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Sun, 24 Apr 2022 18:24:53 GMT (envelope-from git) Date: Sun, 24 Apr 2022 18:24:53 GMT Message-Id: <202204241824.23OIOrL9014359@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Joseph Mingrone Subject: git: e2c4d38d4835 - main - biology/hyphy: Update to 2.5.38 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jrm X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: e2c4d38d483537ebe27531c71a9359aae6135354 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1650824693; 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mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jrm: URL: https://cgit.FreeBSD.org/ports/commit/?id=e2c4d38d483537ebe27531c71a9359aae6135354 commit e2c4d38d483537ebe27531c71a9359aae6135354 Author: Joseph Mingrone AuthorDate: 2022-04-19 16:21:42 +0000 Commit: Joseph Mingrone 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 - 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 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 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 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 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 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 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 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 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 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 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 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]; - }