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release version 1.5.1
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@bqminh
bqminh committed Nov 8, 2016
1 parent 5c3e0c4 commit 52fb428
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Showing 6 changed files with 38 additions and 11 deletions.
2 changes: 1 addition & 1 deletion CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ add_definitions(-DIQ_TREE)
# The version number.
set (iqtree_VERSION_MAJOR 1)
set (iqtree_VERSION_MINOR 5)
set (iqtree_VERSION_PATCH "1-beta")
set (iqtree_VERSION_PATCH "1")

set(BUILD_SHARED_LIBS OFF)

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12 changes: 6 additions & 6 deletions phyloanalysis.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1797,10 +1797,10 @@ void runTreeReconstruction(Params &params, string &original_model, IQTree &iqtre

uint64_t mem_required = iqtree.getMemoryRequired();

if (mem_required >= total_mem*0.9) {
if (mem_required >= total_mem*0.95 && !iqtree.isSuperTree()) {
// switch to memory saving mode
if (params.lh_mem_save != LM_MEM_SAVE) {
params.max_mem_size = (total_mem*0.9)/mem_required;
params.max_mem_size = (total_mem*0.95)/mem_required;
params.lh_mem_save = LM_MEM_SAVE;
mem_required = iqtree.getMemoryRequired();
cout << "NOTE: Switching to memory saving mode using " << (mem_required / 1073741824.0) << " GB ("
Expand All @@ -1812,10 +1812,10 @@ void runTreeReconstruction(Params &params, string &original_model, IQTree &iqtre
params.max_mem_size = 0.0;
mem_required = iqtree.getMemoryRequired();
}
if (mem_required >= total_mem) {
cerr << "ERROR: Your RAM is below minimum requirement of " << (mem_required / 1073741824.0) << " GB RAM" << endl;
outError("Memory saving mode cannot work, switch to another computer!!!");
}
}
if (mem_required >= total_mem) {
cerr << "ERROR: Your RAM is below minimum requirement of " << (mem_required / 1073741824.0) << " GB RAM" << endl;
outError("Memory saving mode cannot work, switch to another computer!!!");
}

//#if defined __APPLE__ || defined __MACH__
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8 changes: 8 additions & 0 deletions phylokernelfma.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -86,12 +86,14 @@ void PhyloTree::setLikelihoodKernelFMA() {

if (params->lk_safe_scaling || leafNum >= params->numseq_safe_scaling) {
switch(aln->num_states) {
/*
case 2:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec4d, SAFE_LH, 2, true>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec4d, SAFE_LH, 2, true>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec4d, SAFE_LH, 2, true>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, SAFE_LH, 2, true>;
break;
*/
case 4:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec4d, SAFE_LH, 4, true>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec4d, SAFE_LH, 4, true>;
Expand All @@ -104,12 +106,14 @@ void PhyloTree::setLikelihoodKernelFMA() {
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec4d, SAFE_LH, 20, true>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, SAFE_LH, 20, true>;
break;
/*
case 64:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec4d, SAFE_LH, 64, true>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec4d, SAFE_LH, 64, true>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec4d, SAFE_LH, 64, true>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, SAFE_LH, 64, true>;
break;
*/
default:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchGenericSIMD<Vec4d, SAFE_LH, true>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervGenericSIMD<Vec4d, SAFE_LH, true>;
Expand All @@ -121,12 +125,14 @@ void PhyloTree::setLikelihoodKernelFMA() {
}

switch(aln->num_states) {
/*
case 2:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec4d, NORM_LH, 2, true>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec4d, NORM_LH, 2, true>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec4d, NORM_LH, 2, true>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, NORM_LH, 2, true>;
break;
*/
case 4:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec4d, NORM_LH, 4, true>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec4d, NORM_LH, 4, true>;
Expand All @@ -139,12 +145,14 @@ void PhyloTree::setLikelihoodKernelFMA() {
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec4d, NORM_LH, 20, true>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, NORM_LH, 20, true>;
break;
/*
case 64:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec4d, NORM_LH, 64, true>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec4d, NORM_LH, 64, true>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec4d, NORM_LH, 64, true>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, NORM_LH, 64, true>;
break;
*/
default:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchGenericSIMD<Vec4d, NORM_LH, true>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervGenericSIMD<Vec4d, NORM_LH, true>;
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8 changes: 8 additions & 0 deletions phylokernelsse.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -91,12 +91,14 @@ void PhyloTree::setLikelihoodKernelSSE() {

if (params->lk_safe_scaling || leafNum >= params->numseq_safe_scaling) {
switch(aln->num_states) {
/*
case 2:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec2d, SAFE_LH, 2>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec2d, SAFE_LH, 2>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec2d, SAFE_LH, 2>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec2d, SAFE_LH, 2>;
break;
*/
case 4:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec2d, SAFE_LH, 4>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec2d, SAFE_LH, 4>;
Expand All @@ -109,12 +111,14 @@ void PhyloTree::setLikelihoodKernelSSE() {
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec2d, SAFE_LH, 20>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec2d, SAFE_LH, 20>;
break;
/*
case 64:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec2d, SAFE_LH, 64>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec2d, SAFE_LH, 64>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec2d, SAFE_LH, 64>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec2d, SAFE_LH, 64>;
break;
*/
default:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchGenericSIMD<Vec2d, SAFE_LH>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervGenericSIMD<Vec2d, SAFE_LH>;
Expand All @@ -126,12 +130,14 @@ void PhyloTree::setLikelihoodKernelSSE() {
}

switch(aln->num_states) {
/*
case 2:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec2d, NORM_LH, 2>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec2d, NORM_LH, 2>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec2d, NORM_LH, 2>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec2d, NORM_LH, 2>;
break;
*/
case 4:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec2d, NORM_LH, 4>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec2d, NORM_LH, 4>;
Expand All @@ -144,12 +150,14 @@ void PhyloTree::setLikelihoodKernelSSE() {
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec2d, NORM_LH, 20>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec2d, NORM_LH, 20>;
break;
/*
case 64:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec2d, NORM_LH, 64>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec2d, NORM_LH, 64>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec2d, NORM_LH, 64>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec2d, NORM_LH, 64>;
break;
*/
default:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchGenericSIMD<Vec2d, NORM_LH>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervGenericSIMD<Vec2d, NORM_LH>;
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8 changes: 8 additions & 0 deletions phylotreeavx.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -90,12 +90,14 @@ void PhyloTree::setLikelihoodKernelAVX() {

if (params->lk_safe_scaling || leafNum >= params->numseq_safe_scaling) {
switch(aln->num_states) {
/*
case 2:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec4d, SAFE_LH, 2>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec4d, SAFE_LH, 2>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec4d, SAFE_LH, 2>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, SAFE_LH, 2>;
break;
*/
case 4:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec4d, SAFE_LH, 4>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec4d, SAFE_LH, 4>;
Expand All @@ -108,12 +110,14 @@ void PhyloTree::setLikelihoodKernelAVX() {
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec4d, SAFE_LH, 20>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, SAFE_LH, 20>;
break;
/*
case 64:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec4d, SAFE_LH, 64>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec4d, SAFE_LH, 64>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec4d, SAFE_LH, 64>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, SAFE_LH, 64>;
break;
*/
default:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchGenericSIMD<Vec4d, SAFE_LH>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervGenericSIMD<Vec4d, SAFE_LH>;
Expand All @@ -125,12 +129,14 @@ void PhyloTree::setLikelihoodKernelAVX() {
}

switch(aln->num_states) {
/*
case 2:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec4d, NORM_LH, 2>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec4d, NORM_LH, 2>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec4d, NORM_LH, 2>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, NORM_LH, 2>;
break;
*/
case 4:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec4d, NORM_LH, 4>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec4d, NORM_LH, 4>;
Expand All @@ -143,12 +149,14 @@ void PhyloTree::setLikelihoodKernelAVX() {
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec4d, NORM_LH, 20>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, NORM_LH, 20>;
break;
/*
case 64:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD<Vec4d, NORM_LH, 64>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD<Vec4d, NORM_LH, 64>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD<Vec4d, NORM_LH, 64>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, NORM_LH, 64>;
break;
*/
default:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchGenericSIMD<Vec4d, NORM_LH>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervGenericSIMD<Vec4d, NORM_LH>;
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11 changes: 7 additions & 4 deletions tools.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -3212,7 +3212,10 @@ void parseArg(int argc, char *argv[], Params &params) {

if (params.do_au_test && params.topotest_replicates == 0)
outError("For AU test please please specify number of bootstrap replicates via -zb option");


if (params.lh_mem_save == LM_MEM_SAVE && params.partition_file)
outError("-mem option does not work with partition models yet");

if (!params.out_prefix) {
if (params.eco_dag_file)
params.out_prefix = params.eco_dag_file;
Expand Down Expand Up @@ -3481,9 +3484,9 @@ void usage_iqtree(char* argv[], bool full_command) {
<< " -zb <#replicates> Performing BP,KH,SH,ELW tests for trees passed via -z" << endl
<< " -zw Also performing weighted-KH and weighted-SH tests" << endl
<< " -au Also performing approximately unbiased (AU) test" << endl
<< endl << "ANCESTRAL SEQUENCE RECONSTRUCTION:" << endl
<< " -asr Compute ancestral states by marginal reconstruction" << endl
<< " -asr-min <prob> Min probability to assign ancestral sequence (default: 0.95)" << endl
// << endl << "ANCESTRAL SEQUENCE RECONSTRUCTION:" << endl
// << " -asr Compute ancestral states by marginal reconstruction" << endl
// << " -asr-min <prob> Min probability to assign ancestral sequence (default: 0.95)" << endl
// << " -wja Write ancestral sequences by joint reconstruction" << endl


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