from_database()

void load_coordinates_from_database	(	utility::sql_database::sessionOP	db_session,
		helix_coord_map &	helix_coords,
		bundle_helices_map &	bundle_helices,
		helix_flipped_map &	helix_flipped
	)

References begin, end, detail::find(), basic::options::OptionKeys::ddg::legacy, basic::options::option, basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), TR, x, predPRE::y, and predPRE::z.

Referenced by main().

main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, BLOCK_SIZE, utility::io::oc::cerr, compute_rms_and_clash_score_for_block_pair(), utility::io::oc::cout, create_node_comparison_table(), gpu_set_args::done, feed_rms_and_clash_scores_to_database(), run_backbone::float, basic::database::get_db_session(), basic::options::OptionKeys::gpu::gpu, gpu_rmsd_programs(), create_a3b_hbs::ii, basic::init(), beta_nonlocal::jj, basic::options::OptionKeys::ddg::legacy, load_coordinates_from_database(), max(), BundlePairRmsdCalculator::max_rmsd, utility::mpi_nprocs(), utility::mpi_rank(), basic::options::OptionKeys::legacy_sewing::num_procs, basic::options::option, option, retrieve_rms_and_clash_scores_from_gpu(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), ship_coordinates_to_gpu(), basic::database::schema_generator::TR, utility_exit_with_message, and basic::options::OptionKeys::wum::wum.

retrieve_rms_and_clash_scores_from_gpu()

void retrieve_rms_and_clash_scores_from_gpu	(	basic::gpu::GPU &	gpu,
		calculation_data_for_one_block_pair &	bpd
	)

References calculation_data_for_one_block_pair::clash_data, calculation_data_for_one_block_pair::d_clash_table, calculation_data_for_one_block_pair::d_good_node_pairs, calculation_data_for_one_block_pair::d_rmsd_table, calculation_data_for_one_block_pair::good_node_pairs, calculation_data_for_one_block_pair::n_good_node_pairs, calculation_data_for_one_block_pair::rms_data, and utility_exit_with_message.

Referenced by main().

ship_coordinates_to_gpu()

void ship_coordinates_to_gpu	(	basic::gpu::GPU &	gpu,
		helix_coord_map const &	helix_coords,
		bundle_helices_map const &	bundle_helices,
		utility::vector1< node_data > &	ndat,
		core::Size	blockid,
		gpu_node_block_ptrs &	block_ptrs
	)

References BLOCK_SIZE, gpu_node_block_ptrs::comparison_coord_ind_list, gpu_node_block_ptrs::comparison_coord_ind_offset, gpu_node_block_ptrs::coords_for_col_calc, gpu_node_block_ptrs::coords_for_col_calc_offset, gpu_node_block_ptrs::coords_for_rms_calc, gpu_node_block_ptrs::d_bundle_ids, create_a3b_hbs::ii, beta_nonlocal::jj, kk, gpu_node_block_ptrs::n_comparison_coords, gpu_node_block_ptrs::n_coords_for_col_calc, gpu_node_block_ptrs::rms_coords_moment_of_inertia, utility::to_string(), and utility_exit_with_message.

Referenced by main().

Variable Documentation

BLOCK_SIZE

int BLOCK_SIZE = 512

static

Referenced by compare_gpu_result_against_cpu(), compute_rms_and_clash_score_for_block_pair(), feed_rms_and_clash_scores_to_database(), main(), and ship_coordinates_to_gpu().

TR

basic::Tracer TR("BundlePairRmsdCalculator") ( "BundlePairRmsdCalculator"  )

static

Author

Tim Jacobs

Referenced by load_coordinates_from_database().