changed timing code

TimoLassmann · Mar 16, 2020 · 4dc6103 · 4dc6103
1 parent f31f541
commit 4dc6103
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Showing 11 changed files with 580 additions and 30 deletions.
diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,8 @@
+2020-03-16  Timo Lassmann 
+
+	* version 3.2.3
+	- replaced timing code with code from the easel lib.
+
 2020-02-23  Timo Lassmann
 
 	* version 3.2.2

diff --git a/configure.ac b/configure.ac
@@ -1,13 +1,13 @@
 
-AC_INIT(kalign, 3.2.2)
+AC_INIT(kalign, 3.2.3)
 
 #AC_CONFIG_AUX_DIR([.])
 
 AC_USE_SYSTEM_EXTENSIONS
 AM_INIT_AUTOMAKE
 AC_PROG_CC
 AC_PROG_CXX
-AC_PROG_RANLIB
+#AC_PROG_RANLIB
 AC_PROG_INSTALL
 AM_SILENT_RULES([no])
 
@@ -91,30 +91,38 @@ AC_PROG_INSTALL
 
 AC_CHECK_LIB([m], [sqrt])
 AC_CHECK_LIB([pthread], [main])
-AC_SEARCH_LIBS([clock_gettime],[rt])
+AC_SEARCH_LIBS([clock_gettime],[rt posix])
 
 # Checks for header files.
 AC_CHECK_HEADERS([math.h float.h stdlib.h unistd.h])
 AC_CHECK_HEADERS([sys/time.h])
+
+AC_CHECK_HEADERS([mach/mach.h])
+
 AC_CHECK_HEADERS([limits.h])
 
+
 AC_C_INLINE
+AC_TYPE_SIZE_T
+AC_TYPE_SSIZE_T
+
+AC_TYPE_INT8_T
 AC_TYPE_INT32_T
 AC_TYPE_INT64_T
-AC_TYPE_INT8_T
-AC_TYPE_SIZE_T
+
+AC_TYPE_UINT8_T
 AC_TYPE_UINT16_T
 AC_TYPE_UINT32_T
 AC_TYPE_UINT64_T
-AC_TYPE_UINT8_T
 # Checks for library functions.
 AC_FUNC_MALLOC
 AC_FUNC_REALLOC
 AC_FUNC_STRNLEN
 AC_FUNC_ERROR_AT_LINE
 AC_CHECK_FUNCS([gettimeofday pow realpath sqrt strstr memset])
-
-
+AC_CHECK_FUNCS([clock_gettime])
+AC_CHECK_FUNCS([gethrtime])
+AC_CHECK_FUNCS([gettimeofday])
 
 AC_CANONICAL_HOST
 case $host_os in

diff --git a/src/Makefile.am b/src/Makefile.am
@@ -17,6 +17,8 @@ bin_PROGRAMS = timescorealn kalign
 kalign_SOURCES = run_kalign.c \
 tldevel.h \
 tldevel.c \
+esl_stopwatch.h \
+esl_stopwatch.c \
 rng.h \
 rng.c \
 global.h \
@@ -56,6 +58,8 @@ TESTS = edist alphabet  misc_test bpm_test rstdin_test
 rwaln_SOURCES = \
 tldevel.h \
 tldevel.c \
+esl_stopwatch.h \
+esl_stopwatch.c \
 rwalign.c \
 alphabet.h \
 alphabet.c \
@@ -65,6 +69,8 @@ rwaln_CPPFLAGS = $(AM_CPPFLAGS) -DRWALIGN_TEST
 timescorealn_SOURCES = \
 tldevel.h \
 tldevel.c \
+esl_stopwatch.h \
+esl_stopwatch.c \
 time_and_score_aln.c \
 msa.h \
 parameters.h \
@@ -79,6 +85,8 @@ misc.c
 bpm_test_SOURCES = \
 tldevel.h \
 tldevel.c \
+esl_stopwatch.h \
+esl_stopwatch.c \
 rng.h \
 rng.c \
 bpm.h \
@@ -109,6 +117,8 @@ alphabet_CPPFLAGS = $(AM_CPPFLAGS) -DITEST_ALPHABET
 edist_SOURCES = \
 tldevel.h \
 tldevel.c \
+esl_stopwatch.h \
+esl_stopwatch.c \
 rng.h \
 rng.c \
 euclidean_dist.h \

diff --git a/src/bisectingKmeans.c b/src/bisectingKmeans.c
@@ -30,7 +30,7 @@
 
 #include "alignment.h"
 #include "pick_anchor.h"
-
+#include "esl_stopwatch.h"
 struct node{
         struct node* left;
         struct node* right;
@@ -90,8 +90,8 @@ int build_tree_kmeans(struct msa* msa, struct aln_param* ap)
         RUNP(dm = d_estimation(msa, anchors, num_anchors,0));//les,int pair)
 
         STOP_TIMER(timer);
-
-        LOG_MSG("Done in %f sec.", GET_TIMING(timer));
+        GET_TIMING(timer);
+        //LOG_MSG("Done in %f sec.", GET_TIMING(timer));
 
         MFREE(anchors);
 
@@ -111,8 +111,8 @@ int build_tree_kmeans(struct msa* msa, struct aln_param* ap)
 
         RUNP(root = bisecting_kmeans(msa,root, dm, samples, numseq, num_anchors, numseq, ap->rng));
         STOP_TIMER(timer);
-
-        LOG_MSG("Done in %f sec.", GET_TIMING(timer));
+        GET_TIMING(timer);
+        //LOG_MSG("Done in %f sec.", GET_TIMING(timer));
 
         label_internal(root, numseq);
 
@@ -126,7 +126,7 @@ int build_tree_kmeans(struct msa* msa, struct aln_param* ap)
                 _mm_free(dm[i]);
         }
         MFREE(dm);
-
+        DESTROY_TIMER(timer);
         return OK;
 ERROR:
         return FAIL;

diff --git a/src/bpm.c b/src/bpm.c
@@ -25,6 +25,8 @@
 
 #include "rng.h"
 
+
+
 #ifdef HAVE_AVX2
 #include <immintrin.h>
 
@@ -40,7 +42,9 @@ __m256i bitShiftRight256ymm (__m256i *data, int count);
 /* Below are test functions  */
 #ifdef BPM_UTEST
 
+
 #include "alphabet.h"
+#include "esl_stopwatch.h"
 
 /* Functions needed for the unit test*/
 uint8_t dyn_256(const uint8_t* t,const uint8_t* p,int n,int m);
@@ -177,38 +181,45 @@ int bpm_test(void)
         double dyn_timing;
         double bpm_timing;
         int timing_iter = 100;
-        fprintf(stdout,"Dyn\tAVX\tDYN/AVX\n");
+        //fprintf(stdout,"Dyn\tAVX\tDYN/AVX\n");
         DECLARE_TIMER(t);
+
+        START_TIMER(t);
         for(i = 0; i < 100;i+=10){
                 RUN(mutate_seq(b,len,i,alphabet->L,rng));
-                START_TIMER(t);
+
                 for(j = 0; j < timing_iter;j++){
                         dyn_score = dyn_256(a,b,len,len);
                 }
-                STOP_TIMER(t);
-                dyn_timing = GET_TIMING(t);
+                //dyn_timing = GET_TIMING(t);
+        }
+        STOP_TIMER(t);
+        GET_TIMING(t);
 
+        START_TIMER(t);
+        for(i = 0; i < 100;i+=10){
+                RUN(mutate_seq(b,len,i,alphabet->L,rng));
 
-                START_TIMER(t);
 #ifdef HAVE_AVX2
                 for(j = 0; j < timing_iter;j++){
                         bpm_score = bpm_256(a,b,len,len);
                 }
 #else
                 bpm_score = dyn_score;
 #endif
-                STOP_TIMER(t);
 
-                bpm_timing = GET_TIMING(t);
 
-                ASSERT(dyn_score == bpm_score, "Scores differ: %d %d.",dyn_score, bpm_score);
-                fprintf(stdout,"%f\t%f\t%f\n",dyn_timing,bpm_timing,  dyn_timing / bpm_timing);
+                //ASSERT(dyn_score == bpm_score, "Scores differ: %d %d.",dyn_score, bpm_score);
+                //fprintf(stdout,"%f\t%f\t%f\n",dyn_timing,bpm_timing,  dyn_timing / bpm_timing);
 
                 /* restore seq */
                 for(j = 0;j < len;j++){
                         b[j] = a[j];
                 }
         }
+        STOP_TIMER(t);
+        GET_TIMING(t);
+        DESTROY_TIMER(t);
         MFREE(alphabet);
         MFREE(a);
         MFREE(b);