Changes:
1. Added TRISTATE_CORRECTION in pairhmm-template-kernel.cc (function stripINITIALIZATION) 2. Added VEC_DIV macros to define-double.h and define-float.h 3. Edited initializeVectors to match Java C++ original: *(ptr_p_MY+r-1) = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_d]; *(ptr_p_YY+r-1) = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_c]; Modified: *(ptr_p_MY+r-1) = ctx.ph2pr[_d]; *(ptr_p_YY+r-1) = ctx.ph2pr[_c];
This commit is contained in:
Karthik Gururaj
parent
5fab96b7ee
commit
8240ea826e
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@ -4,3 +4,5 @@
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tests
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.deps
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hmm_Mohammad
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pairhmm-template-main
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*.swp
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19
Makefile
19
Makefile
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@ -1,4 +1,4 @@
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#OMPCFLAGS=-fopenmp
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OMPCFLAGS=-fopenmp
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#OMPLDFLAGS=-lgomp
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#CFLAGS=-O2 -std=c++11 -W -Wall -march=corei7-avx -Wa,-q -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas
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@ -7,7 +7,7 @@
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JAVA_ROOT=/opt/jdk1.7.0_25/
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JNI_COMPILATION_FLAGS=-D_REENTRANT -fPIC -I${JAVA_ROOT}/include -I${JAVA_ROOT}/include/linux
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CFLAGS=-g -W -Wall -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas -xAVX
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CFLAGS=-O3 -W -Wall -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas -xAVX
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CXXFLAGS=$(CFLAGS)
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CC=icc
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@ -16,11 +16,12 @@ CXX=icc
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LDFLAGS=-lm $(OMPLDFLAGS)
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#BIN:=pairhmm-1-base #pairhmm-2-omp pairhmm-3-hybrid-float-double pairhmm-4-hybrid-diagonal pairhmm-5-hybrid-diagonal-homogeneus pairhmm-6-onlythreediags pairhmm-7-presse pairhmm-8-sse #pairhmm-dev
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BIN:=libJNILoglessPairHMM.so #pairhmm-2-omp pairhmm-3-hybrid-float-double pairhmm-4-hybrid-diagonal pairhmm-5-hybrid-diagonal-homogeneus pairhmm-6-onlythreediags pairhmm-7-presse pairhmm-8-sse #pairhmm-dev
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BIN:=libJNILoglessPairHMM.so pairhmm-template-main
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#SOURCES=pairhmm-1-base.cc input.cc
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SOURCES=org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc hmm_mask.cc
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OBJECTS=$(SOURCES:.cc=.o)
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LIBSOURCES=org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc hmm_mask.cc
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SOURCES=$(LIBSOURCES) pairhmm-template-main.cc
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LIBOBJECTS=$(LIBSOURCES:.cc=.o)
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DEPDIR=.deps
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DF=$(DEPDIR)/$(*).d
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@ -28,11 +29,11 @@ all: $(BIN)
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-include $(addprefix $(DEPDIR)/,$(SOURCES:.cc=.d))
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pairhmm-1-base: pairhmm-1-base.o input.o
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$(CXX) -o $@ $^ $(LDFLAGS)
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pairhmm-template-main: pairhmm-template-main.o hmm_mask.o
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$(CXX) -fopenmp -o $@ $^ $(LDFLAGS)
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libJNILoglessPairHMM.so: $(OBJECTS)
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$(CXX) -shared -o libJNILoglessPairHMM.so $(OBJECTS)
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libJNILoglessPairHMM.so: $(LIBOBJECTS)
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$(CXX) -shared -o $@ $(LIBOBJECTS)
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%.o: %.cc
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@mkdir -p $(DEPDIR)
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@ -23,6 +23,7 @@
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#undef VEC_ADD
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#undef VEC_SUB
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#undef VEC_MUL
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#undef VEC_DIV
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#undef VEC_BLEND
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#undef VEC_BLENDV
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#undef VEC_CAST_256_128
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@ -82,6 +83,9 @@
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#define VEC_MUL(__v1, __v2) \
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_mm256_mul_pd(__v1, __v2)
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#define VEC_DIV(__v1, __v2) \
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_mm256_div_pd(__v1, __v2)
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#define VEC_BLEND(__v1, __v2, __mask) \
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_mm256_blend_pd(__v1, __v2, __mask)
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@ -23,6 +23,7 @@
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#undef VEC_ADD(__v1, __v2)
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#undef VEC_SUB(__v1, __v2)
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#undef VEC_MUL(__v1, __v2)
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#undef VEC_DIV(__v1, __v2)
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#undef VEC_BLEND(__v1, __v2, __mask)
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#undef VEC_BLENDV(__v1, __v2, __maskV)
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#undef VEC_CAST_256_128(__v1)
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@ -83,6 +84,9 @@
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#define VEC_MUL(__v1, __v2) \
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_mm256_mul_ps(__v1, __v2)
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#define VEC_DIV(__v1, __v2) \
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_mm256_div_ps(__v1, __v2)
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#define VEC_BLEND(__v1, __v2, __mask) \
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_mm256_blend_ps(__v1, __v2, __mask)
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@ -438,7 +438,7 @@ void test_mask_computations (testcase& tc, int tcID, bool printDebug=false) {
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//cout << "Finished validating entry " << endl ;
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}
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#ifdef HMM_MASK_MAIN
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int main () {
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#define BATCH_SIZE 10000
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@ -482,3 +482,4 @@ int main () {
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return 0 ;
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}
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#endif
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@ -15,6 +15,10 @@
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#include <immintrin.h>
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#include <emmintrin.h>
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#include <omp.h>
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using namespace std;
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//#define DEBUG3 1
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#define DEBUG 1
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#include "template.h"
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@ -22,7 +26,6 @@
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#include "shift_template.c"
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#include "pairhmm-template-kernel.cc"
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using namespace std;
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#define MM 0
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@ -32,22 +35,17 @@ using namespace std;
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#define MY 4
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#define YY 5
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//#define DEBUG3 1
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#define DEBUG 1
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template<class T>
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string to_string(T obj)
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class LoadTimeInitializer
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{
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stringstream ss;
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string ret_string;
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ss.clear();
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ss << std::scientific << obj;
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ss >> ret_string;
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ss.clear();
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return ret_string;
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}
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public:
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LoadTimeInitializer() //will be called when library is loaded
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{
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ConvertChar::init();
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}
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};
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LoadTimeInitializer g_load_time_initializer;
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void debug_dump(string filename, string s, bool to_append, bool add_newline=true)
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void debug_dump(string filename, string s, bool to_append, bool add_newline)
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{
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ofstream fptr;
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fptr.open(filename.c_str(), to_append ? ofstream::app : ofstream::out);
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@ -157,8 +157,18 @@ template<class NUMBER> void GEN_INTRINSIC(initializeVectors, PRECISION)(int ROWS
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*(ptr_p_GAPM+r-1) = ctx._(1.0) - ctx.ph2pr[_c];
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*(ptr_p_MX+r-1) = ctx.ph2pr[_i];
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*(ptr_p_XX+r-1) = ctx.ph2pr[_c];
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*(ptr_p_MY+r-1) = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_d];
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*(ptr_p_YY+r-1) = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_c];
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*(ptr_p_MY+r-1) = ctx.ph2pr[_d];
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*(ptr_p_YY+r-1) = ctx.ph2pr[_c];
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#ifdef DEBUG3
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debug_dump("transitions_jni.txt",to_string(*(ptr_p_MM+r-1) ),true);
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debug_dump("transitions_jni.txt",to_string(*(ptr_p_GAPM+r-1)),true);
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debug_dump("transitions_jni.txt",to_string(*(ptr_p_MX+r-1) ),true);
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debug_dump("transitions_jni.txt",to_string(*(ptr_p_XX+r-1) ),true);
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debug_dump("transitions_jni.txt",to_string(*(ptr_p_MY+r-1) ),true);
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debug_dump("transitions_jni.txt",to_string(*(ptr_p_YY+r-1) ),true);
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#endif
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//*(ptr_p_MY+r-1) = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_d];
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//*(ptr_p_YY+r-1) = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_c];
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}
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NUMBER *ptr_distm1D = (NUMBER *)distm1D;
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@ -166,6 +176,9 @@ template<class NUMBER> void GEN_INTRINSIC(initializeVectors, PRECISION)(int ROWS
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{
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int _q = tc->q[r-1] & 127;
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ptr_distm1D[r-1] = ctx.ph2pr[_q];
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#ifdef DEBUG3
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debug_dump("priors_jni.txt",to_string(ptr_distm1D[r-1]),true);
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#endif
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}
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}
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@ -187,13 +200,18 @@ template<class NUMBER> inline void GEN_INTRINSIC(stripINITIALIZATION, PRECISION)
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NUMBER zero = ctx._(0.0);
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NUMBER init_Y = ctx.INITIAL_CONSTANT / (tc->haplen);
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UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0);
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#define TRISTATE_CORRECTION_FACTOR 3.0
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UNION_TYPE packed3; packed3.d = VEC_SET1_VAL(TRISTATE_CORRECTION_FACTOR);
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/* compare rs and N */
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//rs = VEC_LDPOPCVT_CHAR((tc->irs+i*AVX_LENGTH));
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//rsN.d = VEC_CMP_EQ(N_packed256, rs);
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distm = distm1D[i];
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_1_distm = VEC_SUB(packed1.d, distm);
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_1_distm = VEC_SUB(packed1.d, distm);
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#ifndef DO_NOT_USE_TRISTATE_CORRECTION
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distm = VEC_DIV(distm, packed3.d);
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#endif
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/* initialize M_t_2, M_t_1, X_t_2, X_t_1, Y_t_2, Y_t_1 */
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M_t_2.d = VEC_SET1_VAL(zero);
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@ -16,7 +16,7 @@
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#define BATCH_SIZE 10000
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//#define RUN_HYBRID
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uint8_t ConvertChar::conversionTable[255] ;
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//uint8_t ConvertChar::conversionTable[255] ;
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int thread_level_parallelism_enabled = false ;
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double getCurrClk() {
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15
template.h
15
template.h
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@ -13,6 +13,7 @@
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#include <immintrin.h>
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#include <ctype.h>
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#include <string>
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#define MROWS 500
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#define MCOLS 1000
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@ -132,6 +133,20 @@ typedef struct
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int *irs;
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} testcase;
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template<class T>
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std::string to_string(T obj)
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{
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stringstream ss;
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string ret_string;
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ss.clear();
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ss << std::scientific << obj;
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ss >> ret_string;
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ss.clear();
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return ret_string;
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}
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void debug_dump(std::string filename, std::string s, bool to_append, bool add_newline=true);
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int normalize(char c);
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