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1. Moved break statement in utils.cc to correct position 

2. Tested sandbox with regions
3. Lots of profiling code from previous commit exists
This commit is contained in:
Karthik Gururaj 2014-02-06 09:32:56 -08:00
parent acda6ca27b
commit 78642944c0
4 changed files with 36 additions and 32 deletions
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3
public/c++/VectorPairHMM/LoadTimeInitializer.cc
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@ -10,6 +10,9 @@ LoadTimeInitializer::LoadTimeInitializer() //will be called when library is loa
#ifndef DISABLE_FTZ #ifndef DISABLE_FTZ
//Very important to get good performance - enable FTZ, converts denormals to 0 //Very important to get good performance - enable FTZ, converts denormals to 0
_MM_SET_FLUSH_ZERO_MODE(_MM_FLUSH_ZERO_ON); _MM_SET_FLUSH_ZERO_MODE(_MM_FLUSH_ZERO_ON);
cout << "FTZ enabled - may decrease accuracy if denormal numbers encountered\n";
#else
cout << "FTZ is not set - may slow down performance if denormal numbers encountered\n";
#endif #endif
m_sumNumReads = 0; m_sumNumReads = 0;
m_sumSquareNumReads = 0; m_sumSquareNumReads = 0;

4
public/c++/VectorPairHMM/Sandbox.java
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@ -272,7 +272,7 @@ public class Sandbox {
//System.err.println(e); //System.err.println(e);
//} //}
Sandbox t = new Sandbox(); Sandbox t = new Sandbox();
t.doEverythingNative(args[0]); //t.doEverythingNative(args[0]);
//t.parseSandboxFile(args[0]); t.parseSandboxFile(args[0]);
} }
} }

7
public/c++/VectorPairHMM/pairhmm-1-base.cc
View File

@ -9,14 +9,14 @@ using namespace std;
int main(int argc, char** argv) int main(int argc, char** argv)
{ {
#define BATCH_SIZE 5 #define BATCH_SIZE 10000
if(argc < 2) if(argc < 2)
{ {
cerr << "Needs path to input file as argument\n"; cerr << "Needs path to input file as argument\n";
exit(0); exit(0);
} }
do_compute(argv[1]); do_compute(argv[1]);
#if 0 return 0;
bool use_old_read_testcase = false; bool use_old_read_testcase = false;
if(argc >= 3 && string(argv[2]) == "1") if(argc >= 3 && string(argv[2]) == "1")
use_old_read_testcase = true; use_old_read_testcase = true;
@ -56,7 +56,6 @@ int main(int argc, char** argv)
testcase tc_in; testcase tc_in;
int break_value = 0; int break_value = 0;
tc_vector.clear(); tc_vector.clear();
g_load_time_initializer.open_sandbox();
while(1) while(1)
{ {
break_value = use_old_read_testcase ? read_testcase(&tc_in, fptr) : break_value = use_old_read_testcase ? read_testcase(&tc_in, fptr) :
@ -144,8 +143,6 @@ int main(int argc, char** argv)
fclose(fptr); fclose(fptr);
else else
ifptr.close(); ifptr.close();
g_load_time_initializer.close_sandbox();
#endif
return 0; return 0;
} }

20
public/c++/VectorPairHMM/utils.cc
View File

@ -79,9 +79,13 @@ int read_testcase(testcase *tc, FILE* ifp)
int x, size = 0; int x, size = 0;
ssize_t read; ssize_t read;
read = getline(&line, (size_t *) &size, ifp == 0 ? stdin : ifp); read = getline(&line, (size_t *) &size, ifp == 0 ? stdin : ifp);
if (read == -1) if (read == -1)
{
free(line);
return -1; return -1;
}
tc->hap = (char *) malloc(size); tc->hap = (char *) malloc(size);
@ -326,7 +330,7 @@ void do_compute(char* filename)
long long accum_values[NUM_PAPI_COUNTERS] = { 0, 0, 0, 0 }; long long accum_values[NUM_PAPI_COUNTERS] = { 0, 0, 0, 0 };
#endif #endif
#define BATCH_SIZE 100000 #define BATCH_SIZE 10000
bool use_old_read_testcase = true; bool use_old_read_testcase = true;
unsigned chunk_size = 100; unsigned chunk_size = 100;
std::ifstream ifptr; std::ifstream ifptr;
@ -459,12 +463,12 @@ void do_compute(char* filename)
#endif #endif
for(unsigned i=0;i<num_testcases;++i) for(unsigned i=0;i<num_testcases;++i)
{ {
delete tc_vector[i].rs; free(tc_vector[i].rs);
delete tc_vector[i].hap; free(tc_vector[i].hap);
delete tc_vector[i].q; free(tc_vector[i].q);
delete tc_vector[i].i; free(tc_vector[i].i);
delete tc_vector[i].d; free(tc_vector[i].d);
delete tc_vector[i].c; free(tc_vector[i].c);
} }
total_count += num_testcases; total_count += num_testcases;
num_testcases = 0; num_testcases = 0;
@ -473,10 +477,10 @@ void do_compute(char* filename)
results_vec.clear(); results_vec.clear();
//curr_batch_size = rand()%BATCH_SIZE + 4; //min batch size //curr_batch_size = rand()%BATCH_SIZE + 4; //min batch size
curr_batch_size = BATCH_SIZE; curr_batch_size = BATCH_SIZE;
}
if(break_value < 0) if(break_value < 0)
break; break;
} }
}
baseline_results.clear(); baseline_results.clear();
results_vec.clear(); results_vec.clear();