Ha14 installation

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Note, these instructions are out of date. Draft instructions are being prepared here: Installation Draft. That page will replace this one shortly.

Prerequisite: install and set up the PSDM suite

It is assumed that the PSDM software distribution has been set up. Developers may additionally want to set up an ssh-agent. Note again that several sites already have cctbx.xfel installed, and that this step can be skipped for regular users not involved in the development of the software. Once cctbx.xfel has been installed it must be set up before it can be used.

Download and extract a source tree

This step has to be performed on a host with Internet access. Not all hosts at SLAC have that, but the members of e.g. psexport pool do. In what follows, the absolute path /path/to/cctbx/sources should be replaced with something more appropriate (a site-wide install will benefit from a location on a shared disk, whereas ~/projects/phenix-src is a common choice among developers). The directory must accessible everywhere cctbx.xfel is to be run.

Regular users

$ mkdir -p /path/to/cctbx/sources
$ cd /path/to/cctbx/sources
$ wget http://cci.lbl.gov/cctbx_build/results/current/cctbx_bundle.tar.gz
$ wget http://adder.lbl.gov/cctbx.xfel/downloads/labelit_bundle_current.tar.gz
$ mkdir cctbx_project
$ tar -xpvzf cctbx_bundle.tar.gz -C cctbx_project --strip-components=1
$ tar -xpvzf labelit_bundle_current.tar.gz


A user account on cci.lbl.gov is required, the name of which is to be substituted for user below.

$ mkdir -p /path/to/cctbx/sources
$ cd /path/to/cctbx/sources
$ svn export svn+ssh://user@cci.lbl.gov/phenix_regression/trunk/phenix_svn_getting_started.csh
$ ./phenix_svn_getting_started.csh user
$ rm phenix_svn_getting_started.csh

Developers may also want to check out the bleeding edge CBFlib sources, as well as sources and auxiliary data for the DIALS project.

 $ svn checkout "http://svn.code.sf.net/p/cbflib/code-0/trunk/CBFlib_bleeding_edge" cbflib
 $ svn checkout "http://svn.code.sf.net/p/dials/code/trunk" dials
 $ svn checkout "svn+ssh://user@cci.lbl.gov/dials_regression/trunk" dials_regression

Create the cxi_user directory

Add the cxi_user directory and its __init__.py module. This defines the default integration algorithm used by cctbx.xfel.

$ mkdir cxi_user
$ cat > cxi_user/__init__.py << EOF
from xfel.mono_simulation.mono_treatment import post_outlier_rejection
from xfel.mono_simulation.mono_treatment import pre_get_predictions

Configure the source tree

To avoid problems with run-time dynamic linking of Python extensions, the Python interpreter required for the next step must be the one provided by the PSDM software distribution. That interpreter can be located using find, e.g.

$ find $SIT_ROOT/sw/external/python -perm /0111 -type f -wholename "*/$SIT_ARCH/*/python" 2> /dev/null

At SLAC this interpreter is located somewhere under /reg/g/psdm/sw/external/python. Then create and initialize the build directory, /path/to/cctbx/build below, using the Python interpreter located using the above find command. The build directory is often located next to the source directory (~/projects/phenix-build is a common developer choice).

Regular users

$ mkdir -p /path/to/cctbx/build
$ cd /path/to/cctbx/build
$ python /path/to/cctbx/sources/cctbx_project/libtbx/configure.py xfel


$ mkdir -p /path/to/cctbx/build
$ cd /path/to/cctbx/build
$ python /path/to/cctbx/sources/cctbx_project/libtbx/configure.py cxi_xdr_xes labelit_regression phenix xfel

Compile the sources

Initialise the running shell using the newly created configuration files. bash-users should

$ . setpaths.sh

while csh-users will instead need to run

% source setpaths.csh

The next step requires a C++ compiler. At SLAC, the members of the psexport pool do not have any compilers installed, but the interactive nodes, reachable via psanacs, do.

$ cd /path/to/cctbx/build
$ make
$ make

Please be sure to run make twice, as shown. On SLAC's interactive nodes, this takes just over 6 minutes. To finalize the installation, see Setup.

External links