Getting Started

Getting started on FNAL servers

Send a ticket requesting access to the COUUP affiliation with the Fermilab Service Desk. This can take up to 2 business days.
Once you have access, ssh into the general purpose virtual machine (GPVM)
```
kinit <username>@FNAL.GOV
ssh -KYX <username>@couppsbcgpvm01.fnal.gov
```
If you see errors relating to permissions in your home directory, try using kinit -f <username>>@fnal.gov to make sure your credentials are being forwarded.
Navigate to the app directory area, then make a new directory for yourself
```
cd /exp/e961/app/users
mkdir <username>
cd <username>
```
Get the code! Setup an SSH key for github if you do not already have one (follow the “Generating a new SSH key” steps), and then add it to you github account. Also copy the key to your home directory on couppsbcgpvm01.fnal.gov to: ~/.ssh/. If you ran the ssh keygen on the couppsbcgpvm01.fnal.gov machine, it will be there already. Then clone the directory into you app users area:
```
git clone git@github.com:SBC-Collaboration/LAr10Ana.git
```
Now you have access to the code on the Fermilab servers! See below for instructions on other things you may want to do next: how to setup the SBCLAr10 conda environment, how to log back into the fermilab servers, how to submit grid jobs, and others.

Logging back into the Fermilab servers

Once you have your account setup, to get back to your app area from your laptop, run:

ssh -KYX <username>@couppsbcgpvm01.fnal.gov
cd /exp/e961/app/users/<username>

You may get an authentication error if you have not run kinit in about a day. In that case, before ssh-ing, run:

kinit -f <username>@FNAL.GOV

Activating the SBCLAr10 Conda Environment

SBC analysis mostly relies on python code, with a few external dependencies. The code is managed in a central conda environment. Once you have the LAr10Ana repository downloaded, navigate to LAr10Ana/. Then run:

source setup.sh

This will setup the conda environment in your current terminal.

Running jupyter notebooks

To run a jupyter notebook, you’ll want to start a server from your terminal and then open it in a browser. First, login to the Fermilab server and forward port 8888:

ssh -KYX <username>@couppsbcgpvm01.fnal.gov -L 8888:localhost:8888

If you see an error in the login that port 8888 is taken, then try again with a different port (8889, for example).

The first time you run a notebook, you’ll want to add the conda environment to your list of available jupyterlab kernels. To do this, navigate to your LAr10Ana directory (cd /path/to/LAr10Ana), and run the commands:

source setup.sh # This activates the conda environment. You'll need to run it every time you create a new terminal connection.
source jupyter_init.sh # This tells jupyter about your conda environment. You only need to run it the first time you run the notebook.

Now you’re ready to start a jupyter notebook! To do this, start from a terminal inside LAr10Ana where you have already activated the conda environment (by running setup.sh). Then, run:

jupyter notebook --no-browser --port <port>

Where <port> is the port you selected in the ssh. A link will print in the terminal. Open it in the browser to access the jupyter notebook. For some example notebooks for accessing SBC-LAr10 data, navigate to nb/examples. Make sure to select the SBC conda (env) kernel when starting a new notebook.

Running Event Display

To run the event display, you’ll need to launch a VNC session on a free port.

Check for VNC ports

See which ports are already in use:

/exp/e961/app/home/coupp/bin/RegisterVNCDesktop

Pick a two-digit number that isn’t taken. For example, 50 would mean your VNC server runs on port 5950.

Register your choice:

/exp/e961/app/home/coupp/bin/RegisterVNCDesktop 50 "Optional short description"

Setup `xstartup`

If you don’t already have ~/.vnc/xstartup, make one. Also create ~/.vnc if needed.

Here’s a working example:

#!/bin/sh

# Unset conflicting environment variables
unset SESSION_MANAGER
unset DBUS_SESSION_BUS_ADDRESS
unset PYTHONHOME PYTHONPATH LD_LIBRARY_PATH LD_PRELOAD

# Load X resources
[ -f $HOME/.Xresources ] && xrdb $HOME/.Xresources

# Start IceWM
exec icewm

Make sure it’s executable:

chmod +x ~/.vnc/xstartup

Start the VNC Server

Use the display number you picked earlier:

vncserver :PORT_NUMBER

Run the Event Display

You will need to port forward your local VNC port to your localhost machine. This can be done using ssh

ssh -L <local_port>:localhost:<remote_port> <user>@<remote_host>

After tunneling you can run the following commands to run the event display

export DISPLAY=:PORT_NUMBER
cd /exp/e961/app/LAr10Ana
source setup.sh
python EventDisplay/eventdisplay/ped.py

VNC Software

You will need to download VNC software and connect to localhost:PORT_NUMBER to view the event display.

For MacOS we recommend using the built in “Screen Sharing” software.
For Windows we recommend using TigerVNC
For Chromebook, try using Remmina (Linux app)