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Description: filter SSE3 intrinsics
src/sse.c is compiled when SSE is active at least. However this file includes
some intrinsics which are specific to SSE3, so adjust the source code to make
sure the -msse3 option has been specified indeed. Unfortunately, this also
means that the code is unusable as is on x86 without proper sse3-support.
Author: Étienne Mollier <emollier@debian.org>
Forwarded: no
Last-Update: 2021-11-17
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- phyml.orig/src/sse.h
+++ phyml/src/sse.h
@@ -22,7 +22,7 @@
#include "times.h"
#include "mixt.h"
-#if (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#if defined(__SSE3__)
void SSE_Update_Partial_Lk(t_tree *tree,t_edge *b_fcus,t_node *n);
void SSE_Update_Eigen_Lr(t_edge *b, t_tree *tree);
--- phyml.orig/src/lk.c
+++ phyml/src/lk.c
@@ -779,7 +779,7 @@
{
#if (defined(__AVX__) || defined(__AVX2__))
tree->site_lk_cat[catg] = AVX_Lk_Core_One_Class_No_Eigen_Lr(p_lk_left,p_lk_rght,Pij_rr,tPij_rr,pi,ns,ambiguity_check,state);
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#elif defined(__SSE3__)
tree->site_lk_cat[catg] = SSE_Lk_Core_One_Class_No_Eigen_Lr(p_lk_left,p_lk_rght,Pij_rr,tPij_rr,pi,ns,ambiguity_check,state);
#else
tree->site_lk_cat[catg] = Lk_Core_One_Class_No_Eigen_Lr(p_lk_left,p_lk_rght,Pij_rr,pi,ns,ambiguity_check,state);
@@ -870,7 +870,7 @@
{
#if (defined(__AVX__) || defined(__AVX2__))
tree->site_lk_cat[catg] = AVX_Lk_Core_One_Class_Eigen_Lr(dot_prod,expl ? expl : NULL,ns);
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#elif defined(__SSE3__)
tree->site_lk_cat[catg] = SSE_Lk_Core_One_Class_Eigen_Lr(dot_prod,expl ? expl : NULL,ns);
#else
tree->site_lk_cat[catg] = Lk_Core_One_Class_Eigen_Lr(dot_prod,expl ? expl : NULL,ns);
@@ -963,7 +963,7 @@
AVX_Lk_dLk_Core_One_Class_Eigen_Lr(dot_prod,
expl ? expl : NULL,
ns,&core_lk,&core_dlk);
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#elif defined(__SSE3__)
SSE_Lk_dLk_Core_One_Class_Eigen_Lr(dot_prod,
expl ? expl : NULL,
ns,&core_lk,&core_dlk);
@@ -1045,7 +1045,7 @@
#if (defined(__AVX__) || defined(__AVX2__))
AVX_Update_Eigen_Lr(b,tree);
return;
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#elif defined(__SSE3__)
SSE_Update_Eigen_Lr(b,tree);
return;
#endif
@@ -1292,7 +1292,7 @@
{
#if (defined(__AVX__) || defined(__AVX2__))
AVX_Update_Partial_Lk(tree,b,d);
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#elif defined(__SSE3__)
SSE_Update_Partial_Lk(tree,b,d);
#else
Default_Update_Partial_Lk(tree,b,d);
--- phyml.orig/src/sse.c
+++ phyml/src/sse.c
@@ -16,7 +16,7 @@
//////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////
-#if ((defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__)) && !((defined __AVX__ || defined __AVX2__)))
+#if (defined(__SSE3__) && !((defined __AVX__ || defined __AVX2__)))
void SSE_Update_Eigen_Lr(t_edge *b, t_tree *tree)
{
--- phyml.orig/src/utilities.h
+++ phyml/src/utilities.h
@@ -38,7 +38,7 @@
#include <xmmintrin.h>
#include <pmmintrin.h>
#include <immintrin.h>
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#elif defined(__SSE3__)
#include <emmintrin.h>
#include <pmmintrin.h>
#endif
@@ -122,7 +122,7 @@
#if (defined __AVX__ || defined __AVX2__)
#define BYTE_ALIGN 32
-#elif (defined(__SSE__) || defined(__SSE2__) || defined __SSE3__)
+#elif defined __SSE3__
#define BYTE_ALIGN 16
#else
#define BYTE_ALIGN 1
@@ -772,8 +772,10 @@
#if (defined(__AVX__) || defined(__AVX2__))
__m256d *_tPij1,*_tPij2,*_pmat1plk1,*_pmat2plk2,*_plk0,*_l_ev,*_r_ev,*_prod_left,*_prod_rght;
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#elif defined(__SSE3__)
__m128d *_tPij1,*_tPij2,*_pmat1plk1,*_pmat2plk2,*_plk0,*_l_ev,*_r_ev,*_prod_left,*_prod_rght;
+#else
+ long *_tPij1,*_tPij2,*_pmat1plk1,*_pmat2plk2,*_plk0,*_l_ev,*_r_ev,*_prod_left,*_prod_rght;
#endif
phydbl *p_lk_left_pi,*l_ev;
@@ -2559,7 +2561,7 @@
#if (defined(__AVX__) || defined(__AVX2__))
#include "avx.h"
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#elif defined(__SSE3__)
#include "sse.h"
#endif
--- phyml.orig/src/free.c
+++ phyml/src/free.c
@@ -378,7 +378,7 @@
Free(tree->p_lk_left_pi);
Free(tree->l_ev);
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
Free(tree->_tPij1);
Free(tree->_tPij2);
Free(tree->_pmat1plk1);
--- phyml.orig/src/make.c
+++ phyml/src/make.c
@@ -29,7 +29,7 @@
const unsigned int ns = tree->mod->ns;
const unsigned int nsns = ns * ns;
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
const unsigned int sz = (int)BYTE_ALIGN / 8;
const unsigned int ncatg = tree->mod->ras->n_catg;
#endif
@@ -76,7 +76,7 @@
tree->_prod_rght = _aligned_malloc(ns / sz * sizeof(__m256d),BYTE_ALIGN);
tree->big_lk_array = _aligned_malloc(((3*tree->n_otu-2)*tree->data->crunch_len*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes)*tree->mod->ns + 2*(2*tree->n_otu-1)*tree->mod->ras->n_catg*tree->mod->ns*tree->mod->ns) * sizeof(phydbl),BYTE_ALIGN);
#endif
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#elif (defined(__SSE3__))
#ifndef WIN32
if(posix_memalign((void **)&tree->dot_prod,BYTE_ALIGN,(size_t)tree->n_pattern*tree->mod->ns*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes)*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
if(posix_memalign((void **)&tree->expl,BYTE_ALIGN,(size_t)3*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes)*tree->mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
@@ -108,7 +108,7 @@
tree->_prod_rght = _aligned_malloc(ns / sz * sizeof(__m128d),BYTE_ALIGN);
tree->big_lk_array = _aligned_malloc(((3*tree->n_otu-2)*tree->data->crunch_len*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes)*tree->mod->ns + 2*(2*tree->n_otu-1)*tree->mod->ras->n_catg*tree->mod->ns*tree->mod->ns) * sizeof(phydbl),BYTE_ALIGN);
#endif
-#elif (!(defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__)))
+#elif (!(defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__)))
tree->dot_prod = (phydbl *)mCalloc(tree->n_pattern*tree->mod->ns*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes),sizeof(phydbl));
tree->expl = (phydbl *)mCalloc(3*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes)*tree->mod->ns,sizeof(phydbl));
tree->p_lk_left_pi = (phydbl *)mCalloc(ns,sizeof(phydbl));
@@ -381,7 +381,7 @@
{
b->p_lk_left = NULL;
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
#ifndef WIN32
if(posix_memalign((void **)&b->p_lk_tip_l,BYTE_ALIGN,(size_t)tree->data->crunch_len*tree->mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
#else
@@ -458,7 +458,7 @@
}
else if(b->rght->tax)
{
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
#ifndef WIN32
if(posix_memalign((void **)&b->p_lk_tip_r,BYTE_ALIGN,(size_t)tree->data->crunch_len*tree->mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
#else
@@ -511,7 +511,7 @@
tree->sum_scale_extra_0 = (int *)mCalloc(tree->data->crunch_len*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes),sizeof(int));
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
#ifndef WIN32
if(posix_memalign((void **)&tree->p_lk_extra_0,BYTE_ALIGN,(size_t)tree->data->crunch_len*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes)*tree->mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
#else
@@ -522,7 +522,7 @@
#endif
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
#ifndef WIN32
if(posix_memalign((void **)&tree->p_lk_tip_extra_0,BYTE_ALIGN,(size_t)tree->data->crunch_len*tree->mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
#else
@@ -540,7 +540,7 @@
tree->sum_scale_extra_1 = (int *)mCalloc(tree->data->crunch_len*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes),sizeof(int));
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
#ifndef WIN32
if(posix_memalign((void **)&tree->p_lk_extra_1,BYTE_ALIGN,(size_t)tree->data->crunch_len*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes)*tree->mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
#else
@@ -551,7 +551,7 @@
#endif
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
#ifndef WIN32
if(posix_memalign((void **)&tree->p_lk_tip_extra_1,BYTE_ALIGN,(size_t)tree->data->crunch_len*tree->mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
#else
@@ -947,7 +947,7 @@
mod->Pij_rr = (vect_dbl *)mCalloc(1,sizeof(vect_dbl));
Init_Vect_Dbl(0,mod->Pij_rr);
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
#ifndef WIN32
if(posix_memalign((void **)&mod->Pij_rr->v,BYTE_ALIGN,(size_t)mod->ras->n_catg*mod->ns*mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
#else
@@ -1061,7 +1061,7 @@
e_frq->pi = (vect_dbl *)mCalloc(1,sizeof(vect_dbl));
e_frq->pi->len = ns;
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
#ifndef WIN32
if(posix_memalign((void **)&e_frq->pi->v,BYTE_ALIGN,(size_t)ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
#else
@@ -1184,7 +1184,7 @@
eig->r_e_vect_im = (phydbl *)mCalloc(ns*ns,sizeof(phydbl));
eig->q = (phydbl *)mCalloc(ns*ns,sizeof(phydbl));
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
#ifndef WIN32
if(posix_memalign((void **)&eig->r_e_vect,BYTE_ALIGN,ns*ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
if(posix_memalign((void **)&eig->l_e_vect,BYTE_ALIGN,ns*ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
|
