Installing the psana2-cctbx toolchain

Step by step installation instructions for getting a native build of CCTBX.XFEL with PSANA-2. Currently these steps have only been tested on Cori PII, a RHEL-7 type system.

Installing the psana-cctbx.xfel toolchain

Firstly, we must ensure that the environment is setup before installing CCTBX.XFEL. The following commands assume a bash environment by default (alternative shells should also work, with alternative instructions given where necessary).

Install Miniconda for Python 2.7.
Once installed, source the conda installation and update the base environment:
```
  source ./miniconda/etc/profile.d/conda.sh
  conda update -y conda
```
Create a conda environment for the installation:
```
 conda create -n myEnv python=2.7
```
Activate the newly created conda environment:
```
 conda activate myEnv
```
Install psana from the LCLS-II conda channel
```
 conda install -c lcls-ii psana
```

Install the following additional dependencies for building and running psana and cctbx:

 conda install future h5py mpich2 wxpython pillow libtiff mock pytest jinja2 scikit-learn tabulate tqdm
 conda install --channel conda-forge orderedset
 python -m pip install procrunner

Create a cctbx.xfel directory, and acquire the bootstrap program for building and installation (--no-check-certificate can often be required):

 mkdir $PERM/cctbx.xfel; cd $PERM/cctbx.xfel
 wget https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py --no-check-certificate

Download and build the cctbx.xfel packages using the conda environment activated python.
```
 python bootstrap.py hot update --builder=dials
```
Get an interactive session on Cori KNL for this step. Assuming C++ compilers exist on the path, the following step will build the XFEL version of cctbx; specify the number of available cores to enable parallel compilation:
```
 python bootstrap.py build --builder=dials --with-python=`which python` --nproc=<# cores available for compile>
```
This step also needs an interactive session. To use the Cray MPI libraries properly on Cori PII, this step is necessary. It uninstalls the mpi4py that comes with conda, switches compilers to Cray and then installs mpi4py from scratch:
```
conda uninstall mpi4py mpich2 --force
module swap PrgEnv-intel PrgEnv-cray
MPICC=cc pip install mpi4py
```

The path environment variables are set up by running the following command:

source $PERM/cctbx.xfel/build/setpaths.sh #Bash users

source $PERM/cctbx.xfel/build/setpaths.csh #csh users

With the above steps the psana2-cctbx.xfel build should now be installed, with all accessible commands working.