From 329ae589f43732251291c37872225696fd7dda09 Mon Sep 17 00:00:00 2001 From: Segei L Kosakovsky Pond Date: Tue, 18 Aug 2020 21:24:02 -0400 Subject: [PATCH] Fixing bugs introduced in 2.5.16 (related to LF scaling); some speed-up tweaks; fixing optimization boundary handling --- src/core/global_things.cpp | 2 +- src/core/hbl_env.cpp | 2 + src/core/include/hbl_env.h | 3 +- src/core/likefunc.cpp | 100 ++++- src/core/matrix.cpp | 2 +- src/core/tree.cpp | 407 +++++++++++------- .../SimpleOptimizations/IntermediateCodon.bf | 2 +- .../hbltests/SimpleOptimizations/LargeNuc.bf | 7 + 8 files changed, 368 insertions(+), 157 deletions(-) diff --git a/src/core/global_things.cpp b/src/core/global_things.cpp index c0afb193e..25f24fd21 100644 --- a/src/core/global_things.cpp +++ b/src/core/global_things.cpp @@ -120,7 +120,7 @@ namespace hy_global { kErrorStringDatasetRefIndexError ("Dataset index reference out of range"), kErrorStringMatrixExportError ("Export matrix called with a non-polynomial matrix argument"), kErrorStringNullOperand ("Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"), - kHyPhyVersion = _String ("2.5.16"), + kHyPhyVersion = _String ("2.5.17"), kNoneToken = "None", kNullToken = "null", diff --git a/src/core/hbl_env.cpp b/src/core/hbl_env.cpp index 88beefc86..be983cd9d 100644 --- a/src/core/hbl_env.cpp +++ b/src/core/hbl_env.cpp @@ -296,6 +296,8 @@ _String const // but rather set the last_fileio_exception variable to the value of the exception status_bar_update_string ("STATUS_BAR_STATUS_STRING"), // used to set the progress message displayed to the user + tolerate_numerical_errors ("TOLERATE_NUMERICAL_ERRORS"), + // if set, numerical errors that would cause termination are instead trated as warnings try_numeric_sequence_match ("TRY_NUMERIC_SEQUENCE_MATCH"), // try matching sequences by 0 (or 1) based index, if matching by name fails true_const ("TRUE"), diff --git a/src/core/include/hbl_env.h b/src/core/include/hbl_env.h index 0b566c280..d12d9c479 100644 --- a/src/core/include/hbl_env.h +++ b/src/core/include/hbl_env.h @@ -201,7 +201,8 @@ namespace hy_env { try_numeric_sequence_match, short_mpi_return, kSCFGCorpus, - verbosity_level_string + verbosity_level_string, + tolerate_numerical_errors; ; diff --git a/src/core/likefunc.cpp b/src/core/likefunc.cpp index 555404741..c1f1aaf11 100644 --- a/src/core/likefunc.cpp +++ b/src/core/likefunc.cpp @@ -5289,6 +5289,7 @@ long _LikelihoodFunction::Bracket (long index, hyFloat& left, hyFloat& middle } while (1) { + while (middle-leftStep <= lowerBound) { if (verbosity_level > 100) { @@ -5330,7 +5331,7 @@ long _LikelihoodFunction::Bracket (long index, hyFloat& left, hyFloat& middle } return -2; } else { - middle=MIN(lowerBound+initialStep*.1,upperBound-rightStep); + middle=lowerBound+2.*leftStep; first = false; } } @@ -5374,7 +5375,7 @@ long _LikelihoodFunction::Bracket (long index, hyFloat& left, hyFloat& middle } return -2; } else { - middle=MAX(upperBound-initialStep*.1,lowerBound+leftStep); + middle=MAX(upperBound-2.*rightStep,lowerBound+leftStep); first = false; } } @@ -8371,7 +8372,9 @@ hyFloat _LikelihoodFunction::ComputeBlock (long index, hyFloat* siteRes, long c #endif hyFloat* thread_results = (hyFloat*) alloca (sizeof(hyFloat)*np); - + /*if (likeFuncEvalCallCount==11035) { + printf ("REGULAR overallScalingFactors = %ld\n", overallScalingFactors[0]); + }*/ #ifdef _OPENMP #if _OPENMP>=201511 #pragma omp parallel for default(shared) schedule(monotonic:guided,1) private(blockID) proc_bind(spread) num_threads (np) if (np>1) @@ -8399,6 +8402,42 @@ hyFloat _LikelihoodFunction::ComputeBlock (long index, hyFloat* siteRes, long c branchIndex, branchIndex >= 0 ? branchValues->list_data: nil); } + + /*if (likeFuncEvalCallCount == 68700) { + + NLToConsole(); + BufferToConsole(df->GetColumn (1141)); + NLToConsole(); + NLToConsole(); + BufferToConsole(df->GetColumn (1140)); + NLToConsole(); + NLToConsole(); + BufferToConsole(df->GetColumn (1142)); + NLToConsole(); + + blockID = 0; + long bl = BlockLength (0); + hyFloat * site_results = new hyFloat [bl]; + t->ComputeTreeBlockByBranch (*sl, + *branches, + tcc, + df, + inc, + conditionalTerminalNodeStateFlag[index], + ssf, + (_Vector*)conditionalTerminalNodeLikelihoodCaches(index), + overallScalingFactors.list_data[index], + blockID * sitesPerP, + (1+blockID) * sitesPerP, + catID, + site_results, + scc, + branchIndex, + branchIndex >= 0 ? branchValues->list_data: nil); + for (long k = 0; k < bl; k++) { + fprintf (stderr, "REGULAR,%ld,%15.12lg\n", k, site_results[k]); + } + }*/ if (np > 1) { @@ -8441,6 +8480,10 @@ hyFloat _LikelihoodFunction::ComputeBlock (long index, hyFloat* siteRes, long c branchIndex >= 0 ? branchValues->list_data: nil); }*/ + + /*if (likeFuncEvalCallCount == 11035) { + printf ("\n\nREGULAR compute result %15.12lg %ld %15.12lg %15.12lg\n", sum, overallScalingFactors.list_data[index], _logLFScaler * overallScalingFactors.list_data[index], sum - _logLFScaler * overallScalingFactors.list_data[index]); + }*/ sum -= _logLFScaler * overallScalingFactors.list_data[index]; @@ -8460,6 +8503,11 @@ hyFloat _LikelihoodFunction::ComputeBlock (long index, hyFloat* siteRes, long c /*for (unsigned long p_id = 0; p_id < indexInd.lLength; p_id++) { printf ("%ld %s = %15.12g\n", p_id, GetIthIndependentVar(p_id)->GetName()->sData, (*parameterValuesAndRanges)(p_id,0)); }*/ + + /*if (likeFuncEvalCallCount==11035) { + printf ("BEFORE CONSTRUCT CACHE overallScalingFactors = %ld\n", overallScalingFactors[0]); + }*/ + #ifdef _OPENMP #if _OPENMP>=201511 #pragma omp parallel for default(shared) schedule(monotonic:guided,1) private(blockID) proc_bind(spread) num_threads (np) if (np>1) @@ -8483,6 +8531,10 @@ hyFloat _LikelihoodFunction::ComputeBlock (long index, hyFloat* siteRes, long c // check results + /*if (likeFuncEvalCallCount==11035) { + printf ("AFTER CONSTRUCT CACHE overallScalingFactors = %ld\n", overallScalingFactors[0]); + }*/ + if (sum > -INFINITY) { hyFloat checksum = t->ComputeLLWithBranchCache (*sl, doCachedComp, @@ -8493,6 +8545,24 @@ hyFloat _LikelihoodFunction::ComputeBlock (long index, hyFloat* siteRes, long c catID, siteRes) - _logLFScaler * overallScalingFactors.list_data[index]; + + /*if (likeFuncEvalCallCount == 68700) { + blockID = 0; + long bl = BlockLength (0); + hyFloat * site_results = new hyFloat [bl]; + t->ComputeLLWithBranchCache (*sl, + doCachedComp, + bc, + df, + 0, + df->GetPatternCount (), + catID, + site_results); + for (long k = 0; k < bl; k++) { + fprintf (stderr, "CACHE,%ld,%15.12lg\n", k, site_results[k]); + } + }*/ + if (fabs ((checksum-sum)/sum) > 1.e-10 * df->GetPatternCount ()) { /*hyFloat check2 = t->ComputeTreeBlockByBranch (*sl, @@ -8512,13 +8582,25 @@ hyFloat _LikelihoodFunction::ComputeBlock (long index, hyFloat* siteRes, long c branchIndex, branchIndex >= 0 ? branchValues->list_data: nil);*/ - _String* node_name = GetIthTree (index)->GetNodeFromFlatIndex(doCachedComp)->GetName(); - - _TerminateAndDump (_String("Internal error in ComputeBranchCache (branch ") & *node_name & - + " ) reversible model cached likelihood = "& _String (checksum, "%20.16g") & ", directly computed likelihood = " & _String (sum, "%20.16g") & - + ". This is most likely because a non-reversible model was incorrectly auto-detected (or specified by the model file in environment variables)."); + _String* node_name = GetIthTree (index)->GetNodeFromFlatIndex(doCachedComp)->GetName(), + err_msg = _String("Internal error in ComputeBranchCache (branch ") & *node_name & + + ", eval #" & likeFuncEvalCallCount &" ) reversible model cached likelihood = "& _String (checksum, "%20.16g") & ", directly computed likelihood = " & _String (sum, "%20.16g") & + + ". This is most likely because a non-reversible model was incorrectly auto-detected (or specified by the model file in environment variables; for smaller errors, this could be due to numerical instability of calculations for larger alignments)."; + + + + if (hy_env::EnvVariableTrue(hy_env::tolerate_numerical_errors)) { + NLToConsole(); + BufferToConsole("***WARNING***\n"); + StringToConsole(err_msg); + NLToConsole(); + } else { + _TerminateAndDump (err_msg); + return -INFINITY; + } - return -INFINITY; + + } } diff --git a/src/core/matrix.cpp b/src/core/matrix.cpp index 91881d6ae..c824085bc 100644 --- a/src/core/matrix.cpp +++ b/src/core/matrix.cpp @@ -2035,7 +2035,7 @@ bool _Matrix::IsReversible(_Matrix* freqs) { } return true; } - } catch (const _String reason) { + } catch (const _String& reason) { ReportWarning (_String ("Reversibility checks failed: ") & reason); return false; } diff --git a/src/core/tree.cpp b/src/core/tree.cpp index b5cf314b8..dd0c62cd4 100644 --- a/src/core/tree.cpp +++ b/src/core/tree.cpp @@ -83,7 +83,7 @@ _TheTree::_maxTimesCharWidth = 0.980392; _String const _TheTree::kTreeOutputLabel ( "TREE_OUTPUT_BRANCH_LABEL"), _TheTree::kTreeOutputTLabel ( "TREE_OUTPUT_BRANCH_TLABEL"), - _TheTree::kTreeOutputFSPlaceH ( "__FONT_SIZE__"); + _TheTree::kTreeOutputFSPlaceH ( "__FONT_SIZE__"); #define DEGREES_PER_RADIAN 57.29577951308232286465 @@ -96,10 +96,12 @@ extern long likeFuncEvalCallCount, matrix_exp_count; -hyFloat _lfScalerPower = 100., -_lfScalerUpwards = pow(2.,_lfScalerPower), -_lfScalingFactorThreshold = 1./_lfScalerUpwards, -_logLFScaler = _lfScalerPower *log(2.); +hyFloat _lfScalerPower = 100., + _lfScalerUpwards = pow(2.,_lfScalerPower), + _lfScalingFactorThreshold = 1./_lfScalerUpwards, + _logLFScaler = _lfScalerPower *log(2.), + _lfMaxScaler = DBL_MAX * 1.e-10, + _lfMinScaler = 1./_lfMaxScaler; @@ -109,11 +111,16 @@ _scalerDividers; #ifdef _SLKP_DEBUG_ /*----------------------------------------------------------------------------------------------------------*/ -void echoNodeList (_SimpleList& theNodes, _SimpleList& leaves, _SimpleList& iNodes) -{ +void echoNodeList (_SimpleList& theNodes, _SimpleList& leaves, _SimpleList& iNodes, _SimpleList& flatParents) { for (long n = 0; n < theNodes.lLength; n++) { - node* nd = (node*)(theNodes(n)in_object)->GetName()->sData); + bool is_leaf = theNodes(n)* nd = (node*)(is_leaf?leaves(theNodes(n)):iNodes(theNodes(n)-leaves.lLength)); + long children = 0; + if (!is_leaf) { + long myIndex = theNodes(n)-leaves.lLength; + flatParents.Each ([&](long v, unsigned long)->void {if (v == myIndex) children++;}); + } + printf ("%ld %ld %s (%d)\n", n, theNodes(n), LocateVar(nd->in_object)->GetName()->get_str(), children); } } @@ -121,6 +128,52 @@ void echoNodeList (_SimpleList& theNodes, _SimpleList& leaves, _SimpleList& iNod /*----------------------------------------------------------------------------------------------------------*/ +hyFloat _computeReductionScaler (hyFloat currentScaler, hyFloat sum, long& didScale) { + if (currentScaler > _lfMinScaler) { + didScale = -1; + sum *= _lfScalingFactorThreshold; + + hyFloat tryScale2 = currentScaler * _lfScalingFactorThreshold, + scaler = _lfScalingFactorThreshold; + + while (sum > _lfScalerUpwards && tryScale2 > _lfMinScaler) { + sum *= _lfScalingFactorThreshold; + currentScaler = tryScale2; + tryScale2 *= _lfScalingFactorThreshold; + scaler *= _lfScalingFactorThreshold; + didScale --; + } + + return scaler; + } + return NAN; +} + +hyFloat _computeBoostScaler (hyFloat currentScaler, hyFloat sum, long& didScale) { + if (currentScaler < _lfMaxScaler) { + didScale = 1; + sum *= _lfScalerUpwards; + + hyFloat tryScale2 = currentScaler * _lfScalerUpwards, + scaler = _lfScalerUpwards; + + while (sum < _lfScalingFactorThreshold && tryScale2 < _lfMaxScaler) { + sum *= _lfScalerUpwards; + currentScaler = tryScale2; + tryScale2 *= _lfScalerUpwards; + scaler *= _lfScalerUpwards; + didScale ++; + } + return scaler; + } /*else { +#pragma omp critical + printf ("Overflow in _computeBoostScaler %15.12lg\n", currentScaler); + }*/ + return NAN; +} + +/*----------------------------------------------------------------------------------------------------------*/ + inline void _handle4x4_pruning_case (double const* childVector, double const* tMatrix, double* parentConditionals, void* transposed_mx) { #ifdef _SLKP_USE_SSE_INTRINSICS double tv [4] __attribute__ ((aligned (16))) = {childVector[0], @@ -3284,15 +3337,15 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList for (long siteID = siteFrom; siteID < siteTo; siteID++, parentConditionals += alphabetDimension) { if (tcc) { - if (parentTCCIBit == _HY_BITMASK_WIDTH_) { + if (__builtin_expect (parentTCCIBit==_HY_BITMASK_WIDTH_,0)) { parentTCCIBit = 0; parentTCCIIndex ++; } - if (siteID > siteFrom && (tcc->list_data[parentTCCIIndex] & bitMaskArray.masks[parentTCCIBit]) > 0) { + if (__builtin_expect(siteID > siteFrom && (tcc->list_data[parentTCCIIndex] & bitMaskArray.masks[parentTCCIBit]) > 0,0)) { if (!isLeaf) { childVector += alphabetDimension; - if (++currentTCCBit == _HY_BITMASK_WIDTH_) { + if (__builtin_expect(++currentTCCBit == _HY_BITMASK_WIDTH_,0)) { currentTCCBit = 0; currentTCCIndex ++; } @@ -3320,7 +3373,7 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList } else { siteState = lNodeFlags[nodeCode*siteCount + siteOrdering.list_data[siteID]] ; } - if (siteState >= 0L) + if (__builtin_expect(siteState >= 0L,1)) // a single character state; sweep down the appropriate column { if (alphabetDimension == 4UL) { @@ -3350,17 +3403,24 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList } } else { if (tcc) { - if ((tcc->list_data[currentTCCIndex] & bitMaskArray.masks[currentTCCBit]) > 0 && siteID > siteFrom) { - for (long k = 0; k < alphabetDimension; k++) { + if (__builtin_expect((tcc->list_data[currentTCCIndex] & bitMaskArray.masks[currentTCCBit]) > 0 && siteID > siteFrom,0)) { + memcpy (childVector,lastUpdatedSite,alphabetDimension*(sizeof (hyFloat))); + /*for (long k = 0; k < alphabetDimension; k++) { childVector[k] = lastUpdatedSite[k]; - } + }*/ } - if (++currentTCCBit == _HY_BITMASK_WIDTH_) { + if (__builtin_expect(++currentTCCBit == _HY_BITMASK_WIDTH_,0)) { currentTCCBit = 0; currentTCCIndex ++; } lastUpdatedSite = childVector; } + /*if (likeFuncEvalCallCount == 11035 && siteOrdering.list_data[siteID] == 1141) { + + fprintf (stderr, "REGULAR,%s,%15.12g,%15.12g,%15.12g,%15.12g,%15.12g\n", currentTreeNode->GetName()->get_str(), + scalingAdjustments[nodeCode*siteCount+siteID], + childVector[0],childVector[1],childVector[2],childVector[3]); + }*/ } /* #ifdef _SLKP_USE_AVX_INTRINSICS @@ -3402,71 +3462,42 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList sum = (parentConditionals [0] + parentConditionals [1]) + (parentConditionals [2] + parentConditionals [3]); - /*if (isnan(sum)) { - char buffer[512]; - long child_count = 0; - for (long k = 0; k < flatParents.lLength; k++) { - child_count += flatParents.list_data [k] == parentCode; + /*if (likeFuncEvalCallCount == 11035) { + if ((siteID == 677 || siteID == 692 || siteID == 774) && currentTreeNode->GetName()->EndsWith("NODE_00027110_64")) { + printf ("[CHECK BEFORE] IN REGULAR COMPUTE %ld %ld (%s/%lg [index = %ld, %ld, %ld, %ld], sum = %lg)\n", likeFuncEvalCallCount, siteID, currentTreeNode->GetName()->get_str(), scalingAdjustments [parentCode*siteCount + siteID], nodeCode, parentCode, siteCount, siteID, sum); } - - snprintf (buffer, 512, "Encountered a NAN in parentConditionals at node %s (%ld code, %ld children of parent), site %ld: %lg %lg %lg %lg (%lg, %lg, %lg, %lg); scaler = %lg", currentTreeNode->GetName()->get_str(), parentCode, child_count, siteID, parentConditionals[0],parentConditionals[1], parentConditionals[2], parentConditionals[3], - childVector[0],childVector[1],childVector[2],childVector[3],_lfScalerUpwards); - HandleApplicationError(buffer); }*/ - if (sum < _lfScalingFactorThreshold && sum > 0.0) { - hyFloat tryScale = scalingAdjustments [parentCode*siteCount + siteID] * _lfScalerUpwards; - - /*if (siteID == 1205) { - #pragma omp critical - { - printf ("Scaling UP at node %s, Sum = %lg, scaler = %lg\n", currentTreeNode->GetName()->get_str(), sum, tryScale); - } - }*/ + if (__builtin_expect(sum < _lfScalingFactorThreshold && sum > 0.0,0)) { + + hyFloat scaler = _computeBoostScaler(scalingAdjustments [parentCode*siteCount + siteID] * _lfScalerUpwards, sum, didScale); - if (tryScale < HUGE_VAL) { - parentConditionals [0] *= _lfScalerUpwards; - parentConditionals [1] *= _lfScalerUpwards; - parentConditionals [2] *= _lfScalerUpwards; - parentConditionals [3] *= _lfScalerUpwards; - localScalerChange += theFilter->theFrequencies.get (siteOrdering.list_data[siteID]); - scalingAdjustments [parentCode*siteCount + siteID] = tryScale; - didScale = 1; + if (didScale) { + parentConditionals [0] *= scaler; + parentConditionals [1] *= scaler; + parentConditionals [2] *= scaler; + parentConditionals [3] *= scaler; + localScalerChange += didScale * theFilter->theFrequencies.get (siteOrdering.list_data[siteID]); + scalingAdjustments [parentCode*siteCount + siteID] *= scaler; } + } else { - if (sum > _lfScalerUpwards) { - if (sum < HUGE_VAL) { // no point scaling an infinity - - didScale = -1; - - hyFloat scaler = scalingAdjustments [parentCode*siteCount + siteID] * _lfScalingFactorThreshold; - //hyFloat save_sum = sum; - sum *= _lfScalingFactorThreshold; - while (sum > _lfScalerUpwards) { - sum *= _lfScalingFactorThreshold; - scaler *= _lfScalingFactorThreshold; - didScale --; - } - - /*#pragma omp critical - if (siteID == 1205) { - printf ("Scaling down from %lg to %lg; scaler %lg, steps %ld\n", save_sum, sum, scaler, didScale); - }*/ - + if (__builtin_expect(sum > _lfScalerUpwards && sum < HUGE_VAL,0)) { + + hyFloat scaler = _computeReductionScaler (scalingAdjustments [parentCode*siteCount + siteID] * _lfScalingFactorThreshold, sum, didScale); + + if (didScale) { parentConditionals [0] *= scaler; parentConditionals [1] *= scaler; parentConditionals [2] *= scaler; parentConditionals [3] *= scaler; - localScalerChange += didScale * theFilter->theFrequencies (siteOrdering.list_data[siteID]); - scalingAdjustments [parentCode*siteCount + siteID] = scaler; - //didScale = -1; + scalingAdjustments [parentCode*siteCount + siteID] *= scaler; } - } - } + childVector += 4; } else { hyFloat sum = 0.0; @@ -3652,34 +3683,49 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList - if (sum < _lfScalingFactorThreshold && sum > 0.0) { - hyFloat tryScale = scalingAdjustments [parentCode*siteCount + siteID] * _lfScalerUpwards; - if (tryScale < HUGE_VAL) { - scalingAdjustments [parentCode*siteCount + siteID] = tryScale; + if (__builtin_expect(sum < _lfScalingFactorThreshold && sum > 0.0,0)) { + + hyFloat scaler = _computeBoostScaler(scalingAdjustments [parentCode*siteCount + siteID] * _lfScalerUpwards, sum, didScale); + + if (didScale) { for (long c = 0; c < alphabetDimension; c++) { - parentConditionals [c] *= _lfScalerUpwards; + parentConditionals [c] *= scaler; } - localScalerChange += theFilter->theFrequencies.get(siteOrdering.list_data[siteID]); - didScale = 1; + localScalerChange += didScale * theFilter->theFrequencies.get (siteOrdering.list_data[siteID]); + scalingAdjustments [parentCode*siteCount + siteID] *= scaler; } + } else { - if (sum > _lfScalerUpwards) { - scalingAdjustments [parentCode*siteCount + siteID] *= _lfScalingFactorThreshold; - for (long c = 0; c < alphabetDimension; c++) { - parentConditionals [c] *= _lfScalingFactorThreshold; + if (__builtin_expect(sum > _lfScalerUpwards,0)) { + if (sum < HUGE_VAL) { // no point scaling an infinity + + hyFloat scaler = _computeReductionScaler (scalingAdjustments [parentCode*siteCount + siteID] * _lfScalingFactorThreshold, sum, didScale); + + if (didScale) { + for (long c = 0; c < alphabetDimension; c++) { + parentConditionals [c] *= scaler; + } + + localScalerChange += didScale * theFilter->theFrequencies (siteOrdering.list_data[siteID]); + scalingAdjustments [parentCode*siteCount + siteID] *= scaler; + } + + //#pragma omp critical + // printf ("SCALE DOWN %lg\n", scaler); + } - localScalerChange -= theFilter->theFrequencies.get (siteOrdering.list_data[siteID]); - didScale = -1; + } } - /*if (sum == 0.) { - printf ("Zeroed out at %d (%d) node %s\n", nodeCode, parentCode, ((_CalcNode*)(isLeaf ? flatCLeaves.GetItem(nodeCode) : flatTree.GetItem(nodeCode)))->GetName()->get_str()); - }*/ childVector += alphabetDimension; } if (didScale) { + /*if (likeFuncEvalCallCount == 11035 && siteOrdering.list_data[siteID] == 1141) { + printf ("SCALED IN REGULAR COMPUTE %ld %ld %ld (%s/%lg)\n", likeFuncEvalCallCount, siteID, didScale, currentTreeNode->GetName()->get_str(), scalingAdjustments [parentCode*siteCount + siteID] ); + }*/ + if (siteCorrectionCounts) { siteCorrectionCounts [siteOrdering.list_data[siteID]] += didScale; } @@ -3694,8 +3740,18 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList hyFloat scM; if (didScale < 0) { scM = _lfScalingFactorThreshold; + if (didScale < -1) { + for (long k = 0; k < -didScale-1; k++) { + scM *= _lfScalingFactorThreshold; + } + } } else { scM = _lfScalerUpwards; + if (didScale > 1) { + for (long k = 1; k < didScale; k++) { + scM *= _lfScalerUpwards; + } + } } @@ -3770,12 +3826,19 @@ hyFloat _TheTree::ComputeTreeBlockByBranch ( _SimpleList hyFloat term; long const site_frequency = theFilter->theFrequencies (siteOrdering.list_data[siteID]); + + if (site_frequency > 1L) { term = log(accumulator) * site_frequency - correction; } else { term = log(accumulator) - correction; } // Kahan sum + + /*if (likeFuncEvalCallCount == 11035) { + fprintf (stderr, "REGULAR, %ld, %ld, %20.15lg, %20.15lg, %20.15lg\n", likeFuncEvalCallCount, siteID, accumulator, correction, term); + }*/ + hyFloat temp_sum = result + term; correction = (temp_sum - result) - term; result = temp_sum; @@ -3832,6 +3895,7 @@ void _TheTree::ComputeBranchCache ( taggedNodes.Populate (flatLeaves.lLength + flatNodes.lLength, 0, 0); + long myParent = brID -flatLeaves.lLength; const long alphabetDimension = theFilter->GetDimension(), @@ -3860,13 +3924,17 @@ void _TheTree::ComputeBranchCache ( } } - /*printf ("\n\nComputeBranchCache at branch %ld; siteOdering %s\n", - brID, _String((_String*)siteOrdering.toStr()).sData); + /* + if (likeFuncEvalCallCount == 11035) { + printf ("\n\nComputeBranchCache at branch %ld; siteOdering %s\n", + brID, _String((_String*)siteOrdering.toStr()).get_str()); - echoNodeList (rootPath,flatLeaves,flatNodes ); + echoNodeList (rootPath,flatLeaves,flatNodes,flatParents); printf ("\n"); - echoNodeList (nodesToProcess,flatLeaves,flatNodes); - */ + echoNodeList (nodesToProcess,flatLeaves,flatNodes,flatParents); + } + */ + hyFloat * state = cache + alphabetDimension * siteFrom, * childVector; @@ -3884,13 +3952,20 @@ void _TheTree::ComputeBranchCache ( state[s] = 0.; } state[siteState] = 1.; + /*if (likeFuncEvalCallCount == 11035 && siteOrdering.list_data[siteID] == 1141) { + printf ("RESOLVED SITE STATE: %15.12g, %15.12g, %15.12g, %15.12g\n", state[0],state[1],state[2],state[3]); + }*/ } else { childVector = lNodeResolutions->theData + (-siteState-1) * alphabetDimension; for (unsigned long s = 0UL; s < alphabetDimension; s++) { state[s] = childVector[s]; } + /*if (likeFuncEvalCallCount == 11035 && siteOrdering.list_data[siteID] == 1141) { + printf ("AMBIGUOUS SITE STATE (%ld): %15.12g, %15.12g, %15.12g, %15.12g\n", siteState, state[0],state[1],state[2],state[3]); + }*/ } } + } else { // an internal branch long nodeCode = brID - flatLeaves.lLength; hyFloat *lastUpdated = iNodeCache + (nodeCode * siteCount + siteFrom) * alphabetDimension; @@ -3934,9 +4009,15 @@ void _TheTree::ComputeBranchCache ( for (long nodeID = 0; nodeID < node_count; nodeID++) { bool notPassedRoot = nodeIDtheData + (-siteState-1) * alphabetDimension; } - canScale = 0; + canScale = false; } else { if (tcc&¬PassedRoot) { if ((tcc->list_data[currentTCCIndex] & bitMaskArray.masks[currentTCCBit]) > 0 && siteID > siteFrom) @@ -4067,58 +4149,69 @@ void _TheTree::ComputeBranchCache ( } } + /*if (likeFuncEvalCallCount == 11035 && siteOrdering.list_data[siteID] == 1141) { + if (!isLeaf && notPassedRoot) { + fprintf (stderr, "CACHE,%s,%15.12g,%15.12g,%15.12g,%15.12g,%15.12g\n", currentTreeNode->GetName()->get_str(), + scalingAdjustments[nodeCode*siteCount+siteID], + childVector[0],childVector[1],childVector[2],childVector[3]); + } + }*/ + hyFloat sum = .0; long didScale = 0; if (alphabetDimension == 4UL) { // special case for nuc data + /*if (likeFuncEvalCallCount == 11035 && siteOrdering.list_data[siteID] == 1141) { + printf ("\n\n%s\n",currentTreeNode->GetName()->get_str()); + printf ("parentConditionals = %15.12g %15.12g %15.12g %15.12g\n", parentConditionals[0],parentConditionals[1],parentConditionals[2],parentConditionals[3]); + printf ("childVector = %15.12g %15.12g %15.12g %15.12g\n", childVector[0],childVector[1],childVector[2],childVector[3]); + printf ("tmatrix[0] = %15.12g %15.12g %15.12g %15.12g\n", tMatrix[0],tMatrix[1],tMatrix[2],tMatrix[3]); + printf ("tmatrix[1] = %15.12g %15.12g %15.12g %15.12g\n", tMatrix[4],tMatrix[5],tMatrix[6],tMatrix[7]); + printf ("tmatrix[2] = %15.12g %15.12g %15.12g %15.12g\n", tMatrix[8],tMatrix[9],tMatrix[10],tMatrix[11]); + printf ("tmatrix[3] = %15.12g %15.12g %15.12g %15.12g\n", tMatrix[12],tMatrix[13],tMatrix[14],tMatrix[15]); + + }*/ + + #ifdef _SLKP_USE_AVX_INTRINSICS _handle4x4_pruning_case (childVector, tMatrix, parentConditionals, tmatrix_transpose); #else _handle4x4_pruning_case (childVector, tMatrix, parentConditionals, nil); #endif + /*if (likeFuncEvalCallCount == 11035 && siteOrdering.list_data[siteID] == 1141) { + printf ("parentConditionals[post child mixin] = %15.12g %15.12g %15.12g %15.12g [can scale = %d]\n", parentConditionals[0],parentConditionals[1],parentConditionals[2],parentConditionals[3],canScale); + }*/ + if (canScale) { sum = (parentConditionals [0] + parentConditionals [1]) + (parentConditionals [2] + parentConditionals [3]); - if (sum < _lfScalingFactorThreshold && sum > 0.0) { - hyFloat tryScale = scalingAdjustments [nodeCode*siteCount + siteID] * _lfScalerUpwards; - if (tryScale < HUGE_VAL) { - parentConditionals[0] *= _lfScalerUpwards; - parentConditionals[1] *= _lfScalerUpwards; - parentConditionals[2] *= _lfScalerUpwards; - parentConditionals[3] *= _lfScalerUpwards; - - localScalerChange += theFilter->theFrequencies (siteOrdering.list_data[siteID]); - didScale = 1; - scalingAdjustments [nodeCode*siteCount + siteID] = tryScale; + + if (__builtin_expect(sum < _lfScalingFactorThreshold && sum > 0.0,0)) { + hyFloat scaler = _computeBoostScaler(scalingAdjustments [nodeCode*siteCount + siteID] * _lfScalerUpwards, sum, didScale); + if (didScale) { + parentConditionals [0] *= scaler; + parentConditionals [1] *= scaler; + parentConditionals [2] *= scaler; + parentConditionals [3] *= scaler; + localScalerChange += didScale * theFilter->theFrequencies.get (siteOrdering.list_data[siteID]); } + } else { - if (sum > _lfScalerUpwards) { + if (__builtin_expect(sum > _lfScalerUpwards,0)) { if (sum < HUGE_VAL) { // no point scaling an infinity - didScale = -1; - - - hyFloat scaler = scalingAdjustments [parentCode*siteCount + siteID] * _lfScalingFactorThreshold; - - sum *= _lfScalingFactorThreshold; - while (sum > _lfScalerUpwards) { - sum *= _lfScalingFactorThreshold; - scaler *= _lfScalingFactorThreshold; - didScale --; - } - - - parentConditionals [0] *= scaler; - parentConditionals [1] *= scaler; - parentConditionals [2] *= scaler; - parentConditionals [3] *= scaler; - - localScalerChange += didScale * theFilter->theFrequencies (siteOrdering.list_data[siteID]); - //didScale = -1; - scalingAdjustments [nodeCode*siteCount + siteID] = scaler; - } + hyFloat scaler = _computeReductionScaler (scalingAdjustments [nodeCode*siteCount + siteID] * _lfScalingFactorThreshold, sum, didScale); + + if (didScale) { + parentConditionals [0] *= scaler; + parentConditionals [1] *= scaler; + parentConditionals [2] *= scaler; + parentConditionals [3] *= scaler; + localScalerChange += didScale * theFilter->theFrequencies (siteOrdering.list_data[siteID]); + } - } + } + } } } childVector += 4L; @@ -4196,34 +4289,55 @@ void _TheTree::ComputeBranchCache ( childVector += alphabetDimension; if (canScale) { - if (sum < _lfScalingFactorThreshold && sum > 0.0) { - hyFloat tryScale = scalingAdjustments [nodeCode*siteCount + siteID] * _lfScalerUpwards; - if (tryScale < HUGE_VAL) { - //printf ("tryScale < HUGE_VAL\n"); + if (__builtin_expect(sum < _lfScalingFactorThreshold && sum > 0.0,0)) { + hyFloat scaler = _computeBoostScaler(scalingAdjustments [nodeCode*siteCount + siteID] * _lfScalerUpwards, sum, didScale); + + if (didScale) { for (unsigned long c = 0UL; c < alphabetDimension; c++) { - parentConditionals [c] *= _lfScalerUpwards; + parentConditionals [c] *= scaler; } - - localScalerChange += theFilter->theFrequencies.get (siteOrdering.list_data[siteID]); - didScale = 1; + localScalerChange += didScale * theFilter->theFrequencies.get (siteOrdering.list_data[siteID]); } - } else { - if (sum > _lfScalerUpwards) { - //printf ("sum > _lfScalerUpwards\n"); - for (unsigned long c = 0UL; c < alphabetDimension; c++) { - parentConditionals [c] *= _lfScalingFactorThreshold; - } + + } else { + if (__builtin_expect(sum > _lfScalerUpwards && sum < HUGE_VAL,0)) { + hyFloat scaler = _computeReductionScaler (scalingAdjustments [nodeCode*siteCount + siteID] * _lfScalingFactorThreshold, sum, didScale); - localScalerChange -= theFilter->theFrequencies.get (siteOrdering.list_data[siteID]); - didScale = -1; + if (didScale) { + for (unsigned long c = 0UL; c < alphabetDimension; c++) { + parentConditionals [c] *= scaler; + } + localScalerChange += didScale * theFilter->theFrequencies (siteOrdering.list_data[siteID]); + } } } } } + /*if (didScale && likeFuncEvalCallCount == 11035) { + printf ("SCALED IN BRANCH CACHE COMPUTE %ld %ld %ld (%s/%lg)\n", likeFuncEvalCallCount, siteID, didScale, currentTreeNode->GetName()->get_str(), scalingAdjustments [parentCode*siteCount + siteID] ); + }*/ + if (didScale&&siteCorrectionCounts) { + // siteCorrectionCounts [siteOrdering.list_data[siteID]] += didScale; - siteRes[siteOrdering.list_data[siteID]] *= didScale<0?_lfScalingFactorThreshold:_lfScalerUpwards; + if (didScale == 1L) { + siteRes[siteOrdering.list_data[siteID]] *= _lfScalerUpwards; + } else { + if (didScale == -1L) { + siteRes[siteOrdering.list_data[siteID]] *= _lfScalingFactorThreshold; + } else { + if (didScale > 0) { + for (long k = 0; k < didScale; k++) { + siteRes[siteOrdering.list_data[siteID]] *= _lfScalerUpwards; + } + } else{ + for (long k = 0; k < -didScale; k++) { + siteRes[siteOrdering.list_data[siteID]] *= _lfScalingFactorThreshold; + } + } + } + } } } } @@ -4288,6 +4402,11 @@ hyFloat _TheTree::ComputeLLWithBranchCache ( } else { term = log(accumulator) - correction; } + + /*if (likeFuncEvalCallCount == 11035) { + fprintf (stderr, "CACHE, %ld, %ld, %20.15lg, %20.15lg, %20.15lg\n", likeFuncEvalCallCount, siteID, accumulator, correction, term); + }*/ + hyFloat temp_sum = result + term; correction = (temp_sum - result) - term; result = temp_sum; diff --git a/tests/hbltests/SimpleOptimizations/IntermediateCodon.bf b/tests/hbltests/SimpleOptimizations/IntermediateCodon.bf index dccf7e593..85311c6ac 100644 --- a/tests/hbltests/SimpleOptimizations/IntermediateCodon.bf +++ b/tests/hbltests/SimpleOptimizations/IntermediateCodon.bf @@ -611,7 +611,7 @@ Model LargeNuc_part_MG94xREV_3x4_model=(LargeNuc_part_MG94xREV_3x4,LargeNuc_part UseModel (LargeNuc_part_MG94xREV_3x4_model); -DataSet flu = ReadDataFile("../data/fluHA_codon.nex"); +DataSet flu = ReadDataFile(PATH_TO_CURRENT_BF + "/../data/fluHA.nex"); Tree LargeNuc_tree = DATAFILE_TREE; diff --git a/tests/hbltests/SimpleOptimizations/LargeNuc.bf b/tests/hbltests/SimpleOptimizations/LargeNuc.bf index 62d47aef5..3159c5fe6 100644 --- a/tests/hbltests/SimpleOptimizations/LargeNuc.bf +++ b/tests/hbltests/SimpleOptimizations/LargeNuc.bf @@ -3129,6 +3129,13 @@ MATRIX 'DMG39_199810' CCCATYAGTCCTATTGAAACTGTACCAGTAAAAAAGCCAGGAATGGATGGCCCAARAGTYAAACAATGGCCATTGACTGARGAAAAAAAAGCATTAATAGAAATCTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAGAATTGGGCCTGATAATCCATATAATACTCCAGTATTTGCYATAAAGAAAAAAGACAGTACTAAATGGAGAAAGYTAGTAGATTTCAGAGARCTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTAYTRGATGTGGGTGATGCATAYTTTTCAATTCCTTTAGATGARTTCAGGAAGTAYACTGCATTTACCATACCTAGTACAAACAATGAGACACCAGGAATTAGATATCAGTACAATGTGCTTCCACAGGGAGGATCACCAGCAATCTTCCAAAGCATGACAAGAATCGAGCCTTTTAGAAAACAAAATYCARACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGARCAAAAATAGAGGAACTGAGACAACATCTGTTGAAGGGATTGACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAGTGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAAAGCTGGACTGTCAATGAYATACAGAAGTTAGTGGGAAAATTAAATTGGGCAAGTATTTACCCRGGGATTAAAGTAAGGCARTTATGTAAACTCCTTAGGGGAACCAAGGCACTAACAGAAGTAGTACCACTAACAAGAGAAGCAGAR; END; +BEGIN TREES; + +TREE T = 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+ + +END TREES; + BEGIN HYPHY; _testDescription = " fit the REV model to an HIV RT alignment with 3112 sequences and 873 nucleotides";