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Compiling ANTs on Linux and Mac OS
This installation guide is for Linux and Mac users. Windows users will need to install the Linux subsystem and then install Git and CMake, as detailed here, before proceeding to clone ANTs and compile using the instructions on this page.
The instructions here will perform a "SuperBuild", which will automatically build the correct versions of ITK (required) and VTK (optional) for ANTs. Most ANTs users will find it easiest to use the SuperBuild. Advanced users can use system ITK or VTK.
A downloadable script to build and install ANTs locally is available here.
Here is a very minimal example. This example works if you have all the necessary tools, including CMake and a supported compiler. The system requirements and installation steps are discussed in more detail below.
git clone https://github.com/ANTsX/ANTs.git
mkdir build install
cd build
cmake \
-DCMAKE_INSTALL_PREFIX=${PWD}/install \
../ANTs 2>&1 | tee cmake.log
make -j 4 2>&1 | tee build.log
cd ANTS-build
make install 2>&1 | tee install.log
A current list of compilers known to build ANTs successfully can be viewed on Travis at
https://travis-ci.org/ANTsX/ANTs
CMake is available as source or a binary package from
You can also install it through a package manager for your system such as yum, apt, or Homebrew.
The current minimum CMake version is 3.10.2.
The exact procedure varies by Mac OS X version. For 10.11 (El Capitan), you need to first install XCode, then get the command line tools. Once XCode is installed, you can get the command line tools from the Terminal, with
xcode-select --install
The developer tools are usually installed in Linux. If not, there are several routes to install the required tools, depending on the Linux installation. Look for "developer tools" packages for your Linux distribution.
git clone https://github.com/ANTsX/ANTs.git
You can also download code snapshots as a ZIP file from Github, but you will still need git installed for the SuperBuild to work.
The build directory must be outside the source tree. Make a build directory, cd to it, then run cmake with command line options or ccmake for the GUI. The build directory is not the final install location. You will set the prefix in CMake where you want to install the executables and libraries, but that is a separate command after the build completes.
# make a build and install dir
mkdir build install
cd build
ccmake ../ANTs
In the GUI, hit 'c' to do an initial configuration. CMake will do some checking and then present options for review. You should set CMAKE_INSTALL_PREFIX to where you want to install ANTs. This needs to be somewhere that you have write access.
If you are behind a firewall that blocks the git protocol, set SuperBuild_ANTS_USE_GIT_PROTOCOL to "OFF". This should use https for all components of the SuperBuild, but see the Troubleshooting section if you have trouble with git operations.
Hit 'c' again to do another round of configuration. If there are no errors, you're ready to generate the make files by pressing 'g'.
Now you are back at the command line, it's time to compile.
make 2>&1 | tee build.log
The last part of the command here records the terminal output to a file build.log. This is optional, but you must do this if you need to report an issue. If you don't have the tee command installed, you can do
make > build.log 2>&1
but you will not see output to the terminal.
To speed up compilation, you can use multiple threads, for example:
make -j 2 2>&1 | tee build.log
will use two threads. Note that multiple threads will require more RAM as well as CPU resources. If your build seems slow for the number of threads, exits with errors, or hangs up entirely, try building with a single thread. You can also save time by turning off RUN_LONG_TESTS in CMake, or by turning off testing entirely.
If all went well, make will exit with code 0, after printing
[100%] Built target ANTS
You can also check for the empty file CMakeFiles/ANTS-complete under the build directory.
After compilation completes, you will see a subdirectory ANTS-build. This is the location from which you will run the install.
cd ANTS-build
make install 2>&1 | tee install.log
This will copy the binaries and libraries to bin/ and lib/ under CMAKE_INSTALL_PREFIX.
Assuming your install prefix was /opt/ANTs, there will now be a binary directory /opt/ANTs/bin, containing the ANTs executables and scripts. The scripts additionally require ANTSPATH to point to the bin directory including a trailing slash.
For the bash shell (default on Mac and some Linux), you need to set
export ANTSPATH=/opt/ANTs/bin/
export PATH=${ANTSPATH}:$PATH
Now check this worked correctly:
which antsRegistration
should print out the full path to antsRegistration, and
antsRegistrationSyN.sh
should print out the usage for that script. You can put the above variable definitions in your shell initialization file, so future sessions will have them set automatically. On a Mac, this is usually ~/.profile, on Linux ~/.bash_profile.
Many ANTs programs use multi-threading. By default, one thread will be generated for every CPU core on the system. This might be acceptable on a single-user machine but in a cluster environment, you will need to restrict the number of threads to be no more than the number of cores you have reserved for use.
Set the environment variable
ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS
to control the number of threads ANTs will use.
On a desktop computer, a sensible value for this is the number of physical cores. For example, on an iMac with a quad-core CPU (8 virtual cores), set this variable to 4, or less than 4 if you want to save more CPU time for other processes.
If you are building the latest source code, you can check the ANTs Travis page to see if the code can compile successfully.
- If the build hangs while attempting to download code, it may be because the Git protocol is blocked by a firewall. Run
ccmakeagain and setSuperBuild_ANTS_USE_GIT_PROTOCOLto "OFF". If that does not work, try altering your settings withgit configto use https instead of git.
You can do this globally on the command line with
git config --global url."https://".insteadOf git://
This will tell git to use https instead of git for all of your projects.
- If the build hangs during compilation of some code, it may be because the build is running out of RAM. You can reduce memory burden by compiling with fewer threads. Disabling testing may also help, set
BUILD_TESTINGtoOFFin CMake. Alternatively, you can increase the memory available to the build process.
If you have multiple compilers, or CMake can't find the right one for some reason, set variables before building:
export CC=/usr/bin/cc
export CXX=/usr/bin/c++
ccmake ~/code/ANTs
-
Try building with a single thread. Resource limits or timeouts can lead to incomplete compilation, resulting in errors.
-
Ensure that you have a compiler that can build ANTs. The ANTs Travis page has a list of compilers that can build the latest code.
If you see something like
CMake Error at cmake_install.cmake:37 (file):
file cannot create directory: /opt/ANTs/bin. Maybe need administrative
privileges.
make: *** [install] Error 1
The fastest way to fix this is with the DESTDIR variable:
make install DESTDIR=/new/install/dir
This will install the binaries in ${DESTDIR}/opt/ANTs/bin. Alternatively, you can reconfigure the install directory with CMake:
cmake -DCMAKE_INSTALL_PREFIX=/new/install/dir .
make install
This is a result of the default compiler optimization using instructions that are not supported by some CPUs.
Try adding the following to the CMake call:
-DSuperBuild_ANTS_C_OPTIMIZATION_FLAGS:STRING= -mtune=native -march=native \
-DSuperBuild_ANTS_CXX_OPTIMIZATION_FLAGS:STRING= -mtune=native -march=native
See the issue for more on this: 764.
If you still have problems, try searching the ANTs issues here on Github and also the discussion forum hosted at Sourceforge.
You may open an issue to report the error and seek help from the ANTs community. Please see the issue template for build issues, and include all the relevant attachments.
For developers and advanced users who are not using the default Superbuild.
If you wish to use a pre-compiled system version of either ITK or VTK, it must be the correct version for the ANTs source you are working from. The ITK version changes most frequently. The required ITK version can be found in the ANTs source here and the VTK version here.