[med-svn] [Git][med-team/raxml][upstream] New upstream version 8.2.13+dfsg

Andreas Tille (@tille) gitlab at salsa.debian.org
Wed Nov 8 20:40:43 GMT 2023 


Andreas Tille pushed to branch upstream at Debian Med / raxml


Commits:
ba942fb1 by Andreas Tille at 2023-11-08T21:31:57+01:00
New upstream version 8.2.13+dfsg
- - - - -


22 changed files:

- + .github/workflows/ci.yaml
- Makefile.HYBRID.gcc
- Makefile.MPI.gcc
- Makefile.PTHREADS.gcc
- Makefile.QuartetMPI.gcc
- Makefile.SSE3.HYBRID.gcc
- Makefile.SSE3.MPI.gcc
- Makefile.SSE3.PTHREADS.gcc
- Makefile.SSE3.QuartetMPI.gcc
- Makefile.SSE3.gcc
- Makefile.gcc
- − README
- + README.md
- axml.c
- bipartitionList.c
- evaluateGenericSpecial.c
- evaluatePartialGenericSpecial.c
- fastDNAparsimony.c
- makenewzGenericSpecial.c
- newviewGenericSpecial.c
- + sse2neon.h
- treeIO.c


Changes:

=====================================
.github/workflows/ci.yaml
=====================================
@@ -0,0 +1,63 @@
+name: CI
+
+on:
+  push:
+    branches:
+    - master
+  pull_request:
+    branches:
+    - master
+
+jobs:
+  build:
+    name: Build on Linux x86_64
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        intrinsics: ["", ".SSE3", ".AVX", ".AVX2"]
+        type: ["", ".PTHREADS", ".MPI", ".HYBRID", ".QuartetMPI"]
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout at v4
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y file openmpi-bin libopenmpi-dev
+
+    - name: Build
+      run: |
+        set -x
+        if [[ -f Makefile${{ matrix.intrinsics }}${{ matrix.type }}.gcc ]]; then
+          make -j -f Makefile${{ matrix.intrinsics }}${{ matrix.type }}.gcc all
+          file raxmlHPC* | grep x86-64
+        fi
+
+  build-aarch64:
+    name: Build on Linux aarch64
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        intrinsics: ["", ".SSE3"]
+        type: ["", ".PTHREADS", ".MPI", ".HYBRID", ".QuartetMPI"]
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout at v4
+
+    - name: Build
+      uses: uraimo/run-on-arch-action at v2
+      with:
+        arch: aarch64
+        distro: ubuntu20.04
+        githubToken: ${{ github.token }}
+        dockerRunArgs: |
+          --volume "${PWD}:/raxml"
+        install: |
+          apt-get update -q -y
+          apt-get install -q -y make gcc file openmpi-bin libopenmpi-dev
+        run: |
+          set -x
+          make -j -f Makefile${{ matrix.intrinsics }}${{ matrix.type }}.gcc all
+          file raxmlHPC* | grep aarch64


=====================================
Makefile.HYBRID.gcc
=====================================
@@ -2,8 +2,14 @@
 
 CC = mpicc 
 
-
-CFLAGS = -D_WAYNE_MPI -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse
+ARCH := $(shell uname -m)
+ifeq ($(ARCH), x86_64)
+ARCH_CFLAGS=-msse
+else ifeq ($(ARCH), aarch64)
+ARCH_CFLAGS=
+endif
+
+CFLAGS = -D_WAYNE_MPI -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS $(ARCH_CFLAGS)
 
 
 LIBRARIES = -lm -pthread


=====================================
Makefile.MPI.gcc
=====================================
@@ -2,8 +2,14 @@
 
 CC = mpicc 
 
-
-CFLAGS = -D_WAYNE_MPI -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -msse
+ARCH := $(shell uname -m)
+ifeq ($(ARCH), x86_64)
+ARCH_CFLAGS=-msse
+else ifeq ($(ARCH), aarch64)
+ARCH_CFLAGS=
+endif
+
+CFLAGS = -D_WAYNE_MPI -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 $(ARCH_CFLAGS)
 
 
 LIBRARIES = -lm


=====================================
Makefile.PTHREADS.gcc
=====================================
@@ -3,8 +3,14 @@
 
 CC = gcc 
 
-
-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ARCH := $(shell uname -m)
+ifeq ($(ARCH), x86_64)
+ARCH_CFLAGS=-msse
+else ifeq ($(ARCH), aarch64)
+ARCH_CFLAGS=
+endif
+
+CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS $(ARCH_CFLAGS) #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
 
 
 LIBRARIES = -lm -pthread


=====================================
Makefile.QuartetMPI.gcc
=====================================
@@ -3,8 +3,14 @@
 
 CC = mpicc
 
-
-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -msse -D_QUARTET_MPI #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ARCH := $(shell uname -m)
+ifeq ($(ARCH), x86_64)
+ARCH_CFLAGS=-msse
+else ifeq ($(ARCH), aarch64)
+ARCH_CFLAGS=
+endif
+
+CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 $(ARCH_CFLAGS) -D_QUARTET_MPI #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
 
 LIBRARIES = -lm
 


=====================================
Makefile.SSE3.HYBRID.gcc
=====================================
@@ -2,7 +2,14 @@
 
 CC = mpicc 
 
-CFLAGS = -D_WAYNE_MPI -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  
+ARCH := $(shell uname -m)
+ifeq ($(ARCH), x86_64)
+ARCH_CFLAGS=-msse3
+else ifeq ($(ARCH), aarch64)
+ARCH_CFLAGS=
+endif
+
+CFLAGS = -D_WAYNE_MPI -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE $(ARCH_CFLAGS) -fomit-frame-pointer -funroll-loops  
 
 LIBRARIES = -lm -pthread 
 


=====================================
Makefile.SSE3.MPI.gcc
=====================================
@@ -2,7 +2,14 @@
 
 CC = mpicc 
 
-CFLAGS = -D_WAYNE_MPI -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  
+ARCH := $(shell uname -m)
+ifeq ($(ARCH), x86_64)
+ARCH_CFLAGS=-msse3
+else ifeq ($(ARCH), aarch64)
+ARCH_CFLAGS=
+endif
+
+CFLAGS = -D_WAYNE_MPI -D__SIM_SSE3 -O2 -D_GNU_SOURCE $(ARCH_CFLAGS) -fomit-frame-pointer -funroll-loops  
 
 LIBRARIES = -lm
 


=====================================
Makefile.SSE3.PTHREADS.gcc
=====================================
@@ -3,7 +3,14 @@
 
 CC = gcc 
 
-CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops  #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ARCH := $(shell uname -m)
+ifeq ($(ARCH), x86_64)
+ARCH_CFLAGS=-msse3
+else ifeq ($(ARCH), aarch64)
+ARCH_CFLAGS=
+endif
+
+CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE $(ARCH_CFLAGS) -O2 -fomit-frame-pointer -funroll-loops  #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
 
 
 LIBRARIES = -lm -pthread 


=====================================
Makefile.SSE3.QuartetMPI.gcc
=====================================
@@ -3,7 +3,14 @@
 
 CC = mpicc
 
-CFLAGS = -D__SIM_SSE3  -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops  -D_QUARTET_MPI #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ARCH := $(shell uname -m)
+ifeq ($(ARCH), x86_64)
+ARCH_CFLAGS=-msse3
+else ifeq ($(ARCH), aarch64)
+ARCH_CFLAGS=
+endif
+
+CFLAGS = -D__SIM_SSE3 $(ARCH_CFLAGS) -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops  -D_QUARTET_MPI #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
 
 LIBRARIES = -lm
 


=====================================
Makefile.SSE3.gcc
=====================================
@@ -3,7 +3,14 @@
 
 CC = gcc 
 
-CFLAGS = -D__SIM_SSE3  -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops  #-pedantic -Wall  -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ARCH := $(shell uname -m)
+ifeq ($(ARCH), x86_64)
+ARCH_CFLAGS=-msse3
+else ifeq ($(ARCH), aarch64)
+ARCH_CFLAGS=
+endif
+
+CFLAGS = -D__SIM_SSE3 $(ARCH_CFLAGS) -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops  #-pedantic -Wall  -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
 
 LIBRARIES = -lm
 


=====================================
Makefile.gcc
=====================================
@@ -3,8 +3,14 @@
 
 CC = gcc 
 
-
-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -msse #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ARCH := $(shell uname -m)
+ifeq ($(ARCH), x86_64)
+ARCH_CFLAGS=-msse
+else ifeq ($(ARCH), aarch64)
+ARCH_CFLAGS=
+endif
+
+CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 $(ARCH_CFLAGS) #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
 
 LIBRARIES = -lm
 


=====================================
README deleted
=====================================
@@ -1,86 +0,0 @@
-Standard RAxML version 8.2.12
-
-============================================================================================================
-
-When using RAxML please cite the following paper:
-
-A. Stamatakis: "RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies". 
-Bioinformatics (2014) 30 (9): 1312-1313.
-
-============================================================================================================
-
-Quick start under Linux:
-
-standard, SSE3 or AVX version?
-
-In general you should try to compile the SSE3 version that makes use of capabilities 
-on relativiely recent processors (most Intel or AMD chips not older than 3-4 years).
-The SSE3 version will run about 40% faster than the non-SSE3 version.
-
-If you have a more recently bought processor (within the last 1-2 years), please also try to compile
-the AVX version which once again uses the capabilities of modern processors better and can be 10-30% faster 
-than the SSE3 version. AVX will work on the Intel i7 (sandy-bridge) series processors as well as on the very recently 
-released AMD Bulldozer systems. 
-
-Compiling should work out of the box with all reasonably recent vesrion of the GNU gcc and Intel icc compilers.
-If you want to use icc replace gcc by icc in the Makefiles.
-
-Please direct all your RAxML questions to our google group (and only after 
-having used the search function!): 
-https://groups.google.com/forum/?hl=de&fromgroups#!forum/raxml
-
-Sequential version:
-
-type:
-"make -f Makefile.gcc"
-"rm *.o"
-or
-"make -f Makefile.SSE3.gcc"
-"rm *.o"
-or
-"make -f Makefile.AVX.gcc"
-"rm *.o"
-
-Pthreads version:
-
-type: 
-"make -f Makefile.PTHREADS.gcc"
-"rm *.o"
-or
-"make -f Makefile.SSE3.PTHREADS.gcc"
-"rm *.o"
-or
-"make -f Makefile.AVX.PTHREADS.gcc"
-"rm *.o"
-
-Coarse-grain MPI version:
-
-type:
-"make -f Makefile.MPI.gcc"
-"rm *.o"
-or
-"make -f Makefile.SSE3.MPI.gcc"
-"rm *.o"
-or
-"make -f Makefile.AVX.MPI.gcc"                            
-"rm *.o"
-
-Hybrid MPI/Pthreads version:
-
-Before using this version, please read this paper here:
-
-http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2010-3.pdf
-
-and look at these slides: 
-
-http://sco.h-its.org/exelixis/resource/doc/Phylo100225.pdf
-
-type:
-"make -f Makefile.HYBRID.gcc" 
-"rm *.o"
-or  
-"make -f Makefile.SSE3.HYBRID.gcc"
-"rm *.o"
-or
-"make -f Makefile.AVX.HYBRID.gcc" 
-"rm *.o" 


=====================================
README.md
=====================================
@@ -0,0 +1,108 @@
+## Standard RAxML version 8.2.12
+
+---
+
+**When using RAxML please cite the following paper:**
+
+*A. Stamatakis: "RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies".* 
+*Bioinformatics (2014) 30 (9): 1312-1313.*
+
+---
+
+### Quick start under Linux:
+
+standard, SSE3 or AVX version?
+
+In general you should try to compile the SSE3 version that makes use of capabilities on relativiely recent processors (most Intel or AMD chips not older than 3-4 years).The SSE3 version will run about 40% faster than the non-SSE3 version.
+
+If you have a more recently bought processor (within the last 1-2 years), please also try to compile the AVX version which once again uses the capabilities of modern processors better and can be 10-30% faster than the SSE3 version. AVX will work on the Intel i7 (sandy-bridge) series processors as well as on the very recently released AMD Bulldozer systems. 
+
+Compiling should work out of the box with all reasonably recent vesrion of the GNU gcc and Intel icc compilers. If you want to use icc replace gcc by icc in the Makefiles. Please direct all your RAxML questions to our google group (and only after having used the search function!): https://groups.google.com/forum/?hl=de&fromgroups#!forum/raxml
+
+#### Sequential version:
+
+type:
+
+`make -f Makefile.gcc`
+
+`rm *.o`
+
+or
+
+`make -f Makefile.SSE3.gcc`
+
+`rm *.o`
+
+or
+
+`make -f Makefile.AVX.gcc`
+
+`rm *.o`
+
+#### Pthreads version:
+
+type: 
+
+`make -f Makefile.PTHREADS.gcc`
+
+`rm *.o`
+
+or
+
+`make -f Makefile.SSE3.PTHREADS.gcc`
+
+`rm *.o`
+
+or
+
+`make -f Makefile.AVX.PTHREADS.gcc`
+
+`rm *.o`
+
+Coarse-grain MPI version:
+
+type:
+
+`make -f Makefile.MPI.gcc`
+
+`rm *.o`
+
+or
+
+`make -f Makefile.SSE3.MPI.gcc`
+
+`rm *.o`
+
+or
+
+`make -f Makefile.AVX.MPI.gcc`
+
+`rm *.o`
+
+#### Hybrid MPI/Pthreads version:
+
+Before using this version, please read this paper here:
+
+http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2010-3.pdf
+
+and look at these slides: 
+
+http://sco.h-its.org/exelixis/resource/doc/Phylo100225.pdf
+
+type:
+
+`make -f Makefile.HYBRID.gcc"`
+
+`rm *.o`
+
+or  
+
+`make -f Makefile.SSE3.HYBRID.gcc`
+
+`rm *.o`
+
+or
+
+`make -f Makefile.AVX.HYBRID.gcc`
+
+`rm *.o`


=====================================
axml.c
=====================================
@@ -66,7 +66,7 @@
 
 #endif
 
-#if ! (defined(__ppc) || defined(__powerpc__) || defined(PPC))
+#if ! (defined(__ppc) || defined(__powerpc__) || defined(PPC) || defined(__aarch64__))
 #include <xmmintrin.h>
 /*
   special bug fix, enforces denormalized numbers to be flushed to zero,
@@ -76,6 +76,8 @@
   #define MM_DAZ_ON    0x0040
   #define MM_DAZ_OFF    0x0000
 */
+#elif __aarch64__
+#include "sse2neon.h"
 #endif
 
 #include "axml.h"


=====================================
bipartitionList.c
=====================================
@@ -46,10 +46,12 @@
 #include "rmq.h" //include range minimum queries for fast plausibility checker
 
 #ifdef __SIM_SSE3
-
+#ifdef __x86_64__
 #include <xmmintrin.h>
 #include <pmmintrin.h>
-
+#elif __aarch64__
+#include "sse2neon.h"
+#endif
 #endif
 
 #ifdef _USE_PTHREADS


=====================================
evaluateGenericSpecial.c
=====================================
@@ -39,11 +39,14 @@
 #include <string.h>
 #include "axml.h"
 
-
 #ifdef __SIM_SSE3
+#ifdef __x86_64__
 #include <xmmintrin.h>
 #include <pmmintrin.h>
 /*#include <tmmintrin.h>*/
+#elif __aarch64__
+#include "sse2neon.h"
+#endif
 #endif
 
 #ifdef _USE_PTHREADS


=====================================
evaluatePartialGenericSpecial.c
=====================================
@@ -41,10 +41,13 @@
 #include "axml.h"
 
 #ifdef __SIM_SSE3
+#ifdef __x86_64__
 #include <xmmintrin.h>
 #include <pmmintrin.h>
+#elif __aarch64__
+#include "sse2neon.h"
+#endif
 #endif
-
 
 /********************** GTRCAT ***************************************/
 


=====================================
fastDNAparsimony.c
=====================================
@@ -61,9 +61,13 @@
 
 #ifdef __SIM_SSE3
 
+#ifdef __x86_64__
 #include <xmmintrin.h>
 #include <pmmintrin.h>
-  
+#elif __aarch64__
+#include "sse2neon.h"
+#endif
+
 #endif
 
 #ifdef __AVX


=====================================
makenewzGenericSpecial.c
=====================================
@@ -44,9 +44,13 @@
 #include "axml.h"
 
 #ifdef __SIM_SSE3
+#ifdef __x86_64__
 #include <xmmintrin.h>
 #include <pmmintrin.h>
 /*#include <tmmintrin.h>*/
+#elif __aarch64__
+#include "sse2neon.h"
+#endif
 #endif
 
 #ifdef _USE_PTHREADS


=====================================
newviewGenericSpecial.c
=====================================
@@ -44,8 +44,13 @@
 #ifdef __SIM_SSE3
 
 #include <stdint.h>
+
+#ifdef __x86_64__
 #include <xmmintrin.h>
 #include <pmmintrin.h>
+#elif __aarch64__
+#include "sse2neon.h"
+#endif
 
 const union __attribute__ ((aligned (BYTE_ALIGNMENT)))
 {


=====================================
sse2neon.h
=====================================
The diff for this file was not included because it is too large.

=====================================
treeIO.c
=====================================
@@ -1437,7 +1437,7 @@ int treeReadLen (FILE *fp, tree *tr, boolean readBranches, boolean readNodeLabel
   if(!tr->rooted && adef->mode == ANCESTRAL_STATES)
     {
       printf("Error: The ancestral state computation mode requires a rooted tree as input, exiting ....\n");
-      exit(0);
+      exit(-1);
     }
 
   if (! treeNeedCh(fp, ')', "in"))                



View it on GitLab: https://salsa.debian.org/med-team/raxml/-/commit/ba942fb1f16a786155b865a1b85f12d9a4405440

-- 
View it on GitLab: https://salsa.debian.org/med-team/raxml/-/commit/ba942fb1f16a786155b865a1b85f12d9a4405440
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