A BG/Q compatible version (can be cross-compiled with XL compiler)

BayesTest.cpp

@@ -547,14 +547,14 @@ double MfgBayesTest::getGridParams(const std::vector<double> &aVars,
     }
 
 // Fill the matrices and compute their eigendecomposition.
-//#ifdef _MSC_VER
-//#pragma omp parallel sections default(none) shared(                            \
+#ifdef _MSC_VER
+#pragma omp parallel sections default(none) shared(                            \
     omega_fg, omega_bg, kappa, q_fg, q_bg, omega_fg_is_one, omega_bg_is_one)
-//#else
-//#pragma omp parallel sections default(shared)
-//#endif
+#else
+#pragma omp parallel sections default(shared)
+#endif
     {
-//#pragma omp section
+#pragma omp section
       {
         if (omega_fg_is_one)
           q_fg.fillMatrix(kappa);
@@ -563,7 +563,7 @@ double MfgBayesTest::getGridParams(const std::vector<double> &aVars,
 
         q_fg.eigenQREV();
       }
-//#pragma omp section
+#pragma omp section
       {
         if (omega_bg_is_one)
           q_bg.fillMatrix(kappa);

CMakeLists.txt

@@ -193,9 +193,4 @@ target_link_libraries(fast ${EXTRA_LIBS})
 
 if(MPI_LIBRARY)
 	target_link_libraries(fast ${MPI_LIBRARY})
-endif(MPI_LIBRARY)
-
-
-
-
-add_subdirectory(bad_cases)
\ No newline at end of file
+endif(MPI_LIBRARY)
\ No newline at end of file

Forest.cpp

@@ -906,16 +906,16 @@ void Forest::computeLikelihoods(const mfgProbabilityMatrixSet &aSet,
     const int len = static_cast<int>(ivs->size());
     const unsigned int *tmp_ivs = &(*ivs)[0];
 
-//#ifdef _MSC_VER
-//#pragma omp parallel for default(none) shared(aSet, len, tmp_ivs, tmp_roots,   \
+#ifdef _MSC_VER
+#pragma omp parallel for default(none) shared(aSet, len, tmp_ivs, tmp_roots,   \
                                               likelihoods) schedule(static)
-//#else
-//#pragma omp parallel for default(shared)
-//#endif
+#else
+#pragma omp parallel for default(shared)
+#endif
     for (int i = 0; i < len; ++i) {
-//#ifndef _MSC_VER
-//#pragma omp task untied
-//#endif
+#ifndef _MSC_VER
+#pragma omp task untied
+#endif
       {
         // Compute likelihood array at the root of one tree (the access order is
         // the fastest)

MathSupport.h

@@ -44,8 +44,8 @@ inline void SetSeedCodeml(int seed, int PrintSeed) {
       seed = 1234567891 * (int)time(NULL) + 1;
     }
 
-    seed = abs(seed);
-
+   //seed = abs(seed);
+   if (seed < 0) seed=-seed;
     // if(PrintSeed) {
     // fseed = fopen("SeedUsed", "w");
     // if(fseed == NULL) std::cout << "can't open file SeedUsed.";
@@ -73,7 +73,12 @@ inline double rndu2Codeml(void) {
   // 32-bit integer assumed.
   // From Ripley (1987) table 2.4 line 4.
 
-  w_rndu = abs(w_rndu * 16807) % 2147483647;
+  //w_rndu = abs(w_rndu * 16807) % 2147483647;
+  if (w_rndu >= 0)
+    w_rndu = (w_rndu * 16807) % 2147483647;
+  else
+    w_rndu = ((-w_rndu) * 16807) % 2147483647;
+    
   if (w_rndu == 0)
     w_rndu = 13;
   return w_rndu / 2147483647.0;

SETPATHS

@@ -13,10 +13,10 @@
 # 2) BG /Q
   export BLAS_LIB_DIR="/bgsys/local/lib64;/opt/ibmcmp/xlf/bg/14.1/lib64"
   export LAPACK_LIB_DIR="/bgsys/local/lib64;/opt/ibmcmp/xlf/bg/14.1/lib64"
-  export NLOPT_LIB_DIR="/home/kali/FastCodeML-1.2.0/FCM-10.06.2014/nlopt-release/lib"
-  export NLOPT_INCLUDE_DIR="/home/kali/FastCodeML-1.2.0/FCM-10.06.2014/nlopt-release/include"
+  export NLOPT_LIB_DIR="/home/shahmirz/lib"
+  export NLOPT_INCLUDE_DIR="/home/shahmirz/include"
   export MATH_LIB_NAMES="esslbg;lapack;m;xlf90_r;xl;xlfmath;esslbg;dl"
-  export BOOST_ROOT="/home/kali/FastCodeML-1.2.0/FCM-10.06.2014/boost-release"
+  export BOOST_ROOT="/bgsys/local/boost/1_59_0"
   export INCLUDE_DIR_MKL="/bgsys/ibm_essl/prod/opt/ibmmath/essl/5.1/include"
   export CXX="/bgsys/drivers/ppcfloor/comm/xl/bin/mpixlcxx"
   export CXXFLAGS="-qstrict -qthreaded -qhalt=e -D_BGQ_COMPILER"