The SIRF-SuperBuild allows the user to download and compile most of the software needed to compile SIRF and Gadgetron, and automatically build SIRF and Gadgetron. There is still a small number of libraries that are not installed by the SuperBuild, see below for more info for your operating system.
The SuperBuild depends on CMake >= 3.7.
If you are building Gadgetron there are a series of additional dependencies, which must be met.
To compile and install SIRF with the SuperBuild follow these steps:
We will assume in these instructions that you want to install the software in `~/devel'. You can of course decide to put it elsewhere. Let's create it first.
mkdir ~/develIf you do not have CMake >= 3.7 install it first (download link). On Ubuntu Linux, you can issue the following commands
wget https://cmake.org/files/v3.7/cmake-3.7.2-Linux-x86_64.sh
sudo mkdir /opt/cmake
sudo bash cmake-3.7.2-Linux-x86_64.sh --prefix=/opt/cmake
export PATH=/opt/cmake/bin:$PATHDuring installation you will be asked to read and accept CMake's license. If you answered the last question during the CMake installation with yes, then you should use
export PATH=/opt/cmake/cmake-3.7.2-Linux-x86_64/bin:$PATH
Note that the above PATH statements won't work if you are running csh. The equivalent would be for instance
set path = ( /opt/cmake/bin $path )You might want to add the PATH line to your start-up file (e.g. .profile or .cshrc).
cd ~
cd devel
git clone https://github.com/CCPPETMR/SIRF-SuperBuild.gitCreate a build directory and configure the software.
Note that if you want to use MATLAB, you need to use (and specify) a compiler supported by MATLAB and might have to tell CMake where MATLAB is located. Please check our SIRF and MATLAB page.
cd ~/devel
mkdir build
cd build
cmake ../SIRF-SuperBuildUse your build environment to build and install the project. On Linux/OSX etc, you would normally use
make -jNwhere N are the number of cores you want to use for the compilation. For Eclipse/XCode/Visual Studio, you could open the project, or try something like
cmake --build . --config ReleaseNote that there is no separate install step.
Gadgetron requires a configuration file. An example is supplied and, as a starting point, this can be copied and used as the real thing:
mv INSTALL/share/gadgetron/config/gadgetron.xml.example INSTALL/share/gadgetron/config/gadgetron.xml
Source a script with the environment variables appropriate for your shell
For instance, for sh/bash/ksh etc
cd ~/devel/build
source INSTALL/bin/env_ccppetmr.shYou probably want to add a similar line (with absolute path) to your .bashrc/.profile.
Or for csh
cd ~/devel/build
source INSTALL/bin/env_ccppetmr.cshYou probably want to add a similar line (with absolute path) to your .cshrc.
To be able to use Gadgetron, a Gadgetron client must already be open in another terminal window. To do this, open a new terminal window and enter:
gadgetron
N.B.: If you didn't add any of the above statements to your .bashrc or .cshrc, you will have to source env_ccpetmr.* again in this terminal first.
Tests for the SIRF-SuperBuild are currently the SIRF tests. The tests can contain tests from all SuperBuild projects. After setting the environment variables and starting Gadgetron, you can run tests as:
cd ~/devel/build
ctest --verboseTypical output will be something like
test 1
Start 1: SIRF_TESTS
1: Test command: /usr/local/bin/ctest "test"
1: Test timeout computed to be: 9.99988e+06
1: Test project /home/sirfuser/devel/SIRF-SuperBuild/SIRF-prefix/src/SIRF-build
1: Start 1: PET_TEST1
1: 1/3 Test #1: PET_TEST1 ........................ Passed 2.94 sec
1: Start 2: MR_FULLY_SAMPLED
1: 2/3 Test #2: MR_FULLY_SAMPLED ................. Passed 3.83 sec
1: Start 3: MR_UNDER_SAMPLED
1: 3/3 Test #3: MR_UNDER_SAMPLED ................. Passed 2.93 sec
1:
1: 100% tests passed, 0 tests failed out of 3
1:
1: Total Test time (real) = 9.70 sec
1/1 Test #1: SIRF_TESTS ....................... Passed 9.70 sec
100% tests passed, 0 tests failed out of 1
Total Test time (real) = 9.70 sec
The user may also run the SIRF tests independently of the SuperBuild. Just enter the SIRF build directory and launch ctest:
cd ~/devel/build
cd SIRF-prefix/src/SIRF-build
ctest --verboseIf you see failures, you might not have followed the above steps correctly, or have some missing Python modules.
We distribute examples for both Python and MATLAB. You can find them as follows:
cd $SIRF_PATH
cd examples
lsSee our related Wiki page for more information.
They can be found here
They can be found here
They can be found here
SIRF depends on many packages. By default, these packages are installed by the Superbuild. However, the user can decide to compile SIRF against their own versions of certain packages. This can be done via the USE_SYSTEM_* options in CMake. For example, if you wish to compile SIRF against a version of Boost that is already on your machine, you could set USE_SYSTEM_BOOST to ON.
This USE_SYSTEM_* function can be used for as many or as few packages as desired. Advantages to building against your own version of certain packages are decreased compilation times and the potential to use newer versions of these packages.
However, we have only tested SIRF with the versions of the required dependencies that are built by default in the Superbuild. If you decide to compile SIRF using system versions of the dependencies, you run a greater risk of something going wrong.
For this reason, we advise new SIRF users to compile with all the USE_SYSTEM_* options disabled. If you decide to use system versions of certain packages, we would be interested to hear about it any compatibility issues that you may run into.
By default, Python and MATLAB executables and libraries are installed under CMAKE_INSTALL_PREFIX/python and CMAKE_INSTALL_PREFIX/matlab, respectively. If you wish for them to be installed elsewhere, you can simply cut and paste these folders to their desired locations.
In this case, you would then need to ensure that PYTHONPATH and MATLABPATH are updated accordingly. This is because the sourced env_ccppetmr will point to the original (old) location.
By default, the SuperBuild will build the latest stable release of SIRF and associated versions of the dependencies. However, the SuperBuild allows the user to change the versions of the projects it's building.
This is done at the configuration stage that happens when you run cmake.
There is a DEVEL_BUILD tag that allows to build the upstream/master versions of all packages (DEVEL_BUILD=ON). In the following table are listed example versions (hashes) of dependencies that are built by the SuperBuild. The current default values can be found in version_config.cmake.
| TAG | DEVEL_BUILD=OFF (default) | DEVEL_BUILD=ON |
|---|---|---|
SIRF_TAG |
v1.0.0 |
origin/master |
STIR_URL |
https://github.com/UCL/STIR | https://github.com/UCL/STIR |
STIR_TAG |
41651b3a2007c58cbf1f7706bb2e269a21e870b1 |
origin/master |
Gadgetron_URL |
https://github.com/gadgetron/gadgetron | https://github.com/gadgetron/gadgetron |
Gadgetron_TAG |
e7eb430673eb3272e8a821b51750c0a2a96dafed |
origin/master |
ISMRMRD_URL |
https://github.com/ismrmrd/ismrmrd | https://github.com/ismrmrd/ismrmrd |
ISMRMRD_TAG |
42d93137cc16c270c8ba065edd2496483161bd21 |
origin/master |
To use the DEVEL_BUILD option one may (on the terminal)
cd ~/devel/build
cmake ../SIRF-SuperBuild -DDEVEL_BUILD=ONAdditionally one may want to use only a specific version of a package. This is achieved by adding the right tag to the command line (see the table above for available tags):
cd ~/devel/build
cmake ../SIRF-SuperBuild -DSIRF_TAG=<a valid hash>Note that the CMake options in the table are Advanced Options. When running the CMake GUI (or ccmake) they will therefore only be visible when you toggle those on.
Warning: All these variables are cached. This means that once set, you have to change them one by one. Setting
DEVEL_BUILD=ON will therefore not work as expected on an existing build. You will need to delete the cached variables first.
You could do
cmake -DDEVEL_BUILD=ON -USIRF_URL -USIRF_TAG -USTIR_URL -USTIR_TAG -UGadgetron_URL -UGadgetron_TAG -UISMRMRD_URL -UISMRMRD_TAG .