zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Minor: added support in C++ sandbox to choose implementation and check 

from command line
This commit is contained in:
Karthik Gururaj 2014-02-09 18:05:35 -08:00
parent a03d83579b
commit d081c19178
3 changed files with 46 additions and 31 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

26
public/c++/VectorPairHMM/pairhmm-1-base.cc
View File

@ -18,10 +18,28 @@ int main(int argc, char** argv)
if(argc >= 3 && string(argv[2]) == "1")
use_old_read_testcase = true;
unsigned chunk_size = 10000;
if(argc >= 4)
chunk_size = strtol(argv[3],0,10);
do_compute(argv[1], use_old_read_testcase, chunk_size);
bool do_check = true;
uint64_t mask = ~(0ull);
for(int i=3;i<argc;++i)
{
if(strncmp(argv[i], "-chunk_size", 15) == 0)
{
++i;
chunk_size = strtol(argv[i],0,10);
}
else
if(strncmp(argv[i], "-mask", 15) == 0)
{
++i;
mask = strtoll(argv[i],0,16);
}
else
if(strncmp(argv[i], "-no-check", 15) == 0)
do_check = false;
}
if(mask != (~0ull))
initialize_function_pointers(mask);
do_compute(argv[1], use_old_read_testcase, chunk_size, do_check);
return 0;
}

49
public/c++/VectorPairHMM/utils.cc
View File

@ -68,7 +68,7 @@ void initialize_function_pointers(uint64_t mask)
g_compute_full_prob_double = compute_full_prob_avxd<double>;
}
else
if(is_sse41_supported() && (mask & (1<< SSE41_CUSTOM_IDX)))
if(is_sse41_supported() && (mask & ((1<< SSE41_CUSTOM_IDX) | (1<<SSE42_CUSTOM_IDX))))
{
cout << "Using SSE4.1 accelerated implementation of PairHMM\n";
g_compute_full_prob_float = compute_full_prob_sses<float>;
@ -299,10 +299,9 @@ uint64_t diff_time(struct timespec& prev_time)
}
//#define DUMP_COMPUTE_VALUES 1
#define CHECK_VALUES 1
#define BATCH_SIZE 10000
#define RUN_HYBRID
void do_compute(char* filename, bool use_old_read_testcase, unsigned chunk_size)
void do_compute(char* filename, bool use_old_read_testcase, unsigned chunk_size, bool do_check)
{
FILE* fptr = 0;
ifstream ifptr;
@ -322,10 +321,7 @@ void do_compute(char* filename, bool use_old_read_testcase, unsigned chunk_size)
uint64_t vector_compute_time = 0;
uint64_t baseline_compute_time = 0;
uint64_t num_double_calls = 0;
bool all_ok = true;
#ifndef CHECK_VALUES
all_ok = false;
#endif
bool all_ok = do_check ? true : false;
while(1)
{
int break_value = use_old_read_testcase ? read_testcase(&tc, fptr) : read_mod_testcase(ifptr,&tc,true);
@ -360,29 +356,30 @@ void do_compute(char* filename, bool use_old_read_testcase, unsigned chunk_size)
results_vec[i] = result;
}
vector_compute_time += diff_time(start_time);
#ifdef CHECK_VALUES
get_time(&start_time);
if(do_check)
{
get_time(&start_time);
#pragma omp parallel for schedule(dynamic,chunk_size)
for(unsigned i=0;i<tc_vector.size();++i)
{
testcase& tc = tc_vector[i];
double baseline_result = compute_full_prob<double>(&tc);
baseline_result = log10(baseline_result) - log10(ldexp(1.0, 1020.0));
baseline_results_vec[i] = baseline_result;
}
baseline_compute_time += diff_time(start_time);
for(unsigned i=0;i<tc_vector.size();++i)
{
double baseline_result = baseline_results_vec[i];
double abs_error = fabs(baseline_result-results_vec[i]);
double rel_error = (baseline_result != 0) ? fabs(abs_error/baseline_result) : 0;
if(abs_error > 1e-5 && rel_error > 1e-5)
for(unsigned i=0;i<tc_vector.size();++i)
{
cout << std::scientific << baseline_result << " "<<results_vec[i]<<"\n";
all_ok = false;
testcase& tc = tc_vector[i];
double baseline_result = compute_full_prob<double>(&tc);
baseline_result = log10(baseline_result) - log10(ldexp(1.0, 1020.0));
baseline_results_vec[i] = baseline_result;
}
baseline_compute_time += diff_time(start_time);
for(unsigned i=0;i<tc_vector.size();++i)
{
double baseline_result = baseline_results_vec[i];
double abs_error = fabs(baseline_result-results_vec[i]);
double rel_error = (baseline_result != 0) ? fabs(abs_error/baseline_result) : 0;
if(abs_error > 1e-5 && rel_error > 1e-5)
{
cout << std::scientific << baseline_result << " "<<results_vec[i]<<"\n";
all_ok = false;
}
}
}
#endif
for(unsigned i=0;i<tc_vector.size();++i)
{
delete tc_vector[i].rs;

2
public/c++/VectorPairHMM/utils.h
View File

@ -39,5 +39,5 @@ enum ProcessorCapabilitiesEnum
#define ENABLE_ALL_HARDWARE_FEATURES 0xFFFFFFFFFFFFFFFFull
uint64_t get_machine_capabilities();
void initialize_function_pointers(uint64_t mask=ENABLE_ALL_HARDWARE_FEATURES);
void do_compute(char* filename, bool use_old_read_testcase=true, unsigned chunk_size=10000);
void do_compute(char* filename, bool use_old_read_testcase=true, unsigned chunk_size=10000, bool do_check=true);
#endif