1.2.0 - BG/Q compatibility (V.Keller, K.Ali)

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@7226 95c5a404-1f88-0410-a6b0-c3f062b6f34a

BUGS

-Parameter optimizers other than "-m 22" are untested and might not converge properly.
+1. Parameter optimizers other than "-m 22" are untested and might not converge properly.
+2. -nt 1 yields results inconsistent with the test case when specified without MPI

BranchSiteModel.h

@@ -74,10 +74,12 @@ protected:
 		  mMaxIterations(aMaxIterations),
 		  mDependencies(aForest, aVerbose),
 		  mNoParallel(aNoParallel),
-		  mSeed(aSeed),
-		  mRelativeError(aRelativeError),
+//		  mSeed(aSeed),
+//		  mRelativeError(aRelativeError),
 		  mFixedBranchLength(aFixedBranchLength),
-		  mBranches(aNumBranches)
+		  mBranches(aNumBranches),
+                  mSeed(aSeed),
+                  mRelativeError(aRelativeError)
 	{
 		setLimits(aNumBranches, static_cast<size_t>(aNumVariables), aFixedBranchLength);
 	}

CHANGELOG

+FastCodeML 1.2.0:
+- (Major) BG/Q compatibility (detail below)
+- (Minor) Removal of -np option (now controlled by -nt), cleanup of std::cout in main.
+---DETAIL
+- BranchSiteModel.cpp
+	> l.52 int to unsigned int
+	> l379-l386 mFixedBranchLength switch logic (uncommitted change).
+- BranchSiteModel.h 
+	> Init order changed
+- CMakeLists.txt
+	> Boost required at 1.55
+- CmdLine.cpp + .h
+	> Removed OPT_FORCE_SERIAL as command line option (replaced with -nt = 1)
+	> Changed init order
+- CompilerHints.h 
+	> Added #defines for __xlC__
+- Forest.cpp + .h 
+	> Formatting + cleaning constructor and mAllBranchesFG member.
+- Genes.cpp 
+	> Formatting output stream.
+- WriteResults.cpp
+	> Output to cout does not compile on BG/Q - commented out.
+- blas.h
+	> _BGQ_COMPILER #defines
+- fast.cpp
+	> Removal of -np option.
+- SETPATHS - example explaining how to set envionment variables per machine.
 FastCodeML 1.1.0:
 - Few corrections to accept pipe character also in sequence names
 - New option to fixed branch lengths (-bl)

CMakeLists.txt

@@ -30,8 +30,8 @@ set(SRCS
 )
 
 
-# Search for Boost version 1.42 minimum
-set(Boost_ADDITIONAL_VERSIONS "1.42" "1.42.0")
+# Search for Boost version 1.55 minimum
+set(Boost_ADDITIONAL_VERSIONS "1.42" "1.42.0" "1.55")
 find_package(Boost 1.42)
 if(Boost_FOUND)
 	include_directories(${Boost_INCLUDE_DIRS})

CmdLine.cpp

@@ -128,7 +128,7 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal)
 		OPT_COMP_TIMES,
 		OPT_TRACE,
 		OPT_NUM_THREADS,
-		OPT_FORCE_SERIAL,
+//		OPT_FORCE_SERIAL,
 		OPT_BRANCH_FROM_FILE,
 		OPT_ONE_HYP_ONLY,
 		OPT_INIT_H0_FROM_H1,
@@ -142,8 +142,7 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal)
 		OPT_CLEAN_DATA,
 		OPT_NO_PRE_STOP,
 		OPT_MAX_ITER,
-		OPT_BRANCH_LENGTH,
-	//	OPT_FG_BRANCHES
+		OPT_BRANCH_LENGTH
 	};
 
 	// Then the definitions of each command line option
@@ -182,8 +181,8 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal)
 		{ OPT_TRACE,			"--trace",				SO_NONE,	"" },
 		{ OPT_NUM_THREADS,		"-nt",					SO_REQ_SEP,	"Number of threads (1 for non parallel execution)" },
 		{ OPT_NUM_THREADS,		"--number-of-threads",	SO_REQ_SEP,	"" },
-		{ OPT_FORCE_SERIAL,		"-np",					SO_NONE,	"Don't use parallel execution" },
-		{ OPT_FORCE_SERIAL,		"--no-parallel",		SO_NONE,	"" },
+		//{ OPT_FORCE_SERIAL,		"-np",					SO_NONE,	"Don't use parallel execution" },
+		//{ OPT_FORCE_SERIAL,		"--no-parallel",		SO_NONE,	"" },
 		{ OPT_BRANCH_FROM_FILE,	"-bf",					SO_NONE,	"Do only the branch marked in the file as foreground branch" },
 		{ OPT_BRANCH_FROM_FILE,	"--branch-from-file",	SO_NONE,	"" },
 		{ OPT_ONE_HYP_ONLY,		"-hy",					SO_REQ_SEP,	"Compute only H0 if 0, H1 if 1" },
@@ -211,9 +210,7 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal)
 		{ OPT_MAX_ITER,			"-mi",					SO_REQ_SEP,	"Maximum number of iterations for the maximizer (default: 10000)" },
 		{ OPT_MAX_ITER,			"--max-iterations",		SO_REQ_SEP,	"" },
         {OPT_BRANCH_LENGTH,      "-bl",                 SO_NONE,    "The length of the brances is fixed"},
-		{OPT_BRANCH_LENGTH,      "--branch-lengths-fixed", SO_NONE,    ""},
-		//{OPT_ALL_BRANCHES,        "-ab",                 SO_NONE,    "Do all the branches as foreground branch (by default it does only the internal branches)"},
-		//{OPT_ALL_BRANCHES,        "--all-branches", SO_NONE,    ""},
+		{OPT_BRANCH_LENGTH,      "--branch-lengths-fixed", SO_NONE,    ""},
 		SO_END_OF_OPTIONS
 	};
 
@@ -316,9 +313,9 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal)
 			mTrace = true;
 			break;
 
-		case OPT_FORCE_SERIAL:
+/*		case OPT_FORCE_SERIAL:
 			mForceSerial = true;
-			break;
+			break;*/
 
 		case OPT_BRANCH_FROM_FILE:
 			mBranchFromFile = true;
@@ -381,17 +378,14 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal)
 
 		case OPT_NUM_THREADS:
             mNumThreads = static_cast<unsigned int>(atoi(args.OptionArg()));
-           if (mNumThreads == 1)
-                mForceSerial = true;
+          /*  if (mNumThreads == 1)
+                mForceSerial = true;*/
             if (mNumThreads <=0) throw FastCodeMLFatal("Invalid number of threads");
 			break;
 
         case OPT_BRANCH_LENGTH:
             mFixedBranchLength = true;
             mBranchLengthsFromFile = true;
-            break;
-        /*case OPT_ALL_BRANCHES:
-            mAllBranchesFG = true;*/
             break;
 		}
 	}

CmdLine.h

@@ -22,7 +22,9 @@ static const unsigned int MAX_ITERATIONS=10000;
 ///
 ///
 class CmdLine
-{
+{
+
+
 public:
 	/// Constructor.
 	///
@@ -60,9 +62,10 @@ public:
 		mInitFromParams(false),
 		mCleanData(false),
 		mStopIfNotLRT(true),
-		mCmdLineImpl(NULL),
-        mFixedBranchLength(false)//,
-     //   mAllBranchesFG(false)
+//		mCmdLineImpl(NULL),
+        	mFixedBranchLength(false),
+                mCmdLineImpl(NULL)
+
 	{}
 
 	/// Destructor.
@@ -80,6 +83,8 @@ public:
 	void parseCmdLine(int aCnt, char **aVal);
 
 
+
+
 public:
 	double			mDeltaValueForGradient;	///< The variable increment to compute gradient (zero means use a hardcoded default value)
 	double			mRelativeError;			///< Relative error to stop maximization
@@ -101,16 +106,17 @@ public:
 	bool			mBranchLengthsFromFile;	///< The initial value of the branch lengths is taken from the phylo tree file
 	bool			mNoMaximization;		///< Only the first step of the likelihood maximization is taken
 	bool			mTrace;					///< Trace the optimization steps
+        unsigned int    	mNumThreads;                    ///< Number of threads (if 1 the parallelization is disabled)
 	bool			mForceSerial;			///< Disable all parallelism
 	bool			mBranchFromFile;		///< Read the foreground branch to use from the phylo tree file (it is marked as #1)
 	bool			mInitH0fromH1;			///< If set starts the H0 computation from the H1 results
 	bool			mInitFromParams;		///< Initialize times from phylo tree and the other from values hardcoded or entered on the command line
 	bool			mCleanData;				///< Remove ambiguous or missing sites from the MSA (genes)
 	bool			mStopIfNotLRT;			///< Stop H0 maximization when LRT cannot be satisfied
-	unsigned int	mNumThreads;			///< Number of threads (if 1 the parallelization is disabled)
-    bool           mFixedBranchLength;     ///<Fixed branch lengths
-   // bool           mAllBranchesFG;  ///<Only internal branches as FG barnches
-
+    	bool          		 mFixedBranchLength;           ///<fixed branch lengths
+
+
+
 private:
 	struct CmdLineImpl;
 	CmdLineImpl* mCmdLineImpl;				///< Implementation so this structure could be used without other modules be aware of its internals

CompilerHints.h

@@ -39,6 +39,15 @@
 #define RESTRICT
 //#define PURE
 
+#elif defined(__xlC__)
+#define ALIGN64
+#define RESTRICT
+
+#elif defined(__xlc__)
+#define ALIGN64
+#define RESTRICT
+
+
 #else
 #warning "Unknown compiler detected"
 #define ALIGN64

Forest.cpp

@@ -285,7 +285,7 @@ bool Forest::getBranchRange(const CmdLine& aCmdLine, size_t& aBranchStart, size_
 	else if(aCmdLine.mBranchStart < UINT_MAX && aCmdLine.mBranchStart >= num_branches)
 	{
 		// Invalid start value, ignoring, do all branches
-		if(aCmdLine.mVerboseLevel >= VERBOSE_INFO_OUTPUT) std::cout << std::endl << "Invalid branch requested. Ignoring" << std::endl;
+		if(aCmdLine.mVerboseLevel >= VERBOSE_INFO_OUTPUT) std::cout << std::endl << "Invalid branch requested. Ignoring" << std::endl; 
 		aBranchStart = 0;
 		aBranchEnd   = num_branches-1;
 	}
@@ -302,7 +302,7 @@ bool Forest::getBranchRange(const CmdLine& aCmdLine, size_t& aBranchStart, size_
 		aBranchStart = static_cast<size_t>(aCmdLine.mBranchStart);
 		if(aCmdLine.mBranchEnd >= num_branches)
 		{
-			if(aCmdLine.mVerboseLevel >= VERBOSE_INFO_OUTPUT) std::cout << std::endl << "Invalid end branch requested. Ignoring" << std::endl;
+			if(aCmdLine.mVerboseLevel >= VERBOSE_INFO_OUTPUT) std::cout << std::endl << "Invalid end branch requested. Ignoring" << std::endl; 
 			aBranchEnd = num_branches-1;
 			if(aBranchStart > 0) do_all = false;
 		}
@@ -622,7 +622,7 @@ void Forest::addAggressiveReduction(ForestNode* aNode)
 
 
 #ifdef NON_RECURSIVE_VISIT
-
+	
 void Forest::prepareNonRecursiveVisit(void)
 {
 	// Clean the list for non-recursive visit to the trees. Clear also the list of respective parents
@@ -673,7 +673,7 @@ void Forest::prepareNonRecursiveVisitWalker(ForestNode* aNode, ForestNode* aPare
 	// Store the nodes in the visit order except the root that should not be visited
 	// Store also the respective parent node
 	if(aParentNode)
-	{
+	{	
 		aVisitList.push_back(aNode);
 		aParentList.push_back(aParentNode);
 	}

Forest.h

@@ -34,12 +34,11 @@ class Forest
 public:
 	/// Constructor
 	///
-	/// @param[in] aVerbose The verbosity level
+	/// @param[in] aVerbose The verbosity level
 	///
-	explicit Forest(unsigned int aVerbose=0/*,
-                    bool aOnlyInternalBranchFG=false*/)
+	explicit Forest(unsigned int aVerbose=0)
 							: mNumSites(0), mCodonFreq(NULL), mInvCodonFreq(NULL), mInv2CodonFreq(NULL),
-							  mNumBranches(0), mNumInternalBranches(0), mMarkedInternalBranch(UINT_MAX), mVerbose(aVerbose)/*, mOnlyInternalBranchFG(aOnlyInternalBranchFG)*/ {}
+							  mNumBranches(0), mNumInternalBranches(0), mMarkedInternalBranch(UINT_MAX), mVerbose(aVerbose) {}
 
 	/// Destructor
 	///
@@ -371,11 +370,6 @@ private:
 #endif
 	unsigned int					mVerbose;					///< If greater than zero prints more info
 	std::multimap<size_t, size_t>	mSitesMappingToOriginal;	///< Map reduced site num. to list of corresponding original sites.
-
-
-/*protected:
-    bool        mAllBranchesFG;     ///< Only internal branches to be processed*/
-
 };
 
 #endif

Genes.cpp

@@ -285,6 +285,8 @@ void Genes::readFile(const char* aFilename, bool aCleanData)
 		std::cout << "Sites:        " << std::setw(6) << mSiteMultiplicity.size() << "/" << ncodons << std::endl;
 		int multi_codons = static_cast<int>(std::count_if(codon_multiplicity.begin(), codon_multiplicity.end(), std::bind2nd(std::greater<unsigned int>(), 1)));
 		std::cout << "Multi codons: " << std::setw(6) << multi_codons << "/" << ncodons << std::endl;
+                std::cout << std::endl<<"------------------------------------"<<std::endl;
+
 	}
 	if(mVerboseLevel >= VERBOSE_MORE_DEBUG)
 	{

SETPATHS

+#!/bin/bash
+#Environment variables for variety of example machines
+#Please set these paths according to your system!
+
+# 1) Local linux
+export BLAS_LIB_DIR="/home/userid/lib" #Path to BLAS library
+export LAPACK_LIB_DIR="/home/userid/lib" #Path to LAPACK library
+export NLOPT_LIB_DIR="/home/userid/lib/nlopt/lib" #Path to NLopt
+export NLOPT_INCLUDE_DIR="/home/userid/lib/nlopt/include"
+export MATH_LIB_NAMES="blas;lapack;lapack;blas;gfortranbegin;gfortran" #Change if your BLAS library is not libblas.a or if your LAPACK library is not liblapack.a. gfortranbegin/gfortran needed for GCC gfortran.
+export CXX="/usr/bin/mpicxx.mpich2" #Set this if using MPI
+
+# 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 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 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"
+  export LDFLAGS="-static"
+
+# 3) Vital-IT
+  export BLAS_LIB_DIR="/software/Utility/OpenBLAS/0.2.5/lib"
+  export LAPACK_LIB_DIR="/software/Utility/OpenBLAS/0.2.5/include"
+  export NLOPT_LIB_DIR="/software/Utility/nlopt/2.3/lib"
+  export NLOPT_INCLUDE_DIR="/software/Utility/nlopt/2.3/include"
+  export MATH_LIB_NAMES="openblas;lapack;gfortranbegin;gfortran"
+  export BOOST_ROOT="/software/lib64/"
+  export CXX="/home/kali/lib/mpi/bin/mpicxx"
+

WriteResults.cpp

@@ -4,7 +4,7 @@
 #include <fstream>
 #include <limits>
 #include "WriteResults.h"
-#include <string>
+#include <string>
 
 void WriteResults::outputResults(void)
 {
@@ -13,7 +13,7 @@ void WriteResults::outputResults(void)
 
 	// Range of branches to be output (for H0 and H1)
 	std::map<size_t, double>::const_iterator im;
-	std::map<size_t, std::string>::const_iterator ims;
+	std::map<size_t, std::string>::const_iterator ims;
 
 	size_t min_branch = std::numeric_limits<size_t>::max();
 	size_t max_branch = 0;
@@ -42,6 +42,8 @@ void WriteResults::outputResults(void)
 	}
 
 	// Write the log-likelihood values (if a value is not present, write NA)
+	
+
 	for(size_t branch = min_branch; branch <= max_branch; ++branch)
 	{
 		out << "Branch: " << std::setw(4) << branch<<std::endl<< std::endl<< "  LnL0: ";
@@ -55,9 +57,10 @@ void WriteResults::outputResults(void)
 		else
 		{
 			out << std::setw(22) << std::setprecision(15) << std::fixed << im->second;
-
-            ims = mParamStr[0].find(branch);
-            out << std::endl<< std::fixed <<"Branch lengths:" << ims->second << std::endl;
+			
+			ims = mParamStr[0].find(branch);
+			// This output does not work on BG/Q.
+                        //out << std::endl<< std::fixed <<"Branch lengths:" << ims->second << std::endl;
 		}
 		out << "  LnL1: ";
 
@@ -70,8 +73,8 @@ void WriteResults::outputResults(void)
 		else
 		{
 			out << std::setw(22) << std::setprecision(15) << std::fixed << im->second;
-
-            ims = mParamStr[1].find(branch);
+
+            ims = mParamStr[1].find(branch);
             out << std::endl<< std::fixed  <<"Branch lengths:" <<ims->second << std::endl;
 		}
 		out << std::endl;
@@ -137,8 +140,8 @@ void WriteResults::savePositiveSelSites(size_t aFgBranch, const std::vector<unsi
 
 	// Save the positive selection sites and corresponding probabilities for later printing
 	mPositiveSelSites[aFgBranch] = std::make_pair(aPositiveSelSites, aPositiveSelSitesProb);
-}
-
+}
+
 void WriteResults::saveParameters(size_t aFgBranch, std::string& aParamStr, unsigned int aHypothesis)
 {
 	// If no file set, then do nothing

blas.h

@@ -29,11 +29,16 @@
 
 #ifdef _BGQ_COMPILER
 #define dsyevr_ dsyevr
+#define ddot_ ddot
+#define dnrm2_ dnrm2
+#define dscal_ dscal
+#define dsyrk_ dsyrk
+#define dsymv_ dsymv
 #endif
 
 
 #ifdef __cplusplus
-extern "C" {
+extern "C" { 
 #endif
 
 /// DSYRK  performs one of the symmetric rank k operations
@@ -292,15 +297,15 @@ double ddot_(const int *n,
 
 
 /// Computes the Euclidean norm of a vector.
-///
+/// 
 /// DNRM2 computes the Euclidean (L2) norm of a double precision real vector
 ///
 /// @param[in]      n  Number of elements in the operand vector.
 /// @param[in]      dx  Array of dimension (n-1) * |incx| + 1. Array x contains the operand vector.
 /// @param[in]      incx  Increment between elements of x.
-///
+/// 
 /// @return Resulting Euclidean norm.
-///
+/// 
 double dnrm2_(const int *n,
 				const double *dx,
 				const int *incx);

fast.cpp

@@ -26,7 +26,7 @@
 #include "BranchSiteModel.h"
 #include "ParseParameters.h"
 #include "VerbosityLevels.h"
-#include "WriteResults.h"
+#include "WriteResults.h"
 
 #ifndef VTRACE
 #ifdef _OPENMP
@@ -49,14 +49,14 @@
 ///
 ///	@param[in] aRgc Number of command line parameters
 /// @param[in] aRgv Command line parameters
-///
-const char* version="1.1.0";
-
+///
+const char* version="1.2.0";
+
 
 int main(int aRgc, char **aRgv)
 {
 	try
-	{
+	{
 
 #ifdef USE_MKL_VML
 	// If used, intitialize the MKL VML library
@@ -74,39 +74,51 @@ int main(int aRgc, char **aRgv)
 
 	// Adjust and report the number of threads that will be used
 #ifdef _OPENMP
-	int num_threads = omp_get_max_threads();
-    //std::cout<<"max num of thr: "<< num_threads <<std::endl;
-
-    if(num_threads < 2 || cmd.mForceSerial || cmd.mNumThreads == 1)
-    {
+	int num_threads = omp_get_max_threads();
+    //std::cout<<"max num of thr: "<< num_threads <<std::endl;
+
+     if((cmd.mNumThreads >=1)&&(cmd.mNumThreads <= (unsigned int)num_threads))
+        num_threads = cmd.mNumThreads;
+    // std::cout<<"num of thr: "<< num_threads <<std::endl;
+
+     omp_set_num_threads(num_threads);
+    /*if (num_threads < 2)
         cmd.mForceSerial = true;
-        num_threads = 1;
-
-    }
-    else if((cmd.mNumThreads >1)&&(cmd.mNumThreads <= num_threads))
-    {
-            num_threads = cmd.mNumThreads;
-    }
-
-    // std::cout<<"num of thr: "<< num_threads <<std::endl;
-     omp_set_num_threads(num_threads);
-
-#else
+     else
+        cmd.mForceSerial = false;*/
+#else
 	cmd.mNumThreads=1;
-	int num_threads = 1;
+	int num_threads = 1;
 	cmd.mForceSerial = true;
-#endif
+#endif
+
+/*#ifdef _OPENMP
+	int num_threads = omp_get_max_threads();
+	if(num_threads < 2 || cmd.mForceSerial)
+	{
+		cmd.mForceSerial = true;
+		num_threads = 1;
+		omp_set_num_threads(1);
+	}
+#else
+	cmd.mForceSerial = true;
+	int num_threads = 1;
+#endif*/
 
 #ifdef USE_MPI
 	// Shutdown messages from all MPI processes except the master
 	if(!hlc.isMaster()) cmd.mVerboseLevel = VERBOSE_NONE;
-#endif
-
-    std::cout <<std::endl<<"------------------"<< std::endl<<"FastCodeML V"<<version<<std::endl<<"------------------"<<std::endl;
+#endif
+
+//    std::cout <<std::endl<<"------------------"<< std::endl<<"FastCodeML V"<<version<<std::endl<<"------------------"<<std::endl;
 	// Write out command line parameters (if not quiet i.e. if verbose level > 0)
 	if(cmd.mVerboseLevel >= VERBOSE_INFO_OUTPUT)
 	{
-													std::cout << std::endl;
+	
+		std::cout << "------------------------------------" << std::endl;
+		std::cout << "FastCodeML V"<<version << std::endl;
+		std::cout << "------------------------------------"<<std::endl;
+		std::cout << std::endl;
 													std::cout << "Tree file:      " << cmd.mTreeFile << std::endl;
 													std::cout << "Gene file:      " << cmd.mGeneFile << std::endl;
 													std::cout << "Verbose level:  " << cmd.mVerboseLevel << " (" << decodeVerboseLevel(cmd.mVerboseLevel) << ')' << std::endl;
@@ -139,7 +151,7 @@ int main(int aRgc, char **aRgv)
 		if(cmd.mDeltaValueForGradient > 0.0)		std::cout << "Delta value:    " << cmd.mDeltaValueForGradient << std::endl;
 													std::cout << "Relative error: " << cmd.mRelativeError << std::endl;
 		if(cmd.mResultsFile)						std::cout << "Results file:   " << cmd.mResultsFile << std::endl;
-        if(cmd.mNumThreads)                         std::cout << "Number of threads: " << cmd.mNumThreads << std::endl;
+        if(cmd.mNumThreads)                         std::cout << "Number of threads: " << cmd.mNumThreads << std::endl;
         if(cmd.mFixedBranchLength)                        std::cerr << "Branch lengths are fixed" << std::endl;
 #ifdef _OPENMP
 		if(num_threads > 1)
@@ -210,7 +222,7 @@ int main(int aRgc, char **aRgv)
 	if(cmd.mVerboseLevel >= VERBOSE_INFO_OUTPUT) timer.start();
 
 	// Create the forest
-	Forest forest(cmd.mVerboseLevel/*, cmd.mOnlyInternalBranchFG*/);
+	Forest forest(cmd.mVerboseLevel);
 
 	// Enclose file loading into a block so temporary structures could be deleted when no more needed
 	{
@@ -376,11 +388,11 @@ int main(int aRgc, char **aRgv)
 					std::cout << "(Doesn't pass LRT, skipping)";
 				std::cout << " Function calls: " << h0.getNumEvaluations() << "   ";
 				std::cout << std::endl << std::endl;
-				if(lnl0 != std::numeric_limits<double>::infinity())
-				{
-                    std::string s0 = h0.printFinalVars(std::cout);
-                    //std::cout<<"EDW0: "<< s0 <<std::endl;
-                    output_results.saveParameters(fg_branch, s0, 0);
+				if(lnl0 != std::numeric_limits<double>::infinity())
+				{
+                    std::string s0 = h0.printFinalVars(std::cout);
+                    //std::cout<<"EDW0: "<< s0 <<std::endl;
+                    output_results.saveParameters(fg_branch, s0, 0);
 				}
 				std::cout << std::endl;
 			}
@@ -393,11 +405,11 @@ int main(int aRgc, char **aRgv)
 					std::cout << std::setprecision(15) << std::fixed << lnl1;
 				std::cout << " Function calls: " << h1.getNumEvaluations();
 				std::cout << std::endl << std::endl;
-				if(lnl1 != std::numeric_limits<double>::infinity())
-				{
-				    std::string s1= h1.printFinalVars(std::cout);
-				    //std::cout<<"EDW1: "<< s1 <<std::endl;
-				    output_results.saveParameters(fg_branch, s1, 1);
+				if(lnl1 != std::numeric_limits<double>::infinity())
+				{
+				    std::string s1= h1.printFinalVars(std::cout);
+				    //std::cout<<"EDW1: "<< s1 <<std::endl;
+				    output_results.saveParameters(fg_branch, s1, 1);
 				}
 				std::cout << std::endl;
 			}
@@ -593,11 +605,8 @@ Usage:
 -r  --trace (no argument)
         Trace the maximization run
 
--nt  --number-of-threads (required argument)
-        Number of threads (1 for non parallel execution)
-
--np   --no-parallel (no argument)
-        Don't use parallel execution
+-nt  --number-of-threads (required argument)
+        Number of threads (1 for non parallel execution)
 
 -bf  --branch-from-file (no argument)
         Do only the branch marked in the file as foreground branch
@@ -636,9 +645,9 @@ Usage:
         Don't stop H0 maximization even if it cannot satisfy LRT (default: stop)
 
 -mi  --max-iterations (required argument)
-        Maximum number of iterations for the maximizer (default: 10000)
-
--bl  --branch-lengths-fixed (no argument)
+        Maximum number of iterations for the maximizer (default: 10000)
+
+-bl  --branch-lengths-fixed (no argument)
         The length of the brances is fixed
 
 @endverbatim