Commit b667924b authored by Leonardo Solis's avatar Leonardo Solis
Browse files

minor corrections

parent b0bfd045
......@@ -211,11 +211,11 @@ test: odock
ASTEX_PDB := 2bsm
ASTEX_NRUN:= 100
ASTEX_POPSIZE := 150
ASTEX_POPSIZE := 500
ASTEX_TESTNAME := test_astex
astex: odock
$(BIN_DIR)/$(TARGET) -ffile ./input_tsri/search-set-astex/$(ASTEX_PDB)/protein.maps.fld -lfile ./input_tsri/search-set-astex/$(ASTEX_PDB)/flex-xray.pdbqt -nrun $(ASTEX_NRUN) -psize $(ASTEX_POPSIZE) -resnam $(ASTEX_TESTNAME) -gfpop 0
$(BIN_DIR)/$(TARGET) -ffile ./input_tsri/search-set-astex/$(ASTEX_PDB)/protein.maps.fld -lfile ./input_tsri/search-set-astex/$(ASTEX_PDB)/flex-xray.pdbqt -nrun $(ASTEX_NRUN) -psize $(ASTEX_POPSIZE) -resnam $(ASTEX_TESTNAME) -gfpop 1
# $(BIN_DIR)/$(TARGET) -ffile ./input_tsri/search-set-astex/$(ASTEX_PDB)/protein.maps.fld -lfile ./input_tsri/search-set-astex/$(ASTEX_PDB)/flex-xray.pdbqt -nrun $(ASTEX_NRUN) -psize $(ASTEX_POPSIZE) -resnam $(ASTEX_TESTNAME) -gfpop 1 | tee ./input_tsri/search-set-astex/intrapairs/$(ASTEX_PDB)_intrapair.txt
......
......@@ -58,6 +58,6 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
//#define NATIVE_PRECISION
#define MAPPED_COPY
//#define GRADIENT_ENABLED
#define GRADIENT_ENABLED
#endif /* DEFINES_H_ */
......@@ -78,16 +78,16 @@ gradient_minimizer(
if (get_local_id(0) == 0)
{
// Choosing a random entity out of the entire population
///*
/*
run_id = get_group_id(0);
entity_id = (uint)(dockpars_pop_size * gpu_randf(dockpars_prng_states));
//entity_id = 0;
//*/
//entity_id = (uint)(dockpars_pop_size * gpu_randf(dockpars_prng_states));
entity_id = 0;
*/
/*
///*
run_id = get_group_id(0) / dockpars_num_of_lsentities;
entity_id = get_group_id(0) % dockpars_num_of_lsentities;
*/
//*/
energy = dockpars_energies_next[run_id*dockpars_pop_size+entity_id];
......
......@@ -409,8 +409,8 @@ filled with clock() */
// Setup here (temporarily?) the gradient and associated parameters.
// This should be ultimately configurable by the user as program exec. flags.
Gradientparameters gradientpars;
gradientpars.max_num_of_iters = 100;
gradientpars.max_num_of_consec_fails = gradientpars.max_num_of_iters / 5;
gradientpars.max_num_of_iters = 30;
gradientpars.max_num_of_consec_fails = (unsigned int)(0.05 * gradientpars.max_num_of_iters);
gradientpars.alpha = 0.000001f; //0.001f; // TODO: find out why 0.001f, 0.0001f (100 runs, 500 popsize) throws segmentation fault
// Set minimum values for input conformation (translation genes as x, y, z)
......@@ -434,16 +434,16 @@ filled with clock() */
mallocBufferObject(context, CL_MEM_READ_ONLY, size_conformation_min_perturbation, &mem_gradpars_conformation_min_perturbation);
memcopyBufferObjectToDevice(command_queue, mem_gradpars_conformation_min_perturbation, gradientpars.conformation_min_perturbation, size_conformation_min_perturbation);
/*
///*
// Initially, the number of entities that undergo gradient-minimization,
// by default, it is the same as the number of entities that undergo gradient-based minimizer
blocksPerGridForEachGradMinimizerEntity = dockpars.num_of_lsentities*mypars->num_of_runs;
*/
//*/
///*
/*
// test, only one entity per reach run, undergoes gradient minimization
blocksPerGridForEachGradMinimizerEntity = mypars->num_of_runs;
//*/
*/
clock_start_docking = clock();
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment