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This page describes smalldata_tools, a suite of code useful for analysis from the xtc data to small(er) hdf5 files at several stages of analysis. While this page is written with smalldata_tools usage in mind, the information here are also of interest to understand the computing infrastructure, ressources, and directory structure.
The smalldatatsmalldata_tools code can be found on git at https://github.com/slac-lcls/smalldata_tools.
At XPP or XCS, the code setup is usually taken care off by the beam line beamline staff. For other hutches, please contact the controls POC or pcds-poc-l
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Where do I find the smalldata_tools code and my data?
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/sdf/data/lcls/ds/<hutch>/<experiment>/results |
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Hence, the smalldata_tools code is setup in:
# Analysis code and results /sdf/data/lcls/ds/<hutch>/<expname>/results/smalldata_tools # smalldata_tools code setup location |
Make experiment folder accessible from JupyerHub session
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From Jupyter hub, click on the "+" symbol on the top left. Select "terminal" and make a soft-link to the experiment folder:
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ln -s /sdf/data/lcls/ds/<hutch>/<experiment>/ ./<link_name> |
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Where to access data
The hdf5 data will be written to:
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/sdf/data/lcls/ds/<hutch>/<experiment>/hdf5/smalldata |
Smalldata analysis workflow
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Ongoing experiment are generally using the online analysis infrastructure, the fast feedback system (ffb). More info on the system here: Fast Feedback System.
This system is faster and provides prioritization to ongoing experiments. Some time after the experiment is over, the access to the data will be locked and only the offline system will be available.
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Often one can work exclusively from the JupyerHub interface (see below). At times it can nonetheless be useful to be able to access the relevant computing system and directories via a terminal.
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ssh -X <ACCOUNT>@pslogin.slac.stanford.edu |
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For the online analysis:
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ssh -X psffb source /reg/g/psdm/etc/psconda.sh -py3 # Environment to use psana, etc |
And for the offline analysis:
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ssh -X psana source /reg/g/psdm/etc/psconda.sh -py3 # Environment to use psana, etc |
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The working directory structure can be confusing, as some of the offline folders are mounted and accessible from the online system. As a rule of thumb, until things are moved away from the online system, one should exclusively work on the ffb.
The results folder should hosts most of users' code, notebooks, etc. This folder lives on the offline system but is mounted on the ffb:
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/cds/data/psdm/<hutch>/<experiment>/results # should hosts most of users' code, notebooks, etc; lives on the offline system but is mounted on the ffb /cds/data/psdm/<hutch> |
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The smalldata_tools working directory generally are:
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<expname>/results/smalldata_ |
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tools # for the offline system (psana) |
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/cds/data/drpsrcf/<hutch>/<expname>/scratch/smalldata_tools |
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# for the fast feedback system (psffb) |
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Access data
The data will be written to:When using the FFB processing, data are written to:
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/cds/data/drpsrcf/<hutch>/<experiment>/scratch/hdf5/smalldata |
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and to:
# When using the FFB processing /cds/data/psdm/<hutch>/<experiment>/hdf5/smalldata |
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# For the processing using the 'SLAC' endpoint / the psana system |
. Data will be moved from the FFB system to this directory within 3-4 weeks after the experiment has ended.
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If you have an error 511 when trying to access the server, please run
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/reg/g/psdm/sw/jupyterhub/psjhub/jhub/generate-keys.sh |
Make experiment folder accessible from
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JupyterHub session
In Jupyter hub, you can only navigate within your home folder. It is thus recommended to create shortcuts (soft-links) to the relevant experiment folders, for ease-of-access.
From Jupyter hub, click on the "+" symbol on the top left. Select "terminal" and make a soft-link to the experiment folder:
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ln -s /cds/data/psdm/<hutch>/<experiment>/ ./<link_name> |
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If the experiment is going to make use of the FFB, make a second soft-link:
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ln -s /cds/data/drpsrcf/<hutch>/<experiment>/ ./<link_name> |
Advanced topics
The results folder is backed-up and for that reason can only hold-up to 10'000 files after which a quota exceeded error will pop up. Users' who wish to build code with more files should do it on the scratch folder (online: /cds/data/drpsrcf/<hutch>/<experiment>/scratch), where there is no file limits (but no back-up).
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Overview
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