Installation

We distribute binary packages from an internal server using the conda package manager, developed for and by the scientific Python community. The internal server can be accessed via a web browser at https://conda.nsls2.bnl.gov from the wired campus network or controls network.

For users outside Brookhaven National Lab, the packages can be built from source.

Installation Procedure

1. The following configuration files in the home directory are touched by this procedure

   .pyOlog.conf
   .condarc
   .config/
     binstar/
   ipython_ophyd/
     profile_ophyd/
     profile_beamline/
   .bashrc
   

   If the beamline does not have NFS home directories, then these files should be stored on the NFS share (/nfs/beamlineid/) and sym-linked into the home directory (possibly not for .bashrc).

2. If needed, fix proxy settings so you can see the Internet

   echo 'export https_proxy=https://proxy:8888' >> ~/.bashrc
   echo 'export http_proxy=http://proxy:8888' >> ~/.bashrc
   source ~/.bashrc
   

3. Set up a configuration file for pyOlog, pyOlog.conf in the home directory.

4. Install miniconda

   wget http://repo.continuum.io/miniconda/Miniconda-3.8.3-Linux-x86_64.sh -O miniconda.sh
   chmod +x miniconda.sh
   ./miniconda.sh -b -p ./mc
   echo "export PATH=`pwd`/mc/bin:\$PATH" >> ~/.bashrc
   source ~/.bashrc
   

   If the beam line does not have NFS home directories then this should be done in the /nfs/beamline directory. This does not need to be sym-linked as the path logic in .bashrc will take care of finding the correct version of conda which will take care of finding the correct environments.

5. Configure channels

   conda install binstar
   binstar config --set url https://conda.nsls2.bnl.gov/api
   conda config --add channels Nikea
   conda config --add channels BEAMLINE
   conda config --add create_default_packages pip
   conda update --all
   

   Where BEAMLINE is the name of the beamline organization you want to install source for (in uppercase – see the table at bottom)

6. Install the collection or analysis stacks create a new environment

   conda create -n env_name package_name
   

   For example, to install the data-collection stack for SRX (assuming that you have SRX in your channels) into an environment named ophyd:

   conda create -n ophyd srx_collection
   

   See table at bottom for list of available packages

7. Enable env

   source activate env_name
   

8. Disable env

   source deactivate env_name
   

Package sources

Beamline	Channel	List of Packages	Collection Package	Analysis Package
SRX (05id)	SRX	https://conda.nsls2.bnl.gov/SRX	srx_collection	srx_analysis
CSX (23id1)	CSX	https://conda.nsls2.bnl.gov/CSX	csx_collection	csx_analysis
CSX (23id2)	CSX2	https://conda.nsls2.bnl.gov/CSX2	csx2_collection	csx2_analysis
XPD (28id)	XPD	https://conda.nsls2.bnl.gov/XPD	xpd_collection	xpd_analysis
HXN (03id)	HXN	https://conda.nsls2.bnl.gov/HXN	hxn_collection	hxn_analysis
CHX (11id)	CHX	https://conda.nsls2.bnl.gov/CHX	chx_collection	chx_analysis
IXS (10id)	IXS	https://conda.nsls2.bnl.gov/IXS	ixs_collection	ixs_analysis

Upgrade

1. Arrange with beamline scientist to schedule upgrade.

2. Copy the conda packages to the organization.:

   binstar copy --to-owner BEAMLINE latest/PACKAGE_NAME/VERSION_STRING
   

3. Activate and update the ophyd environment:

   source activate ophyd
   conda update --all
   

4. Make an archival copy of the new environment, named ophyd-TODAY’S DATE

   conda create -n ophyd-`date +"%Y-%m-%d"` --clone ophyd
   

5. To capture a snap shot of the current code state

   conda list --export > installed_packages.txt
   

6. Create entry in OLog to record the upgrade.

IPython profile

This section covers the setup of the ipython profile for ophyd. Realistically there are three important considerations.

1. Where are you going to put the ipython profile?

   • There is an environmental variable IPYTHONDIR that changes where the ipython –profile=some_profile command line argument points.

   • There is a command line argument ipython --ipythondir=some_directory that can change

2. Run this command: ipython profile create ipython_ophyd

3. These lines must be added to the ipython_config.py file which is located at $IPYTHONDIR/profile_ophyd/ipython_config.py

   c.StoreMagics.autorestore = True
   c.InteractiveShellApp.extensions = ['ophyd.session',
                                       'pyOlog.cli.ipy']
   c.TerminalIPythonApp.pylab = 'auto'
   

4. Copy over the README.md file from here to $IPYTHONDIR/profile_ophyd/startup/README.md

5. Running ipython --profile=ophyd should now successfully start up ophyd. To check that it is working, run wh_pos at the ipython prompt and make sure that an error is not thrown.

6. To start adding positioners and detectors, see the currently active profiles for CSX1, CSX2, SRX, XPD, CHX, HXN, and IXS

Potential Pitfalls

OLog issues

1. The owner of the logbooks in olog should be ologs-log.

XServer Issues with ssh

xhost +