Online Reconstruction Tools

Introduction

A new set of components has been developed to replace the now deprecated Monitoring Application. Instead of having all functionality implemented within a single application, the online reconstruction and monitoring has been split up into several different programs in order to provide a scalable and flexible system, which requires much less configuration for shifters who just need to look at the plots. A server creates and manages stations that run the online reconstruction in headless mode. A command line client and interactive console allows the user to send commands to the server and receive responses. Finally, a number of GUI clients such as JAS3 and a Java web application can connect to a remote AIDA tree which shows an aggregated set of plots from all of the stations.

Installation

The online reconstruction server and client are part of the HPS Java project.

Start by creating a scratch area on your machine where you can work with the tools.

mkdir /scratch && cd /scratch

You do not have to use this exact directory, but it is recommended to have a dedicated directory for online reconstruction configuration files. The instructions in this documentation will generally assume that you are working within this directory.

The updated online reconstruction tools are currently on a branch of HPS Java, which you can checkout and build using a command such as:

git clone https://github.com/JeffersonLab/hps-java
cd hps-java
git checkout online-recon-dev
mvn clean install -DskipTests

Now, you should install the online reconstruction scripts into your work area:

# Go into online recon module within the hps-java project
cd online-recon

# Install the online recon run scripts to your work dir
mvn install -DskipTests -DskipCheckstyle -DassembleDirectory=/scratch

# Optionally add the script directory to the path.
export PATH=/scratch/bin:$PATH

The online reconstruction run scripts should now be installed to the /scratch/bin directory, and you should be ready to test the client and server.

Starting the Server 

The server cannot startup without an accessible and running ET ring present.

The important ET connection parameters for this can be specified in an initial server config file like:

et.buffer=/tmp/ETBuffer
et.host=localhost
et.port=11111

These are the hostname where the ET ring is running, the port it is using for connections, and the name of the buffer file. They need to match either the actual running ET ring in Hall B or one started by the user on their machine.

You can launch the server now using a command like::

hps-recon-server --host localhost --port 22222 -w $PWD/stations -c my.cfg &

The --host switch should specify a valid network hostname or IP address for the server to use.

The --port switch can be used to set an alternate port for the TCP/IP socket to listen on (by default it is actually 22222).

For testing and development, it is preferable to use the generic localhost but this is not provided as a default. Otherwise, this should be a valid system (DNS?) name, or leave it blank to use the actual system name.

Instead of writing to your terminal, the server will create a log file at logs/server.log which you can tail to check the server's log messages using a command like tail -f logs/server.log to see the server logs from handling client requests.

You can leave out the --host to have the server and client use the actual system name (usually equivalent to the result of the uname command on Linux).

Client Command Line

Now you can connect to the running server using the online recon client:

hps-recon-client --host localhost -c station.prop

An initial configuration can be provided to the client using the -c switch.

You can create an initial file called station.prop which will usually have settings specific to the data format/year like detector name, run number, reconstruction steering file:

lcsim.detector=HPS-PhysicsRun2016-Pass2
lcsim.run=7798
lcsim.steering=/org/hps/steering/recon/PhysicsRun2016OnlineRecon.lcsim

These settings are usually going to be specific to the year of the HPS data being read from the ET ring. The above are settings based on the 2016 physics reconstruction.

The client can also be used without a config file (the server may have been started with one to provide valid defaults).

Client Console

If you run the client without any command options, it will opens the interactive online reconstruction console which can be used to configure, create, start/stop and remove stations that run the HPS physics event reconstruction on data from the ET ring.

hps-recon-client --host localhost

Whenever you see online> it means the command is run in the online reconstruction console, not the system shell (like bash).

Type help into the console to show the documentation for the client command line interface:

online>help

This is the output of the above command:

GENERAL

    help - print general information
    help [cmd] - print information for specific command
    exit - quit the console

SETTINGS

    port [port] - set the server port
    host [host]- set the server hostname
    file [filename] - write server output to a file
    append [true|false] - true to append to output file or false to overwrite
    terminal - redirect server output back to the terminal

COMMANDS

    config - Set new server configuration properties
    create - Create a new station
    list - List station information in JSON format
    log - Tail log file of station (hit any key to stop tailing)
    remove - Remove a station that is inactive
    save - Save the current set of plots to a ROOT or AIDA file
    set - Set a configuration property
    shutdown - Shutdown the server
    start - Start a station that is inactive
    status - Show server and station status
    stop - Stop a station

You can set the connection settings to the server using the port and host commands, though the defaults should usually work fine.

If the server was started with a custom port or it is running with a particular hostname, this can be specified like:

online> port 12345
online> host myactualhostname

By default, output from the server read by the client is printed to the console, but it can be saved to a log file using commands such as:

online> file client.log
online> append true

Configuration of the online reconstruction stations can be set using:

# lcsim detector name for conditions
online>set lcsim.detector HPS-PhysicsRun2016-Pass2

# run number for conditions
online>set lcsim.run 7798

# lcsim steering resource
online>set lcsim.steering /org/hps/steering/recon/PhysicsRun2016OnlineRecon.lcsim

online>set lcsim.detector HPS-PhysicsRun2016-Pass2

FIXME: This example is very specific to 2016 data.

The steering file should contain a Driver that extends the RemoteAidaDriver, in order to provide station plot data to the server.

A single station with the above configuration can be created using:

online>create 1

The argument is the number of stations you want the server to create, which can potentially scale reliably to around the number of cores on your machine.

online>create 8

You will need to test how many stations you can run simultaneously given the specific configuration being used and the number of plots being created/updated.

Stations that have been created but not started are in the inactive state. Stations which are inactive have no running system process and no registration in the plot aggregation engine that adds plots from different stations, so their plots will not be shown in the remote tree.

Inactive stations can be started using a command like:

online>start

The start command can also take a list of station IDs to start:

online>start 1 2 3 ...

Many of the online recon commands are similar in that they take no arguments (usually meaning all stations or all stations in a certain state) or a space-delimited list of station IDs as in the above example.

Once a station is started, it will process events from the ET ring or sit in wait mode waiting for more data to appear.

The status of the stations and the ET ring can be checked using:

online>status

Log data can be streamed from each station using its station ID as an argument:

online>log 1

When streaming log data from one of the stations you can hit any key on the keyboard to exit.

Stop all jobs:

online>stop

Stop stations by ID:

online>stop 1 2 3

Remove all inactive stations (active stations need to be stopped first before they are removable).

online>remove

Remove stations by ID:

online>remove 1 2 3

Save some plots to an AIDA file:

online>save myplots.aida

JAS3 can be used to view AIDA plots.

Save some plots to a ROOT file:

online>save myplots.root

You can use rootbrowse command to look at the plots saved in the ROOT format.

When you'll all done, shutdown the server using a command like:

online>shutdown 5

This will wait 5 seconds before stopping and destroying all stations and cleanly shutting down the server and its connection to the ET ring.

Running a Command File

hps-recon-client --host localhost my.cmd

Accessing the Plot Data using a Web Application

Setup the Web Application

First install Tomcat and start it (not covered here). I used the 9.0.41 version.

Download and build the webapp from github:

git clone https://github.com/JeremyMcCormick/hps-online-recon-webapp
cd hps-online-recon-webapp
mvn clean install war:war -DskipTests

Now go to the Tomcat manager webpage, usually at:
http://localhost:8080/manager/html

Click Choose File in the manager and select the war file at hps-online-recon-webapp/target/HPSRecon.jar

Click Deploy to start the webapp. If there is a previous installation of the war file, then first click on Undeploy under Applications to remove it, or this step will fail.

Should there be trouble with the application, error messages can be found in the Tomcat log files at $TOMCAT_DIR/logs

The connection to the remote AIDA server is defined in hps-online-recon-webapp/src/main/webapp/WEB-INF/web.xml

The default value is:

<context-param>
    <param-name>hps.online.recon.connection</param-name>
    <param-value>//localhost:3001/HPSRecon</param-value>
</context-param>

Should the AIDA server's settings be changed, this MUST be updated and the webapp redeployed.

To force a reload of cached AIDA data (e.g. at the start of a new run), click Reload on the webapp in the admin panel:

View the Plots in the Browser

Anyone can view the combined plots in a webpage, provided the aggregator is running and the URL is accessible.

Go to the webpage to view the plots, which would typically be:

http://localhost:8080/HPSRecon/

If there is an error, probably the online reconstruction server is not running.

The plots should show in the frame on the left of the window:

They are organized by folders (directories) in the aida tree.

Click on one of the plots to show it:

Viewing plots in JAS3

The remote AIDA tree can be viewed in real-time using JAS3 as a client.

Installation of JAS3 is not covered. You need to install the "Remote AIDA Plugin" from the Plugin Manager as well as the standard AIDA plugin (no other plugins should be required).

Once installed and restarted (ignore any errors from the plugin manager), go to Tools > Remote AIDA > Connect and enter the correct settings for your remote AIDA tree:

TODO: graphic here of JAS3 connection params

These are the defaults but this may differ depending on the server's configuration.

Plots should refresh automatically (every 2s by default)

Click on the combined or remote plots in the tree and style them interactively...

TODO: Run a Java main() or Jython script to create AIDA plot pages/regions/styles/etc.

Installing the ET Ring Software

If you are running outside Hall B for testing purposes, the ET project is required for creating a local ET ring and using a producer to stream EVIO files onto it. (This is not needed for actual data runs in Hall B.)

# download and untar sources
https://coda.jlab.org/drupal/system/files/et-16.1.tgz
tar -zxvf et-16.1.tgz

# fix up build files (for some reason this is needed even with Python 2?)
cd et-16.1.GIT
2to3-2.7 -w ./coda.py ./SConstruct
autopep8 -i SConstruct
autopep8 -i coda.py

# build it
export CODA=`pwd`
scons install

# setup the environment (need to do this everytime you run)
export LD_LIBRARY_PATH=${CODA}/Linux-x86_64/lib
export PATH=${CODA}/Linux-x86_64/bin:${CODA}/Linux-x86_64/bin/examples:$PATH

The scons command may not be present in your environment (installation not covered here).

FIXME: The ET installation requires some hacking of the build files. (Checkin to git fork?)

Running the ET Ring

If you are testing and not taking data from a run then you need to start your own ET server to provide EVIO events, using a command like:

et_start -rb 8000000 -sb 8000000 -nd -p 11111 -f /tmp/ETBuffer -s 20000 -n 1000 -v -d

This starts the ET ring on port 11111 and uses a "standard" location for the swap file (buffer).

The -s argument specifics the max event size.

The -n argument is how many events can be present in the ET ring at once (???).

The other settings are mainly to try and improve the network performance of the tool by setting generous read/write buffers and using the no delay flag.

Experiment with the settings that seem to work best for your machine.

Running an Event Producer

To do anything useful with the ET ring, we need to stream HPS event data onto it, which can be done using a command like:

hps-recon-producer -p 11111 -h localhost -e 1 -f /tmp/ETBuffer -l ./evio_files.txt -s 20000 -d 10

The text file contains a list of EVIO files that should be compatible with the settings on the client/server (e.g. 2016 data for the example settings from above).

These settings need to match those of the ET start from above or you will not be able to connect.

TODO: Experiment with using broadcast mode to pickup any running ET rings.

Online Reconstruction Drivers and Steering Files

x

Stuff

For previous runs, the Monitoring Application has been used to run the reconstruction off of the ET ring and produce plots in a custom Java GUI.

This tool has some serious limitations such as:

• Requiring a large amount of configuration for each reconstruction station
• Not being able to scale horizontally by utilizing multiple CPUs to run reconstruction in parallel
• Taking a lot of system memory per process
• Being monolithic and difficult to extend/improve
• Using a no longer maintained plotting backend based on JFreeChart

With these limitations in mind, a new systems was developed around components such as a server, client, and reconstruction (ET) stations. Instead of all the components being run in the same system process, each reconstruction station is given its own system process and dedicated station on the ET ring. The stations run in headless mode (not displaying graphics) and provide real-time plot data using a remote AIDA tree which can be connected to and browsed/displayed as the data is streaming from the ET ring over an RMI connection. The server manages the aggregation of plot and performance data from each reconstruction station. A simple event bus was developed to replace the loop-based system in the old monitoring app. A client provides a command line and console interface for creating, starting, monitoring, stopping and removing stations managed by the server. Commands are sent to the server as JSON using a TCP/IP socket connection, and the server may send back a JSON response or stream data back to the client (e.g. for streaming station log data).

Histograms are booked and filled within the station's Driver code. The plots are stored in an AIDA tree which is remotely accessible (read only). The server mounts these station trees into its remote tree and performs aggregation of histograms, clouds, and profiles into a combined tree. One to three dimensional histograms are supported, depending on the type (profiles have no 3D type). The combined histogram data can be saved to ROOT or AIDA files.

Display clients such as JAS3 or a Java webapp can connect to the server's remote tree and view both the remote (station) plots and the combined plots in real time.