Click here to go to the corresponding page for the latest version of DIALS
Installation for Developers¶
Setting up a Development Environment on Linux or Mac¶
Prerequisites: make and change to a working directory to contain the new source code and build. Then download these bootstrap modules:
wget https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py
or if wget is not available:
curl https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py > bootstrap.py
Then:
python bootstrap.py --builder=dials
Explanation: Several steps are performed: hot, update, base, build. If desired, they can be run individually at the command line:
python bootstrap.py --builder=dials hot
python bootstrap.py --builder=dials update
python bootstrap.py --builder=dials base
python bootstrap.py --builder=dials build
- “hot” downloads static tarballs containing prerequisite dependencies, to the module directory
- “update” anonymously checks out or updates source code for dials and cctbx, to the module directory
- “base” downloads and installs python and third party python packages to the base directory
- “build” configures and compiles dials and cctbx
The DIALS builder pulls code from repositories in multiple locations. If you are a developer with an account at cci.lbl.gov you can add –cciuser=<your cci user name>. This will allow you to make commits back to the source tree. Similarly, if you have a source forge account, you can add –sfuser=<your source forge user name>. If you have an account at GitHub and have installed a registered SSH key on your machine, you can add –git-ssh.
For subsequent login sessions, be sure to set the environment in order to use the command-line dispatchers:
source build/setpaths.sh # or setpaths.csh for tcsh
Additional packages can be installed in the modules directory, e.g., download the dials_regression tarball from the main dials web page. Additional modules may be configured as in this example:
libtbx.configure dials_regression
Restarting the Base Install if One Component Fails¶
It has required quite a bit of experimentation to get the “base” install correct. Here is a procedure to restart the base install if it dies in the middle, and needs to be restarted. First, the top of the base output gives a list of python packages to be installed. On linux it looks something like this:
python numpy hdf5 biopython freetype gettext glib expat fontconfig render pixman png tiff cairo gtk fonts wxpython
matplotlib pyopengl imaging reportlab misc
Identify the subset of packages that has failed to install; as an example assume that wxpython and subsequent packages still need to be installed. Then run the base installer using the just-installed python as the “with-python” base:
python modules/cctbx_project/libtbx/auto_build/install_base_packages.py \
--with-python=`pwd`/base/bin/python wxpython matplotlib pyopengl imaging reportlab misc
Creating a Relocatable Installer Bundle on Linux¶
Starting with the developer build just created, we can create a tarball suitable for public distribution. Caveat is that we build our 64-bit installer on Centos 5.4, so that most conceivable users will be installing on a more modern OS back-compatible with the installer.
Change to the working directory used above. Then:
./modules/dials/installer/dials_installer.sh
..creates an installer called tmp/dials-installer-dev.tar.gz
This can be relocated to a new directory, untarred, then:
cd dials-installer-dev
./install -h [prints a help message]
./install --prefix=[absolute path for relocated dials installation]
Building Using Your Own Custom Python¶
Using your own python to configure and build DIALS requires the dependencies listed above to already be installed and properly configured. Instruct the builder to use your python thusly:
python bootstrap.py --builder=dials --with-python=<absolute path to your python binary>
This will run the ‘hot’ and ‘update’ steps as normal, skip the ‘base’ step that would normally download and build python and necessary DIALS python dependencies, and finally run the ‘build’ step with the python you specified. Note that the DIALS team doesn’t recommend this procedure, but it can be necessary if using DIALS in concert with other packages.
Downloading the DIALS regression test data¶
The DIALS regression test data, needed for some of the DIALS tests, can be obtained here:
cd ../modules
curl http://dials.diamond.ac.uk/developers/dials_regression.tgz > dials_regression.tgz
tar -xzvf dials_regression.tgz
libtbx.configure dials_regression
For those with svn access to the CCI server, it can also be obtained as follows. Checkout the data into the cctbx source directory and configure as follows, replacing “USERNAME” for your username:
cd ../modules
svn checkout svn+ssh://USERNAME@cci.lbl.gov/dials_regression/trunk dials_regression
libtbx.configure dials_regression
