Speed up Docker build

[paulromano]

Description

This PR makes a few updates to our Dockerfile to speed up build times:

• Instead of building Embree from source it uses the apt package
• Similarly, pugixml, libfmt, and Catch2 are installed from apt
• Avoids building tests for MOAB and DAGMC

The Embree change alone should shave off 15-20 min of build time.

Checklist

• I have performed a self-review of my own code
• I have run clang-format (version 15) on any C++ source files (if applicable)
• I have followed the style guidelines for Python source files (if applicable)
• I have made corresponding changes to the documentation (if applicable)
• I have added tests that prove my fix is effective or that my feature works (if applicable)

[GuySten]

If we use fmt and pugixml from apt, we should not include them as submodules.

[paulromano]

We include the submodules as a backup so that people are not required to have them installed already. However, if they do have them installed and find_package finds them, the submodules don't get built.

[shimwell]

I am running this locally and getting a warning and error. I think the warning was there before the PR but is anyone else getting Unable to locate package libcatch2-dev.

The CI doesn't test this docker build till it is pushed to develop so this is why I was building locally

docker build -t openmc_dagmc --build-arg build_dagmc=on --build-arg compile_cores=4 .
[+] Building 11.6s (5/12)                                                                                                                                                docker:default
 => [internal] load build definition from Dockerfile                                                                                                                               0.1s
 => => transferring dockerfile: 8.63kB                                                                                                                                             0.0s
 => [internal] load metadata for docker.io/library/ubuntu:24.04                                                                                                                    0.6s
 => [internal] load .dockerignore                                                                                                                                                  0.0s
 => => transferring context: 2B                                                                                                                                                    0.0s
 => CACHED [dependencies 1/7] FROM docker.io/library/ubuntu:24.04@sha256:d1e2e92c075e5ca139d51a140fff46f84315c0fdce203eab2807c7e495eff4f9                                          0.0s
 => ERROR [dependencies 2/7] RUN apt-get update -y &&     apt-get upgrade -y &&     apt-get install -y         python3-pip python-is-python3 wget git build-essential cmake       10.8s
------                                                                                                                                                                                  
 > [dependencies 2/7] RUN apt-get update -y &&     apt-get upgrade -y &&     apt-get install -y         python3-pip python-is-python3 wget git build-essential cmake         mpich libmpich-dev libhdf5-serial-dev libhdf5-mpich-dev         libpng-dev libpugixml-dev libfmt-dev libcatch2-dev python3-venv &&     apt-get autoremove:                                         
0.366 Get:1 http://archive.ubuntu.com/ubuntu noble InRelease [256 kB]                                                                                                                   
0.522 Get:2 http://security.ubuntu.com/ubuntu noble-security InRelease [126 kB]                                                                                                         
0.631 Get:3 http://archive.ubuntu.com/ubuntu noble-updates InRelease [126 kB]                                                                                                           
0.696 Get:4 http://archive.ubuntu.com/ubuntu noble-backports InRelease [126 kB]
0.760 Get:5 http://archive.ubuntu.com/ubuntu noble/universe amd64 Packages [19.3 MB]
1.083 Get:6 http://security.ubuntu.com/ubuntu noble-security/multiverse amd64 Packages [34.8 kB]
1.227 Get:7 http://security.ubuntu.com/ubuntu noble-security/universe amd64 Packages [1242 kB]
1.689 Get:8 http://archive.ubuntu.com/ubuntu noble/restricted amd64 Packages [117 kB]
1.690 Get:9 http://archive.ubuntu.com/ubuntu noble/main amd64 Packages [1808 kB]
1.744 Get:10 http://archive.ubuntu.com/ubuntu noble/multiverse amd64 Packages [331 kB]
1.752 Get:11 http://archive.ubuntu.com/ubuntu noble-updates/multiverse amd64 Packages [38.1 kB]
1.753 Get:12 http://archive.ubuntu.com/ubuntu noble-updates/universe amd64 Packages [2017 kB]
1.938 Get:13 http://archive.ubuntu.com/ubuntu noble-updates/main amd64 Packages [2275 kB]
2.006 Get:14 http://security.ubuntu.com/ubuntu noble-security/main amd64 Packages [1883 kB]
2.072 Get:15 http://archive.ubuntu.com/ubuntu noble-updates/restricted amd64 Packages [3471 kB]
2.141 Get:16 http://security.ubuntu.com/ubuntu noble-security/restricted amd64 Packages [3262 kB]
2.380 Get:17 http://archive.ubuntu.com/ubuntu noble-backports/universe amd64 Packages [34.6 kB]
2.381 Get:18 http://archive.ubuntu.com/ubuntu noble-backports/main amd64 Packages [49.5 kB]
3.500 Fetched 36.5 MB in 3s (11.3 MB/s)
3.500 Reading package lists...
4.762 Reading package lists...
5.879 Building dependency tree...
6.104 Reading state information...
6.166 Calculating upgrade...
6.477 The following packages will be upgraded:
6.478   gcc-14-base libgcc-s1 libgnutls30t64 libstdc++6
6.926 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
6.926 Need to get 1923 kB of archives.
6.926 After this operation, 9216 B of additional disk space will be used.
6.926 Get:1 http://archive.ubuntu.com/ubuntu noble-updates/main amd64 gcc-14-base amd64 14.2.0-4ubuntu2~24.04.1 [51.0 kB]
7.438 Get:2 http://archive.ubuntu.com/ubuntu noble-updates/main amd64 libstdc++6 amd64 14.2.0-4ubuntu2~24.04.1 [792 kB]
7.993 Get:3 http://archive.ubuntu.com/ubuntu noble-updates/main amd64 libgcc-s1 amd64 14.2.0-4ubuntu2~24.04.1 [78.4 kB]
8.009 Get:4 http://archive.ubuntu.com/ubuntu noble-updates/main amd64 libgnutls30t64 amd64 3.8.3-1.1ubuntu3.5 [1001 kB]
8.371 debconf: delaying package configuration, since apt-utils is not installed
8.436 Fetched 1923 kB in 2s (1172 kB/s)
(Reading database ... 4381 files and directories currently installed.)
8.474 Preparing to unpack .../gcc-14-base_14.2.0-4ubuntu2~24.04.1_amd64.deb ...
8.482 Unpacking gcc-14-base:amd64 (14.2.0-4ubuntu2~24.04.1) over (14.2.0-4ubuntu2~24.04) ...
8.540 Setting up gcc-14-base:amd64 (14.2.0-4ubuntu2~24.04.1) ...
(Reading database ... 4381 files and directories currently installed.)
8.593 Preparing to unpack .../libstdc++6_14.2.0-4ubuntu2~24.04.1_amd64.deb ...
8.625 Unpacking libstdc++6:amd64 (14.2.0-4ubuntu2~24.04.1) over (14.2.0-4ubuntu2~24.04) ...
8.724 Setting up libstdc++6:amd64 (14.2.0-4ubuntu2~24.04.1) ...
(Reading database ... 4381 files and directories currently installed.)
8.773 Preparing to unpack .../libgcc-s1_14.2.0-4ubuntu2~24.04.1_amd64.deb ...
8.781 Unpacking libgcc-s1:amd64 (14.2.0-4ubuntu2~24.04.1) over (14.2.0-4ubuntu2~24.04) ...
8.834 Setting up libgcc-s1:amd64 (14.2.0-4ubuntu2~24.04.1) ...
(Reading database ... 4381 files and directories currently installed.)
8.881 Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu3.5_amd64.deb ...
8.889 Unpacking libgnutls30t64:amd64 (3.8.3-1.1ubuntu3.5) over (3.8.3-1.1ubuntu3.4) ...
8.964 Setting up libgnutls30t64:amd64 (3.8.3-1.1ubuntu3.5) ...
8.993 Processing triggers for libc-bin (2.39-0ubuntu8.7) ...
9.053 Reading package lists...
10.42 Building dependency tree...
10.71 Reading state information...
10.74 E: Unable to locate package libcatch2-dev
------

 1 warning found (use docker --debug to expand):
 - UndefinedVar: Usage of undefined variable '$LD_LIBRARY_PATH' (line 59)
Dockerfile:64
--------------------
  63 |     # Install and update dependencies from Debian package manager
  64 | >>> RUN apt-get update -y && \
  65 | >>>     apt-get upgrade -y && \
  66 | >>>     apt-get install -y \
  67 | >>>         python3-pip python-is-python3 wget git build-essential cmake \
  68 | >>>         mpich libmpich-dev libhdf5-serial-dev libhdf5-mpich-dev \
  69 | >>>         libpng-dev libpugixml-dev libfmt-dev libcatch2-dev python3-venv && \
  70 | >>>     apt-get autoremove
  71 |     
--------------------
ERROR: failed to build: failed to solve: process "/bin/sh -c apt-get update -y &&     apt-get upgrade -y &&     apt-get install -y         python3-pip python-is-python3 wget git build-essential cmake         mpich libmpich-dev libhdf5-serial-dev libhdf5-mpich-dev         libpng-dev libpugixml-dev libfmt-dev libcatch2-dev python3-venv &&     apt-get autoremove" did not complete successfully: exit code: 100

[paulromano]

Thanks for testingit out @shimwell! Apparently libcatch2-dev wasn't present as an apt package until Ubuntu 25.04. The correct name for Ubuntu 24.04 is catch2. I just updated that and built locally and it seems to work now.

[shimwell]

Thanks for the speed improvements, keen to see this as it will help keep the reduce CI usage. I committed a small change to get rid of a warning, hope this is ok.