git: e2c4d38d4835 - main - biology/hyphy: Update to 2.5.38
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Date: Sun, 24 Apr 2022 18:24:53 UTC
The branch main has been updated by jrm:
URL: https://cgit.FreeBSD.org/ports/commit/?id=e2c4d38d483537ebe27531c71a9359aae6135354
commit e2c4d38d483537ebe27531c71a9359aae6135354
Author: Joseph Mingrone <jrm@FreeBSD.org>
AuthorDate: 2022-04-19 16:21:42 +0000
Commit: Joseph Mingrone <jrm@FreeBSD.org>
CommitDate: 2022-04-24 18:24:30 +0000
biology/hyphy: Update to 2.5.38
Upstream changes: https://github.com/veg/hyphy/compare/2.5.36...2.5.38
Sponsored by: The FreeBSD Foundation
---
biology/hyphy/Makefile | 2 +-
biology/hyphy/distinfo | 6 +-
.../patch-src_core_include_function__templates.h | 10 --
biology/hyphy/files/patch-src_core_matrix.cpp | 70 +---------
.../hyphy/files/patch-src_core_tree__evaluator.cpp | 154 ---------------------
5 files changed, 11 insertions(+), 231 deletions(-)
diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile
index 9f1d25f3fd12..80ae747bc589 100644
--- a/biology/hyphy/Makefile
+++ b/biology/hyphy/Makefile
@@ -1,5 +1,5 @@
PORTNAME= hyphy
-DISTVERSION= 2.5.36
+DISTVERSION= 2.5.38
CATEGORIES= biology
MAINTAINER= jrm@FreeBSD.org
diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo
index db30c7c8c9e3..0e642ff3cb29 100644
--- a/biology/hyphy/distinfo
+++ b/biology/hyphy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1643865503
-SHA256 (veg-hyphy-2.5.36_GH0.tar.gz) = c48a077deff3e06cadffa94cd5e91ab659b0ebc6cb60a0d090747bfeff69aae1
-SIZE (veg-hyphy-2.5.36_GH0.tar.gz) = 5362425
+TIMESTAMP = 1650376110
+SHA256 (veg-hyphy-2.5.38_GH0.tar.gz) = 1b66af17f9f7dd0e9951a9bd3b106b95bf5915a78523973ba79af64f970770d6
+SIZE (veg-hyphy-2.5.38_GH0.tar.gz) = 5365153
diff --git a/biology/hyphy/files/patch-src_core_include_function__templates.h b/biology/hyphy/files/patch-src_core_include_function__templates.h
deleted file mode 100644
index 7ca06b1cc56a..000000000000
--- a/biology/hyphy/files/patch-src_core_include_function__templates.h
+++ /dev/null
@@ -1,10 +0,0 @@
---- src/core/include/function_templates.h.orig 2022-02-21 19:44:45 UTC
-+++ src/core/include/function_templates.h
-@@ -156,7 +156,6 @@ void ArrayForEach(ARG_TYPE *array, unsigned long dimen
- template <typename ARG_TYPE>
- void InitializeArray(ARG_TYPE *array, unsigned long dimension,
- ARG_TYPE &&value) {
-- #pragma clang loop unroll_count(8)
- #pragma GCC unroll 4
- for (unsigned long i = 0UL; i < dimension; i++) {
- array[i] = value;
diff --git a/biology/hyphy/files/patch-src_core_matrix.cpp b/biology/hyphy/files/patch-src_core_matrix.cpp
index 0d5720b2751b..a4a280d2d94c 100644
--- a/biology/hyphy/files/patch-src_core_matrix.cpp
+++ b/biology/hyphy/files/patch-src_core_matrix.cpp
@@ -1,6 +1,6 @@
---- src/core/matrix.cpp.orig 2022-02-21 19:46:34 UTC
+--- src/core/matrix.cpp.orig 2022-04-24 18:04:11 UTC
+++ src/core/matrix.cpp
-@@ -3391,7 +3391,6 @@ void _Matrix::AddMatrix (_Matrix& storage, _Matrix
+@@ -3405,7 +3405,6 @@ void _Matrix::AddMatrix (_Matrix& storage, _Matrix
#pragma GCC unroll 4
#pragma clang loop vectorize(enable)
#pragma clang loop interleave(enable)
@@ -8,31 +8,7 @@
#pragma GCC ivdep
#pragma ivdep
for (long idx = 0; idx < upto; idx+=16) {
-@@ -3410,7 +3409,6 @@ void _Matrix::AddMatrix (_Matrix& storage, _Matrix
- #pragma GCC unroll 4
- #pragma clang loop vectorize(enable)
- #pragma clang loop interleave(enable)
-- #pragma clang loop unroll(enable)
- #pragma GCC ivdep
- #pragma ivdep
- for (long idx = 0; idx < upto; idx+=8) {
-@@ -3440,7 +3438,6 @@ void _Matrix::AddMatrix (_Matrix& storage, _Matrix
- #pragma GCC unroll 4
- #pragma clang loop vectorize(enable)
- #pragma clang loop interleave(enable)
-- #pragma clang loop unroll(enable)
- for (long idx = 0; idx < upto; idx+=16) {
- CELL_OP (idx);
- CELL_OP (idx+4);
-@@ -3454,7 +3451,6 @@ void _Matrix::AddMatrix (_Matrix& storage, _Matrix
- #pragma GCC unroll 4
- #pragma clang loop vectorize(enable)
- #pragma clang loop interleave(enable)
-- #pragma clang loop unroll(enable)
- #pragma GCC ivdep
- #pragma ivdep
- for (long idx = 0; idx < upto; idx+=8) {
-@@ -3895,7 +3891,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
+@@ -3909,7 +3908,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
#pragma GCC unroll 4
#pragma clang loop vectorize(enable)
#pragma clang loop interleave(enable)
@@ -40,7 +16,7 @@
for (long k = 0; k < vDim; k+=4) {
__m256d D4, B4;
DO_GROUP_OP (D4, B4, k);
-@@ -3946,7 +3941,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
+@@ -3960,7 +3958,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
#pragma GCC unroll 4
#pragma clang loop vectorize(enable)
#pragma clang loop interleave(enable)
@@ -48,15 +24,7 @@
for (long k = 0; k < vDim; k+=2) {
__m128d D4, B4;
DO_GROUP_OP1 (D4, B4, k);
-@@ -3998,7 +3992,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
- #pragma GCC unroll 4
- #pragma clang loop vectorize(enable)
- #pragma clang loop interleave(enable)
-- #pragma clang loop unroll(enable)
- for (long k = 0; k < vDim; k+=2) {
- float64x2_t D4, B4;
- DO_GROUP_OP1 (D4, B4, k);
-@@ -4163,7 +4156,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
+@@ -4177,7 +4174,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
#pragma GCC unroll 4
#pragma clang loop vectorize(enable)
#pragma clang loop interleave(enable)
@@ -64,7 +32,7 @@
for (long k = 0; k < dimm4; k+=4) {
__m256d D4, B4;
DO_GROUP_OP (D4, B4, k);
-@@ -4271,7 +4263,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
+@@ -4285,7 +4281,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
#pragma GCC unroll 4
#pragma clang loop vectorize(enable)
#pragma clang loop interleave(enable)
@@ -72,15 +40,7 @@
for (long k = 0; k < dimm4; k+=2) {
__m128d D4, B4;
DO_GROUP_OP1 (D4, B4, k);
-@@ -4380,7 +4371,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
- #pragma GCC unroll 4
- #pragma clang loop vectorize(enable)
- #pragma clang loop interleave(enable)
-- #pragma clang loop unroll(enable)
- for (long k = 0; k < dimm4; k+=2) {
- float64x2_t D4, B4;
- DO_GROUP_OP1 (D4, B4, k);
-@@ -4441,7 +4431,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
+@@ -4455,7 +4450,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
#pragma GCC unroll 8
#pragma clang loop vectorize(enable)
#pragma clang loop interleave(enable)
@@ -88,19 +48,3 @@
for (long k = 0, column = j*hDim; k < vDim; k++, column ++) {
resCell += row[k] * secondArg.theData [column];
}
-@@ -5822,7 +5811,6 @@ _Matrix* _Matrix::Exponentiate (hyFloat scale_to, b
- #pragma GCC unroll 4
- #pragma clang loop vectorize(enable)
- #pragma clang loop interleave(enable)
-- #pragma clang loop unroll(enable)
- for (long c = from; c < compressedIndex[r]; c++, i++) {
- theIndex[i] = compressedIndex[c+hDim] * vDim + r;
- }
-@@ -6988,7 +6976,6 @@ hyFloat _Matrix::Sqr (hyFloat* _hprestrict_ sta
- #pragma GCC unroll 4
- #pragma clang loop vectorize(enable)
- #pragma clang loop interleave(enable)
-- #pragma clang loop unroll(enable)
- #pragma GCC ivdep
- #pragma ivdep
- for (long k = 0; k < loopBound; k+=4) {
diff --git a/biology/hyphy/files/patch-src_core_tree__evaluator.cpp b/biology/hyphy/files/patch-src_core_tree__evaluator.cpp
deleted file mode 100644
index 3adcafaf5866..000000000000
--- a/biology/hyphy/files/patch-src_core_tree__evaluator.cpp
+++ /dev/null
@@ -1,154 +0,0 @@
---- src/core/tree_evaluator.cpp.orig 2022-02-21 19:48:41 UTC
-+++ src/core/tree_evaluator.cpp
-@@ -127,7 +127,6 @@ inline double _sse_sum_2 (__m128d const & x) {
- template<long D> inline void __ll_handle_matrix_transpose (hyFloat const * __restrict transitionMatrix, hyFloat * __restrict tMatrixT) {
- long i = 0L;
- for (long r = 0L; r < D; r++) {
-- #pragma unroll(4)
- #pragma GCC unroll 4
- for (long c = 0L; c < D; c++, i++) {
- tMatrixT[c*D+r] = transitionMatrix[i];
-@@ -154,7 +153,6 @@ template<long D> inline bool __ll_handle_conditional_a
- }
- }*/
-
-- #pragma unroll(4)
- #pragma GCC unroll 4
- for (long k = 0L; k < D; k++) {
- parentConditionals[k] *= tMatrix[siteState+D*k];
-@@ -172,7 +170,6 @@ template<long D> inline bool __ll_handle_conditional_a
- } else {
- if (tcc) {
- if (__builtin_expect((tcc->list_data[currentTCCIndex] & bitMaskArray.masks[currentTCCBit]) > 0 && siteID > siteFrom,0)) {
-- #pragma unroll(4)
- #pragma GCC unroll 4
- for (long k = 0L; k < D; k++) {
- childVector[k] = lastUpdatedSite[k];
-@@ -200,7 +197,6 @@ inline bool __ll_handle_conditional_array_initializati
- }
- if (__builtin_expect(siteState >= 0L,1)) {
- // a single character state; sweep down the appropriate column
-- #pragma unroll(4)
- #pragma GCC unroll 4
- for (long k = 0L; k < D; k++) {
- parentConditionals[k] *= tMatrix[siteState+D*k];
-@@ -212,7 +208,6 @@ inline bool __ll_handle_conditional_array_initializati
- } else {
- if (tcc) {
- if (__builtin_expect((tcc->list_data[currentTCCIndex] & bitMaskArray.masks[currentTCCBit]) > 0 && siteID > siteFrom,0)) {
-- #pragma unroll(4)
- #pragma GCC unroll 4
- for (long k = 0L; k < D; k++) {
- childVector[k] = lastUpdatedSite[k];
-@@ -542,7 +537,6 @@ template<long D> inline void __ll_product_sum_loop (hy
- #pragma GCC unroll 8
- #pragma clang loop vectorize(enable)
- #pragma clang loop interleave(enable)
-- #pragma clang loop unroll(enable)
- for (long c = 0; c < D; c++)
- accumulator += tMatrix[c] * childVector[c];
-
-@@ -558,7 +552,6 @@ inline void __ll_product_sum_loop_generic (hyFloat con
- #pragma GCC unroll 8
- #pragma clang loop vectorize(enable)
- #pragma clang loop interleave(enable)
-- #pragma clang loop unroll(enable)
- for (long c = 0; c < D; c++)
- accumulator += tMatrix[c] * childVector[c];
-
-@@ -595,7 +588,6 @@ template<long D, bool ADJUST> inline void __ll_loop_ha
- fprintf (stderr, "UP %ld (%ld) %lg\n", didScale, parentCode, scaler);
- }*/
- if (didScale) {
-- #pragma unroll(4)
- #pragma GCC unroll 4
- for (long c = 0; c < D; c++) {
- parentConditionals [c] *= scaler;
-@@ -626,7 +618,6 @@ template<long D, bool ADJUST> inline void __ll_loop_ha
- }*/
-
- if (didScale) {
-- #pragma unroll(4)
- #pragma GCC unroll 4
- for (long c = 0; c < D; c++) {
- parentConditionals [c] *= scaler;
-@@ -657,7 +648,6 @@ template<bool ADJUST> inline void __ll_loop_handle_sca
- hyFloat scaler = _computeBoostScaler(scalingAdjustments [parentCode*siteCount + siteID] * _lfScalerUpwards, sum, didScale);
-
- if (didScale) {
-- #pragma unroll(8)
- #pragma GCC unroll 8
- for (long c = 0; c < D; c++) {
- parentConditionals [c] *= scaler;
-@@ -679,7 +669,6 @@ template<bool ADJUST> inline void __ll_loop_handle_sca
- hyFloat scaler = _computeReductionScaler (scalingAdjustments [parentCode*siteCount + siteID] * _lfScalingFactorThreshold, sum, didScale);
-
- if (didScale) {
-- #pragma unroll(8)
- #pragma GCC unroll 8
- for (long c = 0; c < D; c++) {
- parentConditionals [c] *= scaler;
-@@ -707,7 +696,6 @@ template<long D> inline void __ll_loop_handle_leaf_cas
- } else {
- for (long k = siteFrom; k < siteTo; k++, pp += D) {
- hyFloat lsf = localScalingFactor[k];
--#pragma unroll(4)
- #pragma GCC unroll 4
- for (long s = 0; s < D; s++) {
- pp[s] = lsf;
-@@ -1585,7 +1573,6 @@ hyFloat _TheTree::ComputeTreeBlockByBranch (
- accumulator = rootConditionals[rootIndex + rootState] * theProbs[rootState];
- rootIndex += alphabetDimension;
- } else {
-- #pragma unroll(4)
- #pragma GCC unroll 4
- for (long p = 0; p < alphabetDimension; p++,rootIndex++) {
- accumulator += rootConditionals[rootIndex] * theProbs[p];
-@@ -1644,7 +1631,6 @@ template<long D> inline bool __lcache_loop_preface (bo
- long siteState = lNodeFlags[nodeCode*siteCount + siteOrdering.list_data[siteID]] ;
- if (siteState >= 0L) {
- unsigned long target_index = siteState;
-- #pragma unroll(4)
- #pragma GCC unroll 4
- for (long k = 0L; k < D; k++, target_index+=D) {
- parentConditionals[k] *= tMatrix[target_index];
-@@ -1659,7 +1645,6 @@ template<long D> inline bool __lcache_loop_preface (bo
- if ((tcc->list_data[currentTCCIndex] & bitMaskArray.masks[currentTCCBit]) > 0 && siteID > siteFrom)
- // the value of this conditional vector needs to be copied from a previously stored site
- // subtree duplication
-- #pragma unroll(4)
- #pragma GCC unroll 4
- for (long k = 0UL; k < D; k++) {
- childVector[k] = lastUpdatedSite[k];
-@@ -1688,7 +1673,6 @@ inline bool __lcache_loop_preface_generic (bool isLeaf
- long siteState = lNodeFlags[nodeCode*siteCount + siteOrdering.list_data[siteID]] ;
- if (siteState >= 0L) {
- unsigned long target_index = siteState;
-- #pragma unroll(4)
- #pragma GCC unroll 4
- for (long k = 0L; k < D; k++, target_index+=D) {
- parentConditionals[k] *= tMatrix[target_index];
-@@ -1704,7 +1688,6 @@ inline bool __lcache_loop_preface_generic (bool isLeaf
- if ((tcc->list_data[currentTCCIndex] & bitMaskArray.masks[currentTCCBit]) > 0 && siteID > siteFrom)
- // the value of this conditional vector needs to be copied from a previously stored site
- // subtree duplication
-- #pragma unroll(4)
- #pragma GCC unroll 4
- for (long k = 0UL; k < D; k++) {
- childVector[k] = lastUpdatedSite[k];
-@@ -1966,7 +1949,6 @@ void _TheTree::ComputeBranchCache (
- unsigned long k3 = 0UL;
- for (unsigned long k = siteFrom; k < siteTo; k++) {
- hyFloat scaler = localScalingFactor[k];
-- #pragma unroll(4)
- #pragma GCC unroll 4
- for (unsigned long k2 = 0UL; k2 < alphabetDimension; k2++, k3++) {
- parentConditionals [k3] = scaler;
-@@ -2474,7 +2456,6 @@ void _TheTree::ComputeBranchCache (
- #pragma GCC unroll 8
- #pragma clang loop vectorize(enable)
- #pragma clang loop interleave(enable)
-- #pragma clang loop unroll(enable)
- for (long k = 0; k < alphabetDimension; k++) {
- sum += parentConditionals[k];
- }