Changed optimization settings for FreeRate parameters

Author: stephaneguindon

Makefile

@@ -209,7 +209,7 @@ AUTOMAKE = ${SHELL} '/Users/guindon/phyml/missing' automake-1.16
 AWK = awk
 CC = gcc
 CCDEPMODE = depmode=gcc3
-CFLAGS = -march=native -Wall -std=c99 -g
+CFLAGS = -std=gnu99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native
 CPPFLAGS = 
 CSCOPE = cscope
 CTAGS = ctags

config.log

@@ -4,13 +4,13 @@ running configure, to aid debugging if configure makes a mistake.
 It was created by PhyML configure 3.3.20250429, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
-  $ ./configure --enable-debug --no-create --no-recursion
+  $ ./configure
 
 ## --------- ##
 ## Platform. ##
 ## --------- ##
 
-hostname = Mac
+hostname = guindon.lirmm.fr
 uname -m = arm64
 uname -r = 24.3.0
 uname -s = Darwin
@@ -30,16 +30,12 @@ Kernel configured for up to 8 processors.
 Processor type: arm64e (ARM64E)
 Processors active: 0 1 2 3 4 5 6 7
 Primary memory available: 8.00 gigabytes
-Default processor set: 477 tasks, 2534 threads, 8 processors
-Load average: 2.33, Mach factor: 5.66
+Default processor set: 410 tasks, 2472 threads, 8 processors
+Load average: 3.15, Mach factor: 4.84
 /bin/machine           = unknown
 /usr/bin/oslevel       = unknown
 /bin/universe          = unknown
 
-PATH: /Users/guindon/anaconda3/bin/
-PATH: /Users/guindon/anaconda3/condabin/
-PATH: /Users/guindon/anaconda3/bin/
-PATH: /Users/guindon/anaconda3/bin/
 PATH: /opt/local/bin/
 PATH: /opt/local/sbin/
 PATH: /opt/homebrew/bin/
@@ -57,6 +53,11 @@ PATH: /opt/X11/bin/
 PATH: /Library/Apple/usr/bin/
 PATH: /Library/TeX/texbin/
 PATH: /usr/local/ncbi/blast/bin/
+PATH: /Users/guindon/anaconda3/bin/
+PATH: /Users/guindon/anaconda3/condabin/
+PATH: /opt/local/bin/
+PATH: /opt/local/sbin/
+PATH: /Users/guindon/.vscode/extensions/ms-python.debugpy-2025.6.0-darwin-arm64/bundled/scripts/noConfigScripts/
 
 
 ## ----------- ##
@@ -385,6 +386,31 @@ configure:5248: checking that generated files are newer than configure
 configure:5254: result: done
 configure:5325: creating ./config.status
 
+## ---------------------- ##
+## Running config.status. ##
+## ---------------------- ##
+
+This file was extended by PhyML config.status 3.3.20250429, which was
+generated by GNU Autoconf 2.71.  Invocation command line was
+
+  CONFIG_FILES    = 
+  CONFIG_HEADERS  = 
+  CONFIG_LINKS    = 
+  CONFIG_COMMANDS = 
+  $ ./config.status 
+
+on guindon.lirmm.fr
+
+config.status:899: creating Makefile
+config.status:899: creating src/Makefile
+config.status:899: creating doc/Makefile
+config.status:899: creating config.h
+config.status:1080: config.h is unchanged
+config.status:1128: executing depfiles commands
+config.status:1205: cd src       && sed -e '/# am--include-marker/d' Makefile         | make -f - am--depfiles
+make: Nothing to be done for `am--depfiles'.
+config.status:1210: $? = 0
+
 ## ---------------- ##
 ## Cache variables. ##
 ## ---------------- ##
@@ -465,7 +491,7 @@ AUTOMAKE='${SHELL} '\''/Users/guindon/phyml/missing'\'' automake-1.16'
 AWK='awk'
 CC='gcc'
 CCDEPMODE='depmode=gcc3'
-CFLAGS='-march=native -Wall -std=c99 -g'
+CFLAGS='-std=gnu99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native'
 CPPFLAGS=''
 CSCOPE='cscope'
 CTAGS='ctags'
@@ -617,44 +643,3 @@ target_alias=''
 #define PHYML 1
 
 configure: exit 0
-
-## ---------------------- ##
-## Running config.status. ##
-## ---------------------- ##
-
-This file was extended by PhyML config.status 3.3.20250429, which was
-generated by GNU Autoconf 2.71.  Invocation command line was
-
-  CONFIG_FILES    = 
-  CONFIG_HEADERS  = 
-  CONFIG_LINKS    = 
-  CONFIG_COMMANDS = 
-  $ ./config.status 
-
-on Mac
-
-config.status:899: creating Makefile
-config.status:899: creating src/Makefile
-config.status:899: creating doc/Makefile
-config.status:899: creating config.h
-config.status:1128: executing depfiles commands
-config.status:1205: cd src       && sed -e '/# am--include-marker/d' Makefile         | make -f - am--depfiles
-make[1]: Nothing to be done for `am--depfiles'.
-config.status:1210: $? = 0
-
-## ---------------------- ##
-## Running config.status. ##
-## ---------------------- ##
-
-This file was extended by PhyML config.status 3.3.20250429, which was
-generated by GNU Autoconf 2.71.  Invocation command line was
-
-  CONFIG_FILES    = 
-  CONFIG_HEADERS  = 
-  CONFIG_LINKS    = 
-  CONFIG_COMMANDS = 
-  $ ./config.status config.h
-
-on Mac
-
-config.status:899: creating config.h

config.status

@@ -420,7 +420,7 @@ $config_commands
 
 Report bugs to <stephane.guindon@lirmm.fr>."
 
-ac_cs_config='--enable-debug'
+ac_cs_config=''
 ac_cs_version="\
 PhyML config.status 3.3.20250429
 configured by ./configure, generated by GNU Autoconf 2.71,
@@ -512,7 +512,7 @@ if $ac_cs_silent; then
 fi
 
 if $ac_cs_recheck; then
-  set X /bin/sh './configure'  '--enable-debug' $ac_configure_extra_args --no-create --no-recursion
+  set X /bin/sh './configure'  $ac_configure_extra_args --no-create --no-recursion
   shift
   \printf "%s\n" "running CONFIG_SHELL=/bin/sh $*" >&6
   CONFIG_SHELL='/bin/sh'
@@ -655,7 +655,7 @@ S["EXEEXT"]=""
 S["ac_ct_CC"]="gcc"
 S["CPPFLAGS"]=""
 S["LDFLAGS"]=""
-S["CFLAGS"]="-march=native -Wall -std=c99 -g"
+S["CFLAGS"]="-std=gnu99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native"
 S["CC"]="gcc"
 S["host_os"]="darwin24.3.0"
 S["host_vendor"]="apple"

doc/Makefile

@@ -162,7 +162,7 @@ AUTOMAKE = ${SHELL} '/Users/guindon/phyml/missing' automake-1.16
 AWK = awk
 CC = gcc
 CCDEPMODE = depmode=gcc3
-CFLAGS = -march=native -Wall -std=c99 -g
+CFLAGS = -std=gnu99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native
 CPPFLAGS = 
 CSCOPE = cscope
 CTAGS = ctags

src/Makefile

@@ -638,7 +638,7 @@ AUTOMAKE = ${SHELL} '/Users/guindon/phyml/missing' automake-1.16
 AWK = awk
 CC = gcc
 CCDEPMODE = depmode=gcc3
-CFLAGS = -march=native -Wall -std=c99 -g
+CFLAGS = -std=gnu99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native
 CPPFLAGS = 
 CSCOPE = cscope
 CTAGS = ctags

src/mixt.c

@@ -4291,14 +4291,14 @@ void MIXT_Kfold_Pos_Cv(t_tree *mixt_tree)
   weights     = NULL;
   tree        = NULL;
 
-  // kfold          = 5;
-  kfold          = 1;
+  kfold          = 5;
+  // kfold          = 1;
   n_prob_vectors = 0;
 
   do
   {
-    // for (int i = 0; i < kfold*5; ++i)
-      for (int i = 0; i < kfold * 1; ++i)
+    for (int i = 0; i < kfold*5; ++i)
+      // for (int i = 0; i < kfold * 1; ++i)
       {
         // Create a copy of the original alignment
         c_seq_cpy = Copy_Cseq(mixt_tree->data, mixt_tree->io, mixt_tree);

src/optimiz.c

@@ -3102,8 +3102,6 @@ void Optimize_Free_Rate(t_tree *mixt_tree, int verbose)
   phydbl lk_before, lk_after;
   tree = mixt_tree;
 
-  /* PhyML_Printf("\n. Optimizing Free_Rate --> %f",mixt_tree->next->a_edges[0]->l->v); */
-
   lk_before = lk_after = UNLIKELY;
 
   do
@@ -3119,7 +3117,27 @@ void Optimize_Free_Rate(t_tree *mixt_tree, int verbose)
               Optimize_Free_Rate_Rr(tree,fast,verbose);
               lk_after = mixt_tree->c_lnL;
 
-              if(lk_after < lk_before - tree->mod->s_opt->min_diff_lk_global)
+
+              if (lk_after < lk_before - tree->mod->s_opt->min_diff_lk_global)
+              {
+                PhyML_Fprintf(stderr, "\n. lk_before: %f lk_after: %f diff: %G",
+                              lk_before, lk_after, lk_before - lk_after);
+                PhyML_Fprintf(stderr, "\n. Err. in file %s at line %d\n",
+                              __FILE__, __LINE__);
+                Exit("");
+              }
+            }        
+          else
+            {
+                fast = YES;
+                lk_before = mixt_tree->c_lnL;
+                Optimize_Free_Rate_Weights(tree,fast,verbose);
+                lk_after = mixt_tree->c_lnL;
+                Optimize_Free_Rate_Rr(tree,fast,verbose);
+                lk_after = mixt_tree->c_lnL;
+
+
+                if (lk_after < lk_before - tree->mod->s_opt->min_diff_lk_global)
                 {
                   PhyML_Fprintf(stderr,"\n. lk_before: %f lk_after: %f diff: %G",lk_before,lk_after,lk_before-lk_after);
                   PhyML_Fprintf(stderr,"\n. Err. in file %s at line %d\n",__FILE__,__LINE__);
@@ -3230,8 +3248,10 @@ void Optimize_Free_Rate_Rr(t_tree *tree, int fast, int verbose)
         {
           phydbl a,c;
 
-          a = tree->mod->ras->gamma_rr_unscaled->v[i] - 2.0;
-          c = tree->mod->ras->gamma_rr_unscaled->v[i] + 2.0;
+          // a = tree->mod->ras->gamma_rr_unscaled->v[i] - 2.0;
+          // c = tree->mod->ras->gamma_rr_unscaled->v[i] + 2.0;
+          a = - 2.0;
+          c = + 2.0;
 
           Generic_Brent_Lk(&(tree->mod->ras->gamma_rr_unscaled->v[i]),
                            a,c,
@@ -3258,8 +3278,10 @@ void Optimize_Free_Rate_Rr(t_tree *tree, int fast, int verbose)
         {
           phydbl a,c;
 
-          a = tree->mod->ras->gamma_rr_unscaled->v[i] - 2.0;
-          c = tree->mod->ras->gamma_rr_unscaled->v[i] + 2.0;
+          // a = tree->mod->ras->gamma_rr_unscaled->v[i] - 2.0;
+          // c = tree->mod->ras->gamma_rr_unscaled->v[i] + 2.0;
+          a = - 2.0;
+          c = + 2.0;
 
           Generic_Brent_Lk(&(tree->mod->ras->gamma_rr_unscaled->v[i]),
                            a,c,
@@ -3302,8 +3324,10 @@ void Optimize_Free_Rate_Weights(t_tree *tree, int fast, int verbose)
     {
       phydbl a,c;
 
-      a = tree->mod->ras->gamma_r_proba_unscaled->v[i] - 2.0;
-      c = tree->mod->ras->gamma_r_proba_unscaled->v[i] + 2.0;
+      // a = tree->mod->ras->gamma_r_proba_unscaled->v[i] - 2.0;
+      // c = tree->mod->ras->gamma_r_proba_unscaled->v[i] + 2.0;
+      a = - 2.0;
+      c = + 2.0;
 
       Generic_Brent_Lk(&(tree->mod->ras->gamma_r_proba_unscaled->v[i]),
                        a,c,
@@ -3312,6 +3336,7 @@ void Optimize_Free_Rate_Weights(t_tree *tree, int fast, int verbose)
                        tree->mod->s_opt->quickdirty,
                        Wrap_Lk,NULL,tree,NULL,NO,NO);      
 
+
       if(fast == YES)
         {
           wm = Weighted_Mean(tree->mod->ras->gamma_rr->v,