configure: do not set -march by default

Author: jdtournier

configure

@@ -86,9 +86,10 @@ ENVIRONMENT VARIABLES
 
     ARCH
         the specific CPU architecture to compile for. This variable will be
-        passed to the compiler using -march=$ARCH. If set to an empty string,
-        no -march flag will be passed to the compiler.  The default is
-        'native'.
+        passed to the compiler using -march=$ARCH. You can use 'ARCH=native' to
+        get the best performance for your system. Note that this will result in
+        executables that may not run on other systems if the same CPU
+        extensions are not available.
 
     CFLAGS
         Any additional flags to the compiler.
@@ -515,11 +516,6 @@ if 'ARCH' in os.environ.keys():
   if march:
     report ('Machine architecture set by ARCH environment variable to: ' + march + '\n')
     cpp_flags += [ '-march='+march ]
-  else:
-    report ('Empty ARCH string found: will not pass -march flag to compiler.\n')
-else:
-  if system != 'darwin':
-    cpp_flags += [ '-march=native' ]
 
 
 

docs/installation/linux_install.rst

@@ -204,22 +204,34 @@ compile *MRtrix3* on a modern distro (within a virtual machine for
 example), package it up, and install it on any Linux system without
 worrying about dependencies.
 
-Important: setting the CPU architecture
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-By default, ``configure`` will cause the build script to generate code
-suitable to run on your current CPU (using the ``-march=native``
-option). This means the executables will likely *not run* on a different
-CPUs with different instruction sets, resulting in 'illegal instruction'
-runtime errors. If you intend to run *MRtrix3* on a variety of different
-systems with a range of CPUs, or you have no idea what the CPU is on
-your target system, it is safest to specify an empty (generic) architecture
-when configuring *MRtrix3*, before invoking ``./build``::
-
-    ARCH= ./configure
+Setting the CPU architecture for optimal performance
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+By default, ``configure`` will cause the build script to produce generic code
+suitable for any current CPU. If you want to ensure optimal performance on your
+system, you can request that ``configure`` produce code tailored to your
+specific CPU architecture, which will allow it to use all available CPU
+instructions and tune the code differently. This can improve performance
+particularly for linear algebra operations as `Eigen
+<http://eigen.tuxfamily.org>`__ will then make use of these extensions.
+However, note that this means the executables produced will likely *not run* on
+a different CPUs with different instruction sets, resulting in 'illegal
+instruction' runtime errors. If you intend to run *MRtrix3* on a variety of
+different systems with a range of CPUs, or you have no idea what the CPU is on
+your target system, it is safest to avoid changing the default. 
+
+Specifying a different CPU architecture is done by setting the ``ARCH`` environment
+variable prior to invoking ``./configure``. The value of this variable will
+then be passed to the compiler via the ``-march`` option. To get the best
+performance *on the current system*, you can specify ``native`` as
+the architecture, leaving it up to the compiler to detect your particular CPU
+and its available instructions. For example::
+
+    export ARCH=native 
+    ./configure
     ./build
 
-For more specific architectures, you can provide any values from the `list of
+For more specific architectures, you can provide any value from the `list of
 specifiers understood by the compiler
 <https://gcc.gnu.org/onlinedocs/gcc-6.2.0/gcc/x86-Options.html#x86-Options>`_,
 for example ``ARCH='sandybridge' ./configure``
@@ -238,7 +250,7 @@ required). Then, from the main *MRtrix3* folder::
 
     ./build clean
     git pull
-    ARCH="" ./configure -static [-nogui]
+    ./configure -static [-nogui]
     ./build
 
 Note that this requires the availability of static versions of the
@@ -341,7 +353,7 @@ required). Then, from the main *MRtrix3* folder::
 
     ./build clean
     git pull
-    ARCH="" ./configure [-nogui]
+    ./configure [-nogui]
     ./build
     ./package_mrtrix -standalone
 

docs/troubleshooting/compiler_error_during_build.rst

@@ -5,7 +5,7 @@ If you encounter an error during the build process that resembles the following:
 
     ERROR: (#/#) [CC] release/cmd/command.o
 
-    /usr/bin/g++-4.8 -c -std=c++11 -pthread -fPIC -march=native -I/home/user/mrtrix3/eigen -Wall -O2 -DNDEBUG -Isrc -Icmd -I./lib -Icmd cmd/command.cpp -o release/cmd/command.o
+    /usr/bin/g++-4.8 -c -std=c++11 -pthread -fPIC -I/home/user/mrtrix3/eigen -Wall -O2 -DNDEBUG -Isrc -Icmd -I./lib -Icmd cmd/command.cpp -o release/cmd/command.o
 
     failed with output
 

docs/troubleshooting/display_issues.rst

@@ -309,7 +309,7 @@ If you encounter an error during the build process that resembles the following:
 
     ERROR: (#/#) [CC] release/cmd/command.o
     
-    /usr/bin/g++-4.8 -c -std=c++11 -pthread -fPIC -march=native -I/home/user/mrtrix3/eigen -Wall -O2 -DNDEBUG -Isrc -Icmd -I./lib -Icmd cmd/command.cpp -o release/cmd/command.o
+    /usr/bin/g++-4.8 -c -std=c++11 -pthread -fPIC -I/home/user/mrtrix3/eigen -Wall -O2 -DNDEBUG -Isrc -Icmd -I./lib -Icmd cmd/command.cpp -o release/cmd/command.o
     
     failed with output