Here are several things you can check to make sure you are ready for the summer school.

Attendee Checklist

To help, we've created a run through below and short Jupyter notebook you can download to demonstrate these steps.

Fermitools Example Run Through

Here's an example session on a Mac. I created a directory called fermi_summer_school  and a file in it called this_is_the_share_directory just so something shows up in a directory listing.  Note that its name does not matter, and you can create it wherever you like or use an existing directory.  This directory will be visible from the container. I then pulled the FermiBottle image from Docker and started it.

(base) user@host % mkdir fermi_summer_school
(base) user@host % cd fermi_summer_school
(base) user@host fermi_summer_school % touch this_is_the_share_directory
(base) user@host fermi_summer_school % ls
(base) user@host fermi_summer_school % docker pull fssc/fermibottle
Pulling from fssc/fermibottle
Digest: sha256:f041b634d1b3a6d3a4e3276c8bac486de47a1839365c0a0826569da40c5a9b47
Status: Image is up to date for fssc/fermibottle
(base) user@host fermi_summer_school % xhost + && \
docker create -it --init \
-e HOST_USER_ID=`id -u $USER` \
-e DISPLAY=host.docker.internal:0 \
-v "`pwd`":/data \
-p 8888:8888 \
fssc/fermibottle being added to access control list
(base) user@host fermi_summer_school % docker ps -a
CONTAINER ID   IMAGE              COMMAND                  CREATED          STATUS    PORTS     NAMES
be68136958ad   fssc/fermibottle   "/opt/docker/bin/ent…"   19 seconds ago   Created             silly_pasteur
(base) user@host fermi_summer_school % docker start be68136958ad
(base) user@host fermi_summer_school % docker attach be68136958ad

You can use either the container id or name of the container to start and attach to it.

This puts me in the container. You should notice that the prompt is now the "fermi" user and the container ID. Note that you only have to run the xhost command once.  If you quit the container, you just have to run the start and attach commands to return to it.

I launched ds9 to make sure X-windows are working. Quit it (assuming it works) and change to the shared directory, which is under /data in the container.

(base) [fermi@be68136958ad ~]$ ds9
(base) [fermi@be68136958ad ~]$ cd /data
(base) [fermi@be68136958ad data]$ ls

Back on the host system, download this file,, and put it in the shared directory. Then, unzip it which will create a directory.

(base) user@host fermi_summer_school % unzip 
   creating: Quick_Test/
  inflating: Quick_Test/Quick_Test.ipynb  
  inflating: Quick_Test/SC00.fits    
  inflating: Quick_Test/3C279_1deg_gti.fits  
(base) user@host fermi_summer_school % ls
Quick_Test/                       this_is_the_share_directory

In the container, you should see the change:

(base) [fermi@be68136958ad data]$ ls
Quick_Test  this_is_the_share_directory

Now start the "fermi" environment and the Jupyter notebook server:

(base) [fermi@be68136958ad data]$ conda activate fermi
(fermi) [fermi@be68136958ad data]$ cd Quick_Test
(fermi) [fermi@be68136958ad Quick_Test]$ ls
3C279_1deg_gti.fits  3C279_1deg_lc.fits  Quick_Test.ipynb  SC00.fits

(fermi) [fermi@be68136958ad data]$ notebook
[I 19:02:00.683 NotebookApp] Loading IPython parallel extension
[I 19:02:00.685 NotebookApp] Serving notebooks from local directory: /data
[I 19:02:00.685 NotebookApp] Jupyter Notebook 6.3.0 is running at:
[I 19:02:00.685 NotebookApp]
[I 19:02:00.685 NotebookApp]  or
[I 19:02:00.685 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 19:02:00.689 NotebookApp] 
    To access the notebook, open this file in a browser:
    Or copy and paste one of these URLs:

You can paste one of the http URLs into the browser (I used the one) on your host machine and should see something like:

Click on the Quick_test.ipynb file to open it. You can then run the notebook by select Cell->Run All from the menu bar.  It runs one of the Fermitools (gtbin) and then creates a lightcurve. You should then end up with a notebook that looks like this:

Congratulations, things seem to be working!

GBM Data Tools Example

The GBM Data Tools tutorials are in Jupyter notebooks.  If you did the example above, you already have a notebook running, but you can't have more than one Jupyter notebook running at a time in FermiBottle by default.  You can use the "Quit" button in the upper right of the Jupyter notebook start page or hit to ctrl-c in the terminal window, which will then prompt you to shut it down.  

The GBM Data Tools are in separate conda environment from the Fermitools.  The GBM team provides the gbm-demos command to launch a list of the tutorial notebooks.

(fermi) [fermi@be68136958ad Quick_Test]$ conda deactivate
(base) [fermi@be68136958ad Quick_Test]$ conda activate fermigbm
(fermigbm) [fermi@be68136958ad Quick_Test]$ 
(fermigbm) [fermi@be68136958ad Quick_Test]$ gbm-demos

Like before, you will need to paste the URL into an external browser and will then find a list of notebooks.  Open the index.ipynb one, which gives more descriptive list of the available tutorials.  Try the first one on the list "GBM Science Data: Time History Spectra" and do Cell->Run All.  It should run quickly and make some plots.  You may see a warning that Basemap is not installed.  That shouldn't be a problem for now.

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