buf fix for scale always

ayresdl · Nov 14, 2018 · 8b8b03e · 8b8b03e
1 parent e859dd3
commit 8b8b03e
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Showing 3 changed files with 7 additions and 4 deletions.
diff --git a/examples/mcmc-nucleotide-medium.nex b/examples/mcmc-nucleotide-medium.nex
@@ -26,7 +26,7 @@ charset 3rd_pos = 3-18792\3;
 partition by_codon = 3:1st_pos,2nd_pos,3rd_pos;
 [partition by_codon = 10:1st_pos,2nd_pos,3rd_pos,4th_pos,5th_pos,6th_pos,7th_pos,8th_pos,9th_pos,10th_pos;]
 
-[set partition=by_codon;]
+set partition=by_codon;
 
 lset applyto=(all) nst=6 rates=invgamma;
 
@@ -47,6 +47,6 @@ set seed=1 swapseed=1;
 
 [mcmc ngen=50000 nruns=1 nchains=1;]
 [mcmc ngen=492 nruns=1 nchains=1 printFreq=1;]
-mcmc ngen=5000 nruns=1 nchains=1 printFreq=1000;
+mcmc ngen=1 nruns=1 nchains=1 printFreq=1000;
 
 end;
diff --git a/src/bayes.h b/src/bayes.h
@@ -32,7 +32,7 @@
 
 #if defined (BEAGLE_ENABLED)
 #include "libhmsbeagle/beagle.h"
-#define BEAGLE_LEVELPASS_ENABLED /* define to send operations to BEAGLE in reverse level order */
+#undef BEAGLE_LEVELPASS_ENABLED /* define to send operations to BEAGLE in reverse level order */
 #endif
 
 /* uncomment the following line when releasing, also modify the VERSION_NUMBER below */

diff --git a/src/mbbeagle.c b/src/mbbeagle.c
@@ -188,6 +188,10 @@ int createBeagleInstance(ModelInfo *m, int nCijkParts, int numGammaCats, int num
     preferredFlags = beagleFlags;
     requiredFlags = 0L;
 
+    if (beagleScalingScheme == MB_BEAGLE_SCALE_ALWAYS) {
+        requiredFlags |= BEAGLE_FLAG_SCALERS_LOG; //BEAGLE_FLAG_SCALERS_RAW;
+        }
+
     if (beagleResourceNumber >= 0 && beagleResourceNumber != 99)
         {
         resource = beagleResourceNumber;
@@ -212,7 +216,6 @@ int createBeagleInstance(ModelInfo *m, int nCijkParts, int numGammaCats, int num
 
         long benchmarkFlags = BEAGLE_BENCHFLAG_SCALING_NONE;
         if (beagleScalingScheme == MB_BEAGLE_SCALE_ALWAYS) {
-            requiredFlags |= BEAGLE_FLAG_SCALERS_LOG; //BEAGLE_FLAG_SCALERS_RAW;
             benchmarkFlags = BEAGLE_BENCHFLAG_SCALING_ALWAYS;
         } else if (beagleScalingScheme == MB_BEAGLE_SCALE_DYNAMIC) {
             benchmarkFlags = BEAGLE_BENCHFLAG_SCALING_DYNAMIC;