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Commit e9c24b8d authored by oshahmir's avatar oshahmir
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Updating default compile options in CMakeLists.txt

parent d5169286
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BayesTest.cpp
View file @ e9c24b8d
......@@ -593,8 +593,8 @@ double MfgBayesTest::getGridParams(const std::vector<double> &aVars,
//if (site==982)
//std::cout<<"before normalization mPriors[site] for cat " << iw << " is "<< mPriors[iw * mNumSites + site] << std::endl;
// debug
//if (site==982)
//std::cout<<"likeliohoods[site] for cat " << iw << " is " << likelihoods[site] << std::endl;
// if (site==982)
// std::cout<<"likeliohoods[site] for cat " << iw << " is " << likelihoods[site] << std::endl;
}
......@@ -616,8 +616,8 @@ double MfgBayesTest::getGridParams(const std::vector<double> &aVars,
mPriors[k * mNumSites + site] = exp(mPriors[k * mNumSites + site] - fh);
// debug
//if (site==982)
//std::cout<<"mPriors[site] for cat " << k << " is "<< mPriors[k * mNumSites + site] << std::endl;
// if (site==982)
// std::cout<<"mPriors[site] for cat " << k << " is "<< mPriors[k * mNumSites + site] << std::endl;
}
scale += fh * aSiteMultiplicity[site];
......@@ -878,10 +878,10 @@ void MfgBayesTest::computeBEB(const std::vector<double> &aVars,
mSiteClassProb[j * mNumSites + site] *= exp(scale1 - fX);
//debug
//if (site==982)
//{
//std::cout << "scale (t=log(fhk[codon_class]) + lnfXs[igrid]): " << scale1 << " fX: " << fX << " site multiplicity " << site_multiplicity[site] <<" prob: " << mSiteClassProb[2 * mNumSites + site] + mSiteClassProb[3 * mNumSites + site] << std::endl;
//}
// if (site==982)
// {
// std::cout << "scale (t=log(fhk[codon_class]) + lnfXs[igrid]): " << scale1 << " fX: " << fX << " site multiplicity " << site_multiplicity[site] <<" prob: " << mSiteClassProb[2 * mNumSites + site] + mSiteClassProb[3 * mNumSites + site] << std::endl;
// }
}
......@@ -955,8 +955,8 @@ void MfgBayesTest::printPositiveSelSites(std::set<int> aFgBranchSet) const {
std::cout << std::setw(6) << im->first + 1 << ' ' << std::fixed
<< std::setprecision(6) << prob << sig << std::endl;
//debug
//if (im->first+1 == 1030)
//std::cout<<"reduced site num for 1030: "<<im->second<<std::endl;
// if (im->first+1 == 1030)
// std::cout<<"reduced site num for 1030: "<<im->second<<std::endl;
}
......
BranchSiteModel.cpp
View file @ e9c24b8d
......@@ -389,8 +389,8 @@ void BranchSiteModel::initFromResult(const std::vector<double> &aPreviousResult,
aValidLen = 0;
//debug
for (std::vector<double>::const_iterator i = aPreviousResult.begin(); i != aPreviousResult.end(); ++i)
std::cout << *i << ' ';
//for (std::vector<double>::const_iterator i = aPreviousResult.begin(); i != aPreviousResult.end(); ++i)
//std::cout << *i << ' ';
// Copy the requested values
mVar.assign(aPreviousResult.begin(),
......
CMakeLists.txt
View file @ e9c24b8d
......@@ -40,17 +40,20 @@ else(Boost_FOUND)
endif(Boost_FOUND)
# Get the configuration switches
# Get the *basic* configuration switches
OPTION(USE_LAPACK "Use BLAS/LAPACK" OFF)
OPTION(USE_MKL_VML "Use Intel MKL vectorized routines" OFF) # could be removed ?
OPTION(USE_OPENMP "Compile with OpenMP support" ON)
OPTION(USE_MPI "Use MPI for high level parallelization" OFF) # could be removed ?
# Get the *advanced* configuration switches (change default values with care, some options are not fully functional)
OPTION(USE_MKL_VML "Use Intel MKL vectorized routines" OFF)
OPTION(USE_MPI "Use MPI for high level parallelization" OFF)
if(NOT WIN32)
OPTION(BUILD_NOT_SHARED "Build FastCodeML not shared" OFF) # could be removed ?
OPTION(BUILD_NOT_SHARED "Build FastCodeML not shared" OFF)
endif(NOT WIN32)
OPTION(BUILD_SEARCH_MPI "Search for MPI installation?" OFF) # could be removed ?
OPTION(USE_ORIGINAL_PROPORTIONS "Use the original CodeML proportion definition" ON) # could be removed ?
SET(USE_LIKELIHOOD_METHOD "Original" CACHE STRING "Select the type of likelihood computation method: Original, NonRecursive, FatVector, DAG") # could be removed ?
OPTION(BUILD_SEARCH_MPI "Search for MPI installation?" OFF)
OPTION(USE_ORIGINAL_PROPORTIONS "Use the original CodeML proportion definition" ON)
SET(USE_LIKELIHOOD_METHOD "Original" CACHE STRING "Select the type of likelihood computation method: Original, NonRecursive, FatVector, DAG")
SET_PROPERTY(CACHE USE_LIKELIHOOD_METHOD PROPERTY STRINGS Original NonRecursive FatVector DAG)
OPTION(USE_IDENTITY_MATRIX "Force identity matrix when time is zero" OFF)
OPTION(USE_CPV_SCALING "Scale conditional probability vectors to avoid under/overflow" ON)
......@@ -71,7 +74,7 @@ if(USE_OPENMP)
endif(USE_OPENMP)
# Search for MPI (could be removed ?)
# Search for MPI
if(USE_MPI)
if(BUILD_SEARCH_MPI)
find_package(MPI)
......@@ -84,7 +87,7 @@ endif(USE_MPI)
# Load the needed paths
set(LINK_DIR_BLAS $ENV{BLAS_LIB_DIR} CACHE PATH "BLAS lib dir")
set(LINK_DIR_LAPACK $ENV{LAPACK_LIB_DIR} CACHE PATH "LAPACK lib dir")
set(INCLUDE_DIR_MKL $ENV{MKL_INCLUDE_DIR} CACHE PATH "MKL include dir") # could be removed ?
set(INCLUDE_DIR_MKL $ENV{MKL_INCLUDE_DIR} CACHE PATH "MKL include dir")
set(INCLUDE_DIR_NLOPT $ENV{NLOPT_INCLUDE_DIR} CACHE PATH "NLopt include dir")
set(LINK_DIR_NLOPT $ENV{NLOPT_LIB_DIR} CACHE PATH "NLopt lib dir")
set(MATH_LIB_NAMES $ENV{MATH_LIB_NAMES} CACHE STRING "Math libraries (Separated by ';')")
......@@ -112,11 +115,11 @@ if(USE_LAPACK)
add_definitions(-DUSE_LAPACK)
endif(USE_LAPACK)
if(MPI_FOUND) # could be removed ?
if(MPI_FOUND)
add_definitions(-DUSE_MPI)
endif(MPI_FOUND)
if(USE_ORIGINAL_PROPORTIONS) # could be removed ?
if(USE_ORIGINAL_PROPORTIONS)
add_definitions(-DUSE_ORIGINAL_PROPORTIONS)
endif(USE_ORIGINAL_PROPORTIONS)
......
CodeMLoptimizer.cpp
View file @ e9c24b8d
......@@ -158,8 +158,8 @@ int Ming2::ming2(FILE *fout, double *f, double x[], const double xl[],
// double f0 = *f = (*fun) (x, n); ++mNumFunCall;
//debug
for (int i=0;i < 100; i++)
printf("x[%d]=%f - ", i,x[i]);
//for (int i=0;i < 100; i++)
//printf("x[%d]=%f - ", i,x[i]);
double f0 = *f = -mModel->computeLikelihood(x, n, mTraceFun);
xtoy(x, x0, n);
......
bad_cases/HBG010916-1.M0.009.nwk
View file @ e9c24b8d
(((((((a0001:0.075468,a0005:0.085411):0.207804,(a0010:0.720769,a0006:0.020905):0.105001):0.012384,(a0000:0.142497,a0012:0.282057)#1:0.018899):0.178792,a0009:0.443433)#1:0.714179,a0008:0.474661):0.143467,a0011:1.098262):0.162709,((a0007:0.348344,(a0003:0.324275,(a0013:0.17518,a0002:0.376901):0.198321):0.112915):0.242393,a0004:0.617143):0.19161);
(((((((a0001:0.075468,a0005:0.085411):0.207804,(a0010:0.720769,a0006:0.020905):0.105001):0.012384,(a0000:0.142497,a0012:0.282057):0.018899):0.178792,a0009:0.443433)#1:0.714179,a0008:0.474661):0.143467,a0011:1.098262):0.162709,((a0007:0.348344,(a0003:0.324275,(a0013:0.17518,a0002:0.376901):0.198321):0.112915):0.242393,a0004:0.617143):0.19161);
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