Physics Derivation Graph: 2025

troubleshooting docker and podman on MacAirbook M2

I have an old MacBook Air running

macOS Catalina v10.15.7 with a 1.8GHz Intel Core i5 and 4GB of RAM
`docker compose version` = 2.2.1
`docker --version` = 20.10.11

I have a new MacBook Air running

macOS Sonoma v14.6.1 with an Apple M2 and 8GB of RAM

Podman on the new MacBook M2

Downloaded

https://github.com/podman-desktop/podman-desktop/releases/download/v1.15.0/podman-desktop-1.15.0-universal.dmg

from https://podman-desktop.io/downloads

Confusingly, 1.15.0 provides Podman 4.9.0 (?)

As per https://stackoverflow.com/a/76488304 I tried

% podman machine stop; podman machine start

Waiting for VM to exit...
Machine "podman-machine-default" stopped successfully
Starting machine "podman-machine-default"
Waiting for VM ...
Mounting volume... /Users:/Users
chattr: Operation not supported while reading flags on /
mkdir: cannot create directory ‘/Users’: Read-only file system
chattr: Operation not supported while reading flags on /
Error: exit status 1

I then tried

% podman machine stop
Waiting for VM to exit...
Machine "podman-machine-default" stopped successfully

% podman machine rm
The following files will be deleted:
...
Are you sure you want to continue? [y/N] y

% podman machine init                                         
Extracting compressed file: podman-machine-default_fedora-coreos-41.20241215.2.0-qemu.aarch64.qcow2: done  
Image resized.
Machine init complete
To start your machine run:
	podman machine start
    
% podman machine start
Starting machine "podman-machine-default"
Waiting for VM ...
Mounting volume... /Users:/Users
chattr: Operation not supported while reading flags on /
mkdir: cannot create directory ‘/Users’: Read-only file system
chattr: Operation not supported while reading flags on /
Error: exit status 1

Running as root doesn't help

% sudo podman machine start
Error: cannot run command "podman machine start" as root

As per https://stackoverflow.com/a/71576242 I tried

% podman machine init --cpus=4 --disk-size=60 --memory=6096 -v $HOME:$HOME
Extracting compressed file: podman-machine-default_fedora-coreos-41.20241215.2.0-qemu.aarch64.qcow2: done  
Image resized.
Machine init complete
To start your machine run:
	podman machine start

% podman machine start
Starting machine "podman-machine-default"
Waiting for VM ...
Mounting volume... /Users/myinitials:/Users/myinitials
chattr: Operation not supported while reading flags on /
mkdir: cannot create directory ‘/Users’: Read-only file system
chattr: Operation not supported while reading flags on /
Error: exit status 1

As a consequence, while I can run the container,

% podman run -it --rm localhost/ui_v8_website_flask_neo4j_webserver /bin/bash 
WARNING: image platform (linux/amd64) does not match the expected platform (linux/arm64)
root@4d006ef73e19:/code#

I am unable to mount the local directory

% podman run -it --rm -v `pwd`:/scratch localhost/ui_v8_website_flask_neo4j_webserver /bin/bash
WARNING: image platform (linux/amd64) does not match the expected platform (linux/arm64)
Error: statfs /Users/bhp/version_control/allofphysicsgraph/ui_v8_website_flask_neo4j: no such file or directory

Uninstall Podman

podman machine stop podman-machine-default
podman machine rm podman-machine-default
podman machine rm
sudo /opt/podman/bin/podman-mac-helper uninstall
sudo rm /etc/paths.d/podman-pkg
sudo rm -rfv /opt/podman
sudo rm -rf /Applications/Podman\ Desktop.app/
sudo rm /var/run/docker.sock
rm -fr ~/.local/share/containers/

Docker on the new MacBook M2

Downloaded https://desktop.docker.com/mac/main/arm64/Docker.dmg from https://docs.docker.com/desktop/setup/install/mac-install/

roles, use cases, and requirements

Tests are based on validating requirements. Requirements are derived from use cases that address the needs of people in specific roles.

Roles

Viewer: sees content on web UI, reads PDF versions. Uses either the web UI or the API.
Editor: adds equations, inference rules, and derivations. Uses either the web UI or the API
Developer: uses the API to build an alternative web UI or runs a service that leverages the PDG
Contributor: edits documentation and source code, fixes bugs. Uses github issue tracker.

Use cases per role

Viewer

reads documentation about PDG
sees the number of derivations

on the navigation page

sees the number of symbols

on the navigation page

sees the number of inference rules

on the navigation page

sees the number of expressions

on the navigation page

sees a list of derivations

accessed from the navigation page

sees a list of expressions

accessed from the navigation page

sees a list of inference rules

accessed from the navigation page

sees a list of symbols

accessed from the navigation page

see a list of derivations that use a specific symbol
see a list of derivations that use a specific inference rule
see a list of derivations that use a specific expression
see the steps of a specific derivation

accessed from the list of derivations

Editor has same as Viewer, plus:
(the following actions require being logged in)

adds a new derivation

accessed from the navigation page
next page is create new step

edits an existing derivation

accessed from the list of derivations
after edit is submitted, return to viewing that derivation

deletes an derivation

accessed from the list of derivations
after delete is confirmed, return to list of derivations

adds a new step

return to derivation

edits an existing step
deletes a step

return to derivation

adds a new expression

return to derivation step

edits an existing expression

change Latex
change relation (e.g., = to >)
change label

deletes an expression
adds a new inference rule
edits an existing inference rule

change number of arguments

deletes an inference rule. (What happens to all the instances of use in various derivations?)
adds a new symbol
edits an existing symbol

change the latex
change the sympy

deletes a symbol. (What happens to all the instances of use in various expressions?)
delete all database content

return to navigation page

For each of the use cases per role,

test in web UI
test in API

what should I work on? many options for tasks TODO

separate the property graph backend from an API and have the web interface call the API
find a lighter weight alternative to neo4j backend
get a minimum viable product working using the existing property graph backend
separate static documentation pages from the dynamic paths
get docker working on my new Mac

That last one is the blocker for everything else, so get docker working on my new Mac is priority. The good news is that the code does run on my old MacBook Air.

Next I'll work on getting a minimum viable product working using the existing property graph backend

Wednesday, January 1, 2025