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Performance and Correctness Improvements #9

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d202112
Fix segfault on large data sets by using heap rather than stack alloc…
Mar 12, 2018
547d44d
add LTO because it's 2018
Mar 14, 2018
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77 changes: 39 additions & 38 deletions sources/BipartitionList.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ along with PhyloBayes. If not, see <http://www.gnu.org/licenses/>.

**********************/

#include <vector>
#include "phylo.h"

// ---------------------------------------------------------------------------------
Expand Down Expand Up @@ -57,7 +58,7 @@ double BPCompare(string* ChainName, int P, string reftreename, int burnin, int e
}
}
BipartitionList** bplist = new BipartitionList*[P];
TaxaParameters* taxaparam = 0;
TaxaParameters* taxaparam = 0;
BipartitionList* refbplist = 0;

if (verbose) {
Expand Down Expand Up @@ -141,13 +142,14 @@ double BPCompare(string* ChainName, int P, string reftreename, int burnin, int e

int bpsize = mergedbplist->GetSize();

double diff[bpsize];
double refdiff[bpsize];
double prob[Q][bpsize];
double length[Q][bpsize];
double meanprob[bpsize];
double refprob[bpsize];
double reflength[bpsize];
vector<double> diff(bpsize);
vector<double> refdiff(bpsize);
vector<vector<double> > prob(Q, vector<double>(bpsize));
vector<vector<double> > length(Q, vector<double>(bpsize));
vector<double> meanprob(bpsize);
vector<double> refprob(bpsize);
vector<double> reflength(bpsize);

for (int k=0; k<bpsize; k++) {
meanprob[k] = 0;
refprob[k] = 0;
Expand Down Expand Up @@ -222,7 +224,7 @@ double BPCompare(string* ChainName, int P, string reftreename, int burnin, int e
meanprob[k] = mean;
}
meandiff /= weight;

if (! bench) {
osp << "total number of bp : " << bpsize << '\n';
osp << "cutoff : " << cutoff << '\n';
Expand Down Expand Up @@ -312,7 +314,7 @@ double BPCompare(string* ChainName, int P, string reftreename, int burnin, int e
}
meandiff /= weight;
// meandiff = sqrt(meandiff);

if (! bench) {
osp << "total number of bp : " << bpsize << '\n';
osp << "cutoff : " << cutoff << '\n';
Expand Down Expand Up @@ -408,7 +410,7 @@ double BPCompare(string* ChainName, int P, string reftreename, int burnin, int e
cout << "meandiff : " << meandiff << '\n';
cout << '\n';
}

ofstream sos((OutFile + ".bpdiff").c_str());
sos << '\n';
sos << "maxdiff : " << maxdiff << '\n';
Expand Down Expand Up @@ -475,7 +477,7 @@ void BipartitionList::BasicAllocation() {
mAllocatedSize = basicsize;
mSize = 0;
mWeight = 0;

mCompatibleArray = 0;

mWeightArray = new double[mAllocatedSize];
Expand Down Expand Up @@ -511,7 +513,7 @@ BipartitionList::BipartitionList(TaxaParameters* inParam) {
BipartitionList::BipartitionList(string filename, int burnin, int every, int until, double cutoff, bool rootonly) {

BasicAllocation();

if (burnin <0) {
if (burnin == -1) {
burnin = -5;
Expand All @@ -525,16 +527,16 @@ BipartitionList::BipartitionList(string filename, int burnin, int every, int unt
}
burnin = - n / burnin;
}

ifstream is(filename.c_str());
PBTree tree;
PBTree tree;
int size = 0;
Ntree = 0;
if (! tree.ReadFromStream(is)) {
return;
}
size = 1;
mParam = new TaxaParameters(&tree);
mParam = new TaxaParameters(&tree);
int cycle = 0;
if (size > burnin) {
if (rootonly) {
Expand Down Expand Up @@ -635,10 +637,10 @@ int BipartitionList::IsEqualTo(BipartitionList* comp) {


void BipartitionList::Prune(PBTree* inTree) {

if (inTree->IsDichotomous()) {
cerr << "in BipartitionList::Prune : warning, tree is dichotomous\n";
}
}
Flush();
inTree->GetRoot()->BipartitionPruning(this);
Modulo();
Expand All @@ -647,7 +649,7 @@ void BipartitionList::Prune(PBTree* inTree) {


void BipartitionList::PruneWithSupports(PBTree* inTree) {

Flush();
inTree->GetRoot()->BipartitionPruningWithSupports(this);
Modulo();
Expand All @@ -664,7 +666,7 @@ BipartitionList::BipartitionList( TreeList* inTreeList, double* weightarray, dou

mParam = inTreeList->GetParameters();
BasicAllocation();

for (int i=0; i<inTreeList->GetSize(); i++) {
BipartitionList tempList(mParam);
inTreeList->GetTree(i)->Trichotomise();
Expand Down Expand Up @@ -694,7 +696,7 @@ BipartitionList::~BipartitionList() {
delete[] mCompatibleArray;
}


// ---------------------------------------------------------------------------------
// Sort(); // reverse order !
// ---------------------------------------------------------------------------------
Expand Down Expand Up @@ -723,12 +725,12 @@ void BipartitionList::Sort() {
}
}
}

// ---------------------------------------------------------------------------------
// GetHisto();
// ---------------------------------------------------------------------------------


void BipartitionList::GetHisto(int* histo, int ncat) {
for (int i=0; i<ncat; i++) {
histo[i] = 0;
Expand All @@ -739,12 +741,12 @@ void BipartitionList::GetHisto(int* histo, int ncat) {
histo[k] ++;
}
}

// ---------------------------------------------------------------------------------
// RegisterWith();
// ---------------------------------------------------------------------------------


int BipartitionList::RegisterWith(TaxaParameters* inParam) {

int ok = 1;
Expand All @@ -770,7 +772,7 @@ int BipartitionList::RegisterWith(TaxaParameters* inParam) {

for (int i=0; i<mSize; i++) {
mBipartitionArray[i]->PermutTaxa(permut);
}
}
delete[] permut;
}
return ok;
Expand All @@ -781,7 +783,7 @@ int BipartitionList::RegisterWith(TaxaParameters* inParam) {
// ---------------------------------------------------------------------------------

void BipartitionList::Truncate(double cutoff) {

int i=0;
while ( (i<mSize) && (GetProb(i) >= cutoff)) {
i++;
Expand All @@ -802,21 +804,21 @@ void BipartitionList::Flush(){
mSize = 0;
mWeight = 0;
}


// ---------------------------------------------------------------------------------
// Pop()
// ---------------------------------------------------------------------------------

void BipartitionList::Pop(){

if (! mSize) {
cerr << "error in BipartitionList : pop called on list of size 0\n";
exit(1);
}
mSize--;
}


// ---------------------------------------------------------------------------------
// Modulo
Expand Down Expand Up @@ -890,20 +892,20 @@ void BipartitionList::Suppress(const Bipartition& bp) {
mBipartitionArray[i]->Suppress(bp);
}
}


// ---------------------------------------------------------------------------------
// GetIndex()
// ---------------------------------------------------------------------------------

int BipartitionList::GetIndex(const Bipartition& inPartition){

int i=0;
while ( (i<mSize) && (*mBipartitionArray[i] != inPartition)) {
i++;
}
if (i == mSize) {
i = -1;
i = -1;
}
return i;
}
Expand Down Expand Up @@ -1015,7 +1017,7 @@ void BipartitionList::Insert(Bipartition inPartition, double weight, double leng
exit(1);
}
}

mSize++;
if (mSize > mAllocatedSize) {
Reallocate();
Expand Down Expand Up @@ -1077,7 +1079,7 @@ void BipartitionList::WriteToStream(ostream& os, int header, int verbose) {
if (header) {
mParam->WriteToStream(os);
}
os << "BipartitionList\n";
os << "BipartitionList\n";
os << "Size " << mSize << '\n';
os << "Weight " << mWeight << '\n';
os << '\n';
Expand Down Expand Up @@ -1113,12 +1115,12 @@ void BipartitionList::ReadFromStream(istream& is) {
mParam->ReadFromStream(is);
}
else if (temp == "BipartitionList") {

int size;
is >> temp >> size >> temp >> mWeight;
cerr << size << '\n';
mSize = 0;

for (int i=0; i<size; i++) {
double prob;
double length;
Expand All @@ -1136,4 +1138,3 @@ void BipartitionList::ReadFromStream(istream& is) {
is >> temp;
}
}

4 changes: 2 additions & 2 deletions sources/Makefile
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
CC=mpic++
CPPFLAGS= -w -O3 -c
LDFLAGS= -O3
CPPFLAGS= -w -O3 -flto -c
LDFLAGS= -O3 -flto
SRCS= TaxonSet.cpp Tree.cpp Random.cpp SequenceAlignment.cpp CodonSequenceAlignment.cpp \
StateSpace.cpp CodonStateSpace.cpp ZippedSequenceAlignment.cpp SubMatrix.cpp \
GTRSubMatrix.cpp CodonSubMatrix.cpp linalg.cpp Chrono.cpp BranchProcess.cpp \
Expand Down