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biology/hyphy: Update to 2.5.38
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Upstream changes: veg/hyphy@2.5.36...2.5.38

Sponsored by:	The FreeBSD Foundation
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@Jehops
Jehops committed Apr 24, 2022
1 parent 3994961 commit e2c4d38
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Showing 5 changed files with 11 additions and 231 deletions.
2 changes: 1 addition & 1 deletion biology/hyphy/Makefile
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@@ -1,5 +1,5 @@
PORTNAME= hyphy
DISTVERSION= 2.5.36
DISTVERSION= 2.5.38
CATEGORIES= biology

MAINTAINER= jrm@FreeBSD.org
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6 changes: 3 additions & 3 deletions biology/hyphy/distinfo
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@@ -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
10 changes: 0 additions & 10 deletions biology/hyphy/files/patch-src_core_include_function__templates.h
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70 changes: 7 additions & 63 deletions biology/hyphy/files/patch-src_core_matrix.cpp
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@@ -1,106 +1,50 @@
--- 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)
- #pragma clang loop unroll(enable)
#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)
- #pragma clang loop unroll(enable)
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)
- #pragma clang loop unroll(enable)
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)
- #pragma clang loop unroll(enable)
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)
- #pragma clang loop unroll(enable)
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)
- #pragma clang loop unroll(enable)
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) {
154 changes: 0 additions & 154 deletions biology/hyphy/files/patch-src_core_tree__evaluator.cpp
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