[WIP] Enable building on non-x86 systems

.gitmodules

@@ -54,7 +54,7 @@
 	url = https://github.com/benedictpaten/sonLib.git
 [submodule "deps/fermi-lite"]
 	path = deps/fermi-lite
-    url = https://github.com/edawson/fermi-lite.git
+	url = https://github.com/mr-c/fermi-lite.git
 [submodule "deps/gbwt"]
 	path = deps/gbwt
 	url = https://github.com/jltsiren/gbwt.git
@@ -116,6 +116,9 @@
 [submodule "vgteam_bbhash"]
 	path = deps/BBHash
 	url = https://github.com/vgteam/BBHash.git
+[submodule "src/simde"]
+	path = src/simde
+	url = https://github.com/nemequ/simde-no-tests
 [submodule "doc/wiki"]
 	path = doc/wiki
 	url = https://github.com/vgteam/vg.wiki.git

.travis.yml

@@ -2,7 +2,6 @@
 
 language: cpp
 compiler: gcc
-sudo: required
 dist: bionic
 # We have some shenanigans to let us cache submodules, and update changed files
 # without messing up mtimes and triggering rebuilds unnecessarily. Travis checks
@@ -15,10 +14,10 @@ before_install:
   - if [[ -e deps ]]; then mv deps deps_cached; fi
   - git submodule update --init --recursive
   - rsync -rv --links --checksum deps/ deps_cached/
-  - rm -Rf deps
+  # - rm -Rf deps
   # Keep the cached deps if the right compiler version was used.
   # Otherwise start fresh
-  - if [[ "$TRAVIS_OS_NAME" == "linux" && -e "deps_cached/gcc$(gcc -dumpversion)" ]]; then mv deps_cached deps; fi
+  # - if [[ "$TRAVIS_OS_NAME" == "linux" && -e "deps_cached/gcc$(gcc -dumpversion)" ]]; then mv deps_cached deps; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" && -e deps_cached/clang ]]; then mv deps_cached deps; fi
   - (ls -lah deps/; ls -lah bin/; ls -lah lib/; ls -lah include/) || true
   - git submodule update --init --recursive
@@ -112,8 +111,6 @@ os:
   - linux
   - osx
 osx_image: xcode12.2
-compiler:
-  - gcc
 env:
   global:
     - DOCS_KEY_ENCRYPTION_LABEL=125272388526
@@ -124,3 +121,5 @@ matrix:
     # We have a special entry to do the docs build
     - os: linux
       env: BUILD_DOCS_ONLY=1
+    - os: linux
+      arch: arm64

Makefile

@@ -17,7 +17,8 @@ CWD:=$(shell pwd)
 CXX ?= g++
 PKG_CONFIG ?= pkg-config
 
-EXE:=vg
+SFX :=
+EXE:=vg$(SFX)
 
 all: $(BIN_DIR)/$(EXE)
 
@@ -182,7 +183,7 @@ else
     CXXFLAGS += -fopenmp
 
     # We care about building for SSE4.2 only and not AVX, to have vaguely portable binaries
-    CXXFLAGS += -msse4.2
+    # CXXFLAGS += -msse4.2
 
     # Note shared libraries are so files
     SHARED_SUFFIX = so

README.md

@@ -66,7 +66,7 @@ At present, you will need GCC version 4.9 or greater, with support for C++14, to
 
 Other libraries may be required. Please report any build difficulties.
 
-Note that a 64-bit OS is required. Ubuntu 18.04 should work. You will also need a CPU that supports SSE 4.2 to run VG; you can check this with `cat /proc/cpuinfo | grep sse4_2`.
+Note that a 64-bit OS is required. Ubuntu 18.04 should work.
 
 When you are ready, build with `. ./source_me.sh && make`, and run with `./bin/vg`.
 

src/crash.cpp

@@ -168,7 +168,7 @@ void emit_stacktrace(int signalNumber, siginfo_t *signalInfo, void *signalContex
         *out << "Caught signal " << signalNumber << " raised at address " << ip << endl;
         // Do our own tracing because backtrace doesn't really work on all platforms.
         stacktrace_manually(*out, signalNumber, ip, bp);
-    #else
+    #elif __x86_64__
         // Linux 64 bit does it this way
         ip = (void*)context->uc_mcontext.gregs[REG_RIP];
         bp = (void**)context->uc_mcontext.gregs[REG_RBP];

src/preflight.cpp

@@ -1,33 +1,11 @@
 #include "preflight.hpp"
 
-#include <iostream>
-#include <cstdlib>
-#include <cpuid.h>
-
 namespace vg {
 
 using namespace std;
 
 void preflight_check() {
 
-    // We assume we are on x86_64 on POSIX (and not Windows).
-    // We use the method of dlib's dlib/simd/simd_check.h
-
-    // Define a place to put the cpuid info
-    unsigned int cpuid_info[4];
-
-    // Call cpuid function 1 (which reports SSE4.2, and other stuff up to original AVX)
-    __cpuid(1, cpuid_info[0], cpuid_info[1], cpuid_info[2], cpuid_info[3]);
-
-    // Bit 20 of result 2 is the SSE 4.2 flag.
-    bool have_sse4_2 = cpuid_info[2] & (1 << 20);
-
-    if (!have_sse4_2) {
-        cerr << "error[vg::preflight_check]: The CPU does not support SSE4.2 instructions. VG cannot run here. "
-            << "Please use a system with SSE4.2 support." << endl;
-        exit(1);
-    }
-
 }
 
 }

src/preflight.hpp

@@ -11,14 +11,7 @@
 
 namespace vg {
 
-/// Define a macro to tell things to be built for every architecture, if possible.
-/// This *doesn't* work on Mac with GNU GCC and Apple libc++, because functions
-/// for x86-64 can't use std::endl, so we exclude that combination.
-#if (!defined(__GNUC__) || !defined(_LIBCPP_VERSION) || !defined(__APPLE__))
-    #define VG_PREFLIGHT_EVERYWHERE __attribute__((__target__("arch=x86-64")))
-#else
-    #define VG_PREFLIGHT_EVERYWHERE
-#endif
+#define VG_PREFLIGHT_EVERYWHERE
 
 /// Run a preflight check to make sure that the system is usable for this build of vg.
 /// Aborts with a helpful message if this is not the case.