[Genabel-commits] r1851 - pkg/OmicABELnoMM/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Oct 27 18:02:36 CET 2014
Author: lckarssen
Date: 2014-10-27 18:02:35 +0100 (Mon, 27 Oct 2014)
New Revision: 1851
Modified:
pkg/OmicABELnoMM/tests/test.cpp
Log:
Cleanup of the code layout of OmicABELnoMM's test.cpp. Code is now (almost?) compliant with our coding style.
No functional changes.
Modified: pkg/OmicABELnoMM/tests/test.cpp
===================================================================
--- pkg/OmicABELnoMM/tests/test.cpp 2014-10-27 16:07:09 UTC (rev 1850)
+++ pkg/OmicABELnoMM/tests/test.cpp 2014-10-27 17:02:35 UTC (rev 1851)
@@ -27,57 +27,82 @@
cout << "\nTotal Results: \t" << out.total_sig_results << endl;
- cout << "\nDuration:\t\t" << out.duration <<" \t"<< out.duration/out.duration*100 << "\n";
+ cout << "\nDuration:\t\t" << out.duration << " \t"
+ << out.duration/out.duration * 100 << "\n";
double missing = (out.duration - (out.acc_loady+out.acc_loadxr
- +out.acc_real_innerloops+out.acc_gemm+out.acc_scorrect));
+ + out.acc_real_innerloops
+ + out.acc_gemm + out.acc_scorrect));
- cout << "Missing Sec:\t\t" << missing <<" \t"<< missing/out.duration*100 << "\n";
+ cout << "Missing Sec:\t\t" << missing << " \t"
+ << missing/out.duration * 100 << "\n";
- missing = (out.acc_real_innerloops - (out.acc_solve+out.acc_sbr +out.acc_stl+out.acc_str+out.acc_other+out.acc_stats+out.acc_storeb+out.acc_inner_scorrect));
+ missing = (out.acc_real_innerloops -
+ (out.acc_solve + out.acc_sbr + out.acc_stl + out.acc_str
+ + out.acc_other + out.acc_stats + out.acc_storeb
+ + out.acc_inner_scorrect));
+
cout << endl;
- cout << "GEMM Sec:\t\t" << out.acc_gemm <<" \t"<< out.acc_gemm/out.duration*100 << "\n";
- cout << "SGenCorr Sec:\t\t" << out.acc_scorrect <<"\t"<< out.acc_scorrect/out.duration*100 << "\n";
+ cout << "GEMM Sec:\t\t" << out.acc_gemm << " \t" <<
+ out.acc_gemm/out.duration * 100 << "\n";
+ cout << "SGenCorr Sec:\t\t" << out.acc_scorrect << "\t"
+ << out.acc_scorrect/out.duration * 100 << "\n";
- cout << "InnerLoops Sec:\t" << out.acc_real_innerloops <<" \t"<< out.acc_real_innerloops/out.duration*100 << "\n";
- cout << "Stl Sec:\t\t" << out.acc_stl <<" \t"<< out.acc_stl/out.duration*100 << "\n";
- cout << "Str Sec:\t\t" << out.acc_str <<"\t"<< out.acc_str/out.duration*100 << "\n";
- cout << "Sbr Sec:\t\t" << out.acc_sbr <<"\t"<< out.acc_sbr/out.duration*100 << "\n";
- cout << "Solve Sec:\t\t" << out.acc_solve <<" \t"<< out.acc_solve/out.duration*100 << "\n";
- cout << "Other Sec:\t\t" << out.acc_other <<" \t"<< out.acc_other/out.duration*100 << "\n";
- cout << "Stats Sec:\t\t" << out.acc_stats <<"\t"<< out.acc_stats/out.duration*100 << "\n";
- cout << "SCorr Sec:\t\t" << out.acc_inner_scorrect <<"\t"<< out.acc_inner_scorrect/out.duration*100 << "\n";
+ cout << "InnerLoops Sec:\t" << out.acc_real_innerloops << " \t"
+ << out.acc_real_innerloops/out.duration * 100 << "\n";
+ cout << "Stl Sec:\t\t" << out.acc_stl << " \t"
+ << out.acc_stl/out.duration * 100 << "\n";
+ cout << "Str Sec:\t\t" << out.acc_str << "\t"
+ << out.acc_str/out.duration * 100 << "\n";
+ cout << "Sbr Sec:\t\t" << out.acc_sbr << "\t"
+ << out.acc_sbr/out.duration * 100 << "\n";
+ cout << "Solve Sec:\t\t" << out.acc_solve << " \t"
+ << out.acc_solve/out.duration * 100 << "\n";
+ cout << "Other Sec:\t\t" << out.acc_other << " \t"
+ << out.acc_other/out.duration * 100 << "\n";
+ cout << "Stats Sec:\t\t" << out.acc_stats << "\t"
+ << out.acc_stats/out.duration * 100 << "\n";
+ cout << "SCorr Sec:\t\t" << out.acc_inner_scorrect << "\t"
+ << out.acc_inner_scorrect/out.duration * 100 << "\n";
- cout << "Missing Sec:\t\t" << missing <<"\t"<< missing/out.duration*100 << "\n";
+ cout << "Missing Sec:\t\t" << missing << "\t"
+ << missing/out.duration * 100 << "\n";
- //cout << "RQy Sec:\t" << out.acc_real_innerloops-out.acc_gemm <<" \t"<< (out.acc_real_innerloops-out.acc_gemm)/out.duration*100 << "\n";
+ // cout << "RQy Sec:\t" << out.acc_real_innerloops-out.acc_gemm
+ // << " \t" << (out.acc_real_innerloops-out.acc_gemm)
+ // / out.duration * 100 << "\n";
cout << endl;
- cout << "Betas Sec:\t\t" << out.acc_storeb <<" \t"<< out.acc_storeb/out.duration*100 << "\n";
- cout << "LoadXR Sec:\t\t" << out.acc_loadxr <<" \t"<< out.acc_loadxr/out.duration*100 << "\n";
- cout << "LoadY Sec:\t\t" << out.acc_loady <<" \t"<< out.acc_loady/out.duration*100 << "\n";
- //cout << endl;
-// cout << "FirstXR Sec:\t" << out.acc_firstAR <<" \t"<< out.acc_firstAR/out.duration*100 << "\n";
-// cout << "FirstY Sec:\t" << out.acc_firstY <<" \t"<< out.acc_firstY/out.duration*100 << "\n";
- //cout << endl;
+ cout << "Betas Sec:\t\t" << out.acc_storeb << " \t"
+ << out.acc_storeb/out.duration * 100 << "\n";
+ cout << "LoadXR Sec:\t\t" << out.acc_loadxr << " \t"
+ << out.acc_loadxr/out.duration * 100 << "\n";
+ cout << "LoadY Sec:\t\t" << out.acc_loady << " \t"
+ << out.acc_loady/out.duration * 100 << "\n";
+ // cout << endl;
+ // cout << "FirstXR Sec:\t" << out.acc_firstAR << " \t"
+ // << out.acc_firstAR/out.duration * 100 << "\n";
+ // cout << "FirstY Sec:\t" << out.acc_firstY << " \t"
+ // << out.acc_firstY/out.duration * 100 << "\n";
+ // cout << endl;
-// cout << "Real StoreB Sec:\t" << out.acc_real_storeb <<" \t"<< out.acc_real_storeb/out.duration*100 << "\n";
-// cout << "Real LoadXR Sec:\t" << out.acc_real_loadxr <<" \t"<< out.acc_real_loadxr/out.duration*100 << "\n";
-// cout << "Real LoadY Sec:\t" << out.acc_real_loady <<" \t"<< out.acc_real_loady/out.duration*100 << "\n";
+ // cout << "Real StoreB Sec:\t" << out.acc_real_storeb << " \t"
+ // << out.acc_real_storeb/out.duration * 100 << "\n";
+ // cout << "Real LoadXR Sec:\t" << out.acc_real_loadxr << " \t"
+ // << out.acc_real_loadxr/out.duration * 100 << "\n";
+ // cout << "Real LoadY Sec:\t" << out.acc_real_loady << " \t"
+ // << out.acc_real_loady/out.duration * 100 << "\n";
- cout << endl<< "Duration:"<< out.duration << endl;
- cout << endl<< "GFLOPS:"<< out.gflops << endl;
+ cout << endl << "Duration:" << out.duration << endl;
+ cout << endl << "GFLOPS:" << out.gflops << endl;
cout << "GFLOPS/s: " << (out.gflops/out.duration) << endl;
- cout <<"Perf: " << (out.gflops/out.duration)/gemm_gflopsPsec << endl ;
+ cout << "Perf: " << (out.gflops/out.duration)/gemm_gflopsPsec << endl;
+}
-
-
-}
-
-int main(int argc, char *argv[] )
+int main(int argc, char *argv[])
{
struct Settings params;
@@ -94,10 +119,6 @@
Algorithm alg;
-
-
-
-
int max_threads = 1;
params.threads = max_threads;
@@ -108,23 +129,24 @@
cout << "Perfromance Test\n" << flush;
double duration, gemmgflops, gemm_gflopsPsec;
- cpu_benchmark((1024.0),5,duration,gemmgflops);
+ cpu_benchmark((1024.0), 5, duration, gemmgflops);
gemm_gflopsPsec = gemmgflops/duration;
cout << "\nGEMM GFLOPS/s " << gemm_gflopsPsec << endl;
struct Outputs out = {0};
// params.use_fake_files = false;
-// !default params
-// alg.applyDefaultParams(params);
- //int factor = 0;//need to repair fakefiles?
-// params.n=2000; params.l=3; params.r=1;
-// params.t=1000; params.tb=min(1000,params.t); params.m=1000; params.mb=min(200,params.m);
-// print_params(params);
-// alg.solve(params, out, P_NEQ_B_OPT_MD);
-// print_output(out, gemm_gflopsPsec);
-//
-//
-// cout << "\nDone\n";
+ // !default params
+ // alg.applyDefaultParams(params);
+ // int factor = 0;//need to repair fakefiles?
+ // params.n=2000; params.l=3; params.r=1;
+ // params.t=1000; params.tb=min(1000, params.t); params.m=1000;
+ // params.mb=min(200, params.m);
+ // print_params(params);
+ // alg.solve(params, out, P_NEQ_B_OPT_MD);
+ // print_output(out, gemm_gflopsPsec);
+ //
+ //
+ // cout << "\nDone\n";
//!-------------------------------------
@@ -143,12 +165,13 @@
params.r = 2;
- params.fnameOutFiles="examples/results/normal";
- params.fnameAL="examples/XL";
- params.fnameAR="examples/XR";
- params.fnameY="examples/Y";
+ params.fnameOutFiles = "examples/results/normal";
+ params.fnameAL = "examples/XL";
+ params.fnameAR = "examples/XR";
+ params.fnameY = "examples/Y";
- params.limit_t = 1000;params.limit_m = params.limit_t *params.r;
+ params.limit_t = 1000;
+ params.limit_m = params.limit_t * params.r;
alg.solve(params, out, P_NEQ_B_OPT_MD);
print_output(out, gemm_gflopsPsec);
@@ -156,92 +179,120 @@
//!MPI
MPI_Finalize();
- //exit(0);
+ // exit(0);
- cout << "\nInteraction Tests\n" << flush;
+ cout << "\nInteraction Tests\n" << flush;
//!-------------------------------------
//!-------------------------------------
//!interactions
- params.fnameOutFiles="examples/results/normal";
- params.fnameAL="examples/interactions/XL";
- params.fnameAR="examples/interactions/XR";
- params.fnameY="examples/interactions/Y";
+ params.fnameOutFiles = "examples/results/normal";
+ params.fnameAL = "examples/interactions/XL";
+ params.fnameAR = "examples/interactions/XR";
+ params.fnameY = "examples/interactions/Y";
- params.use_interactions=true;params.r = 2;
- params.limit_t = 50;params.limit_m = params.limit_t *params.r;
- //params.limit_n = 1000;
- params.fname_excludelist="examples/exclude_individuals.txt";
+ params.use_interactions = true;
+ params.r = 2;
+ params.limit_t = 50;
+ params.limit_m = params.limit_t * params.r;
+ // params.limit_n = 1000;
+ params.fname_excludelist = "examples/exclude_individuals.txt";
string source_path = "examples/interactions/INT";
- string out_path[] = {"examples/results/single_inter_","examples/results/multi_inter_"};
- string out_keep[] = {"","keep_"};
- string dosagename[]={"","add_","dom_","res_","mylin_","myadd_"};
- int dosage_r[]={1,2,2,2,1,2};
+ string out_path[] = {"examples/results/single_inter_",
+ "examples/results/multi_inter_"};
+ string out_keep[] = {"", "keep_"};
+ string dosagename[] = {"", "add_", "dom_", "res_", "mylin_", "myadd_"};
+ int dosage_r[] = {1, 2, 2, 2, 1, 2};
//!--------------No Model-----------------------
- string test_names[] = {"0","1","R","R1","R0","10", "11", "011", "1RR"};
- string keep_test_names[] = {"R","R0", "RR"};
- uint32_t exected_res_single[] = {0,(uint32_t)params.limit_t,0,(uint32_t)params.limit_t,0,0,0,0,(uint32_t)params.limit_t};
- uint32_t exected_res_mult[] = {0,(uint32_t)params.limit_t,0,(uint32_t)params.limit_t,0,(uint32_t)params.limit_t,2*(uint32_t)params.limit_t,(uint32_t)2*params.limit_t,(uint32_t)params.limit_t};
- uint32_t exected_res_single_keep[] = {(uint32_t)params.limit_t,0,(uint32_t)params.limit_t};
- uint32_t exected_res_mult_keep[] = {(uint32_t)params.limit_t,(uint32_t)params.limit_t,(uint32_t)2*params.limit_t};
+ string test_names[] = {"0", "1", "R", "R1", "R0", "10", "11", "011", "1RR"};
+ string keep_test_names[] = {"R", "R0", "RR"};
+ uint32_t exected_res_single[] = {0, (uint32_t)params.limit_t, 0,
+ (uint32_t)params.limit_t, 0, 0, 0,
+ 0, (uint32_t)params.limit_t};
+ uint32_t exected_res_mult[] = {0, (uint32_t)params.limit_t, 0,
+ (uint32_t)params.limit_t, 0,
+ (uint32_t)params.limit_t,
+ 2 *(uint32_t)params.limit_t,
+ (uint32_t)2 *params.limit_t,
+ (uint32_t)params.limit_t};
+ uint32_t exected_res_single_keep[] = {(uint32_t)params.limit_t, 0,
+ (uint32_t)params.limit_t};
+ uint32_t exected_res_mult_keep[] = {(uint32_t)params.limit_t,
+ (uint32_t)params.limit_t,
+ (uint32_t)2 *params.limit_t};
- for(int j = 0; j < 2; j++ )
+ for (int j = 0; j < 2; j++ )
{
- params.use_multiple_interaction_sets=j;
- for(int k = 0; k < 2; k++ )
+ params.use_multiple_interaction_sets = j;
+ for (int k = 0; k < 2; k++)
{
- params.keep_depVar=k;
- for(int d = 0; d < 6; d++ )
+ params.keep_depVar = k;
+ for (int d = 0; d < 6; d++)
{
params.dosages = d;
- params.model = d-1;
+ params.model = d - 1;
params.r=dosage_r[d];
params.fname_dosages = "examples/dosages_";
params.fname_dosages += std::to_string(params.r);
params.fname_dosages += ".txt";
- if(params.keep_depVar)
+ if (params.keep_depVar)
{
-
- for(int i = 0; i < 3; i++ )
+ for (int i = 0; i < 3; i++ )
{
- params.fnameOutFiles=out_path[j]+out_keep[k]+dosagename[d]+keep_test_names[i];
+ params.fnameOutFiles = out_path[j] +
+ out_keep[k] + dosagename[d] + keep_test_names[i];
cout << params.fnameOutFiles << endl;
- params.fname_interactions=source_path+keep_test_names[i];
+ params.fname_interactions = source_path +
+ keep_test_names[i];
memset(&out, 0, sizeof(out));
alg.solve(params, out, P_NEQ_B_OPT_MD);
- cout << "\nTotal Results: \t" << out.total_sig_results << endl;
+ cout << "\nTotal Results: \t"
+ << out.total_sig_results << endl;
cout << "=========================================\n";
- if(d!=3)
+ if (d != 3)
{
- if(j==0)
- myassert(exected_res_single_keep[i] <= out.total_sig_results,"Unexpected number of Results, check manually!");
+ if (j == 0)
+ {
+ myassert(exected_res_single_keep[i] <=
+ out.total_sig_results,
+ "Unexpected number of Results, check manually!");
+ }
else
- myassert(exected_res_mult_keep[i] <= out.total_sig_results,"Unexpected number of Results, check manually!");
+ {
+ myassert(exected_res_mult_keep[i] <=
+ out.total_sig_results,
+ "Unexpected number of Results, check manually!");
+ }
}
}
-
}
else
{
- for(int i = 0; i < 9; i++ )
+ for (int i = 0; i < 9; i++ )
{
//cout << "=========================================\n";
- params.fnameOutFiles=out_path[j]+out_keep[k]+dosagename[d]+test_names[i];
+ params.fnameOutFiles=out_path[j] + out_keep[k] +
+ dosagename[d] + test_names[i];
cout << params.fnameOutFiles << endl;
- params.fname_interactions=source_path+test_names[i];
+ params.fname_interactions=source_path + test_names[i];
memset(&out, 0, sizeof(out));
alg.solve(params, out, P_NEQ_B_OPT_MD);
- cout << "\nTotal Results: \t" << out.total_sig_results << endl;
+ cout << "\nTotal Results: \t"
+ << out.total_sig_results << endl;
cout << "=========================================\n";
- if(d!=3)
+ if (d != 3)
{
- if(j==0)
- myassert(exected_res_single[i] <= out.total_sig_results,"Unexpected number of Results, check manually!");
+ if (j == 0)
+ myassert(exected_res_single[i] <=
+ out.total_sig_results,
+ "Unexpected number of Results, check manually!");
else
- myassert(exected_res_mult[i] <= out.total_sig_results,"Unexpected number of Results, check manually!");
+ myassert(exected_res_mult[i] <=
+ out.total_sig_results,
+ "Unexpected number of Results, check manually!");
}
}
}
@@ -250,7 +301,6 @@
cout << "===============KEEP=============\n";
}
cout << "==================MULTI=========================\n";
-
}
//!-------------------------------------
//!interactions END
@@ -260,24 +310,25 @@
//!-------------------------------------
//!dosages alone
//!-------------------------------------
- string out_dos_path[] = {"examples/results/dosages_","examples/results/dosages_excl_"};
+ string out_dos_path[] = {"examples/results/dosages_",
+ "examples/results/dosages_excl_"};
- for(int j = 0; j < 2; j++ )
+ for (int j = 0; j < 2; j++)
{
- params.fname_excludelist="";
- if(j)
- params.fname_excludelist="examples/exclude_individuals.txt";
+ params.fname_excludelist = "";
+ if (j)
+ params.fname_excludelist = "examples/exclude_individuals.txt";
- for(int d = 0; d < 6; d++ )
+ for (int d = 0; d < 6; d++)
{
params.dosages = d;
params.model = d-1;
- params.r=dosage_r[d];
+ params.r = dosage_r[d];
params.fname_dosages = "examples/dosages_";
params.fname_dosages += std::to_string(params.r);
params.fname_dosages += ".txt";
- params.fnameOutFiles=out_dos_path[j]+dosagename[d];
+ params.fnameOutFiles = out_dos_path[j] + dosagename[d];
cout << params.fnameOutFiles << endl;
memset(&out, 0, sizeof(out));
@@ -285,11 +336,11 @@
cout << "\nTotal Results: \t" << out.total_sig_results << endl;
cout << "=========================================\n";
- if(d!=3)
+ if (d != 3)
{
- myassert((uint32_t)params.limit_t <= out.total_sig_results,"Unexpected number of Results, check manually!");
+ myassert((uint32_t)params.limit_t <= out.total_sig_results,
+ "Unexpected number of Results, check manually!");
}
-
}
}
@@ -306,9 +357,8 @@
cout << "Misc tests" << endl;
- for (int th = 1; th < max_threads+1; th++)
+ for (int th = 1; th < max_threads + 1; th++)
{
-
omp_set_num_threads(th);
blas_set_num_threads(th);
params.threads = th;
@@ -356,8 +406,5 @@
cout << "\nTest finished succesfully\n";
-
-
-
return 0;
}
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