---
title: "Linux & Docker Basics"
subtitle: "Lecture 15"
author: "Dr. Colin Rundel"
footer: "Sta 663 - Spring 2026"
format:
  revealjs:
    theme: slides.scss
    transition: fade
    slide-number: true
    self-contained: true
execute: 
  echo: true
---

```{r setup, message=FALSE, warning=FALSE, include=FALSE}
{{< include _setup.R >}}
```


## {background-image="https://images.squarespace-cdn.com/content/v1/660d89dc96ccfa3a66eeb7ef/1712262249220-NGDRJVOCHGLMO8AM2HF0/sticker-cosplaying-as-a-sysadmin.png?format=1500w" background-size=50%}

::: {.aside}
Source - Jeff Geerling / [Red Shirt Jeff](https://www.redshirtjeff.com/shop/p/cosplaying-as-a-sysadmin-stickers)
:::

# Duke VCM

##


![](imgs/Docker/vcm1.png){fig-align="center" width="100%"}

<br/><br/>

::: {.center}
[vcm.duke.edu](https://vcm.duke.edu/)
:::

##

![](imgs/Docker/vcm2.png){fig-align="center" width="100%"}


##

![](imgs/Docker/vcm3.png){fig-align="center" width="100%"}

# Getting Started

## Connecting

::: {.xsmall}
```shell
rundel@tbBook [~]$ ssh cr173@vcm-52470.vm.duke.edu
```
:::
. . .

::: {.xsmall}
```
The authenticity of host 'vcm-52470.vm.duke.edu (67.159.69.176)' can't be established.
ED25519 key fingerprint is SHA256:fSZfURPpnL4M+0bWv6S3jMYtalAeKZWSLH6DR+sxOe0.
This key is not known by any other names.
Are you sure you want to continue connecting (yes/no/[fingerprint])? 
```
:::

. . .

::: {.xsmall}
```
Warning: Permanently added 'vcm-52470.vm.duke.edu' (ED25519) to the list of known hosts.
cr173@vcm-52470.vm.duke.edu's password:
```
:::

. . .

::: {.xsmall}
```
Welcome to Ubuntu 24.04.4 LTS (GNU/Linux 6.8.0-100-generic x86_64)

 * Documentation:  https://help.ubuntu.com
 * Management:     https://landscape.canonical.com
 * Support:        https://ubuntu.com/pro

 System information as of Tue Feb 24 09:50:33 PM EST 2026

  System load:    0.0               Processes:             150
  Usage of /home: 2.1% of 17.93GB   Users logged in:       0
  Memory usage:   28%               IPv4 address for eth0: 67.159.65.108
  Swap usage:     16%

 * Strictly confined Kubernetes makes edge and IoT secure. Learn how MicroK8s
   just raised the bar for easy, resilient and secure K8s cluster deployment.

   https://ubuntu.com/engage/secure-kubernetes-at-the-edge

Expanded Security Maintenance for Applications is not enabled.

0 updates can be applied immediately.

Enable ESM Apps to receive additional future security updates.
See https://ubuntu.com/esm or run: sudo pro status


*** System restart required ***
** Important Notice about your VCM VM **

This server is set to patch daily via unattended upgrades, and will be shut off every day.
Learn about unattended upgrades for ubuntu: https://linuxcapable.com/how-to-configure-unattended-upgrades-on-ubuntu-linux/
```
:::

## {background-image="imgs/Docker/linux_tree.png" background-size=contain}

```{css}
/*| echo: false*/
.reveal pre code {
  text-wrap-mode: nowrap !important;
}
```


## Determining Distribution

::: {.panel-tabset}

### Ubuntu / Debian

::: {.xxsmall}
```shell
cr173@vcm-52470:~$ cat /etc/os-release
```

```
PRETTY_NAME="Ubuntu 24.04.2 LTS"
NAME="Ubuntu"
VERSION_ID="24.04"
VERSION="24.04.2 LTS (Noble Numbat)"
VERSION_CODENAME=noble
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=noble
LOGO=ubuntu-logo
```
:::

### Fedora / RHEL

::: {.xxsmall}
```shell
cr173@germain [~]$ cat /etc/os-release
```

```
NAME="Fedora Linux"
VERSION="40 (Server Edition)"
ID=fedora
VERSION_ID=40
VERSION_CODENAME=""
PLATFORM_ID="platform:f40"
PRETTY_NAME="Fedora Linux 40 (Server Edition)"
ANSI_COLOR="0;38;2;60;110;180"
LOGO=fedora-logo-icon
CPE_NAME="cpe:/o:fedoraproject:fedora:40"
HOME_URL="https://fedoraproject.org/"
DOCUMENTATION_URL="https://docs.fedoraproject.org/en-US/fedora/f40/system-administrators-guide/"
SUPPORT_URL="https://ask.fedoraproject.org/"
BUG_REPORT_URL="https://bugzilla.redhat.com/"
REDHAT_BUGZILLA_PRODUCT="Fedora"
REDHAT_BUGZILLA_PRODUCT_VERSION=40
REDHAT_SUPPORT_PRODUCT="Fedora"
REDHAT_SUPPORT_PRODUCT_VERSION=40
SUPPORT_END=2025-05-13
VARIANT="Server Edition"
VARIANT_ID=server
```
:::
:::


# System Details

## Filesystem Hierarchy Standard {.scrollable}

::: {.columns}

::: {.column width=50% .small}

See Wikipedia's [article](https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard) 

<br class="small"/>

Some common folders:

* `/bin/` & `/usr/bin/` - executables

* `/etc/` - configuration files

* `/lib*/` & `/usr/lib*/` - Static and shared libraries

* `/usr/include/` - header files

* `/home/` - user home directories

* `/var/` - logs

* `/tmp/` - temporary files

:::

::: {.column width=50%}

::: {.panel-tabset}

### Primary

::: {.xxsmall .limit400}
```{.shell}
tree -d -L 1 /
```

```
/
├── bin -> usr/bin
├── bin.usr-is-merged
├── boot
├── cdrom
├── dev
├── etc
├── home
├── lib -> usr/lib
├── lib64 -> usr/lib64
├── lib.usr-is-merged
├── media
├── mnt
├── opt
├── proc
├── root
├── run
├── sbin -> usr/sbin
├── sbin.usr-is-merged
├── snap
├── srv
├── sys
├── tmp
├── usr
└── var

25 directories
```
:::


### Secondary

::: {.xxsmall}
```shell
cr173@algebra2 [~]$ tree -d -L 1 /usr
```

```
/usr
├── bin
├── games
├── include
├── lib
├── lib64
├── libexec
├── local
├── sbin
├── share
└── src

11 directories
```
:::
:::

:::

:::


## Basic Filesystem Navigation

::: {.small}
| Command | Description |
|:--------|:------------|
| `pwd` | Print working directory |
| `ls` | List directory contents (`-l` long, `-a` include hidden) |
| `cd <dir>` | Change directory |
| `cd ..` | Move up one level |
| `cd ~` | Go to home directory |
| `mkdir <dir>` | Create a directory |
| `rm <file>` | Remove a file (`-r` for directories, `-f` force) |
| `cp <src> <dst>` | Copy file or directory (`-r` for directories) |
| `mv <src> <dst>` | Move or rename file/directory |
| `cat <file>` | Print file contents |
| `less <file>` | Page through file contents |
:::

. . .

Useful shortcuts: `.` = current directory, `..` = parent, `~` = home


# Installing packages with `apt` (Ubuntu, Debian, etc.)

## Update the package list

::: {.xsmall}
```shell
apt update
```

```
Reading package lists... Done
E: Could not open lock file /var/lib/apt/lists/lock - open (13: Permission denied)
E: Unable to lock directory /var/lib/apt/lists/
W: Problem unlinking the file /var/cache/apt/pkgcache.bin - RemoveCaches (13: Permission denied)
W: Problem unlinking the file /var/cache/apt/srcpkgcache.bin - RemoveCaches (13: Permission denied)
```
:::

. . .

![](https://imgs.xkcd.com/comics/sandwich.png){fig-align="center" width="33%"}

::: {.xsmall .center}
[XKCD 149 - Sandwich](https://xkcd.com/149/)
:::


## Update the package list

::: {.xsmall}
```shell
sudo apt update
```

```
[sudo] password for cr173: 
Hit:1 http://archive.linux.duke.edu/ubuntu focal InRelease
Get:2 http://archive.linux.duke.edu/ubuntu focal-updates InRelease [114 kB]
Hit:3 https://falcon-dl.oit.duke.edu/ubuntu focal InRelease
Get:4 http://archive.linux.duke.edu/ubuntu focal-backports InRelease [108 kB]
Get:5 http://archive.linux.duke.edu/ubuntu focal-security InRelease [114 kB]
Get:6 http://archive.linux.duke.edu/ubuntu focal-updates/main amd64 Packages [1,711 kB]
Get:7 http://archive.linux.duke.edu/ubuntu focal-updates/main i386 Packages [628 kB]
Get:8 http://archive.linux.duke.edu/ubuntu focal-updates/main Translation-en [320 kB]
Get:9 http://archive.linux.duke.edu/ubuntu focal-updates/restricted amd64 Packages [917 kB]
Get:10 http://archive.linux.duke.edu/ubuntu focal-updates/restricted Translation-en [131 kB]
Get:11 http://archive.linux.duke.edu/ubuntu focal-updates/universe amd64 Packages [916 kB]
Get:12 http://archive.linux.duke.edu/ubuntu focal-updates/universe i386 Packages [676 kB]
Get:13 http://archive.linux.duke.edu/ubuntu focal-updates/universe Translation-en [204 kB]
Get:14 http://archive.linux.duke.edu/ubuntu focal-updates/universe amd64 c-n-f Metadata [20.4 kB]
Get:15 http://archive.linux.duke.edu/ubuntu focal-security/main i386 Packages [416 kB]
Get:16 http://archive.linux.duke.edu/ubuntu focal-security/main amd64 Packages [1,383 kB]
Get:17 http://archive.linux.duke.edu/ubuntu focal-security/main Translation-en [239 kB]
Get:18 http://archive.linux.duke.edu/ubuntu focal-security/restricted amd64 Packages [859 kB]
Get:19 http://archive.linux.duke.edu/ubuntu focal-security/restricted Translation-en [122 kB]
Get:20 http://archive.linux.duke.edu/ubuntu focal-security/universe i386 Packages [547 kB]
Get:21 http://archive.linux.duke.edu/ubuntu focal-security/universe amd64 Packages [696 kB]
Get:22 http://archive.linux.duke.edu/ubuntu focal-security/universe Translation-en [122 kB]
Get:23 http://archive.linux.duke.edu/ubuntu focal-security/universe amd64 c-n-f Metadata [14.1 kB]
Fetched 10.3 MB in 3s (4,100 kB/s)
Reading package lists... Done
Building dependency tree
Reading state information... Done
1 package can be upgraded. Run 'apt list --upgradable' to see it.
```
:::


## Installing R

::: {.xxsmall}
```shell
sudo apt install r-base
```

```
[sudo] password for cr173:
```
```
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
  build-essential bzip2-doc cpp cpp-9 dpkg-dev fakeroot fontconfig fontconfig-config fonts-dejavu-core g++ g++-9 gcc gcc-9 gcc-9-base gfortran gfortran-9 icu-devtools
  libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl libasan5 libatomic1 libauthen-sasl-perl libblas-dev libblas3 libbz2-dev libcairo2 libcc1-0
  libdata-dump-perl libdatrie1 libdpkg-perl libdrm-amdgpu1 libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libencode-locale-perl libfakeroot libfile-basedir-perl
  libfile-desktopentry-perl libfile-fcntllock-perl libfile-listing-perl libfile-mimeinfo-perl libfont-afm-perl libfontconfig1 libfontenc1 libgcc-9-dev libgfortran-9-dev
  libgfortran5 libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libharfbuzz0b libhtml-form-perl libhtml-format-perl
  libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6
  libicu-dev libio-html-perl libio-socket-ssl-perl libio-stringy-perl libipc-system-simple-perl libisl22 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8
  libjpeg8-dev liblapack-dev liblapack3 libllvm12 liblsan0 liblwp-mediatypes-perl liblwp-protocol-https-perl liblzma-dev libmailtools-perl libmpc3 libmpfr6 libncurses-dev
  libncurses5-dev libnet-dbus-perl libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1
  libpciaccess0 libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpixman-1-0 libpng-dev libpng-tools libquadmath0
  libreadline-dev libsensors-config libsensors5 libsm6 libstdc++-9-dev libtcl8.6 libthai-data libthai0 libtie-ixhash-perl libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl
  libtsan0 libubsan1 liburi-perl libvulkan1 libwayland-client0 libwebp6 libwww-perl libwww-robotrules-perl libx11-protocol-perl libx11-xcb1 libxaw7 libxcb-dri2-0 libxcb-dri3-0
  libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 libxfixes3 libxft2 libxi6
  libxinerama1 libxkbfile1 libxml-parser-perl libxml-twig-perl libxml-xpathengine-perl libxmu6 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxv1
  libxxf86dga1 libxxf86vm1 make mesa-vulkan-drivers perl-openssl-defaults pkg-config r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools
  r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html
  r-recommended unzip x11-common x11-utils x11-xserver-utils xdg-utils zip zlib1g-dev
Suggested packages:
  cpp-doc gcc-9-locales debian-keyring g++-multilib g++-9-multilib gcc-9-doc gcc-multilib autoconf automake libtool flex bison gdb gcc-doc gcc-9-multilib gfortran-multilib
  gfortran-doc gfortran-9-multilib gfortran-9-doc libcoarrays-dev libdigest-hmac-perl libgssapi-perl liblapack-doc bzr icu-doc libcrypt-ssleay-perl liblzma-doc ncurses-doc
  readline-doc lm-sensors libstdc++-9-doc tcl8.6 tk8.6 libauthen-ntlm-perl libunicode-map8-perl libunicode-string-perl xml-twig-tools make-doc elpa-ess r-doc-info | r-doc-pdf
  r-mathlib texlive-base texlive-latex-base texlive-plain-generic texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils texlive-latex-recommended texlive-latex-extra
  texinfo mozilla | www-browser mesa-utils nickle cairo-5c xorg-docs-core
The following NEW packages will be installed:
  build-essential bzip2-doc cpp cpp-9 dpkg-dev fakeroot fontconfig fontconfig-config fonts-dejavu-core g++ g++-9 gcc gcc-9 gcc-9-base gfortran gfortran-9 icu-devtools
  libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl libasan5 libatomic1 libauthen-sasl-perl libblas-dev libblas3 libbz2-dev libcairo2 libcc1-0
  libdata-dump-perl libdatrie1 libdpkg-perl libdrm-amdgpu1 libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libencode-locale-perl libfakeroot libfile-basedir-perl
  libfile-desktopentry-perl libfile-fcntllock-perl libfile-listing-perl libfile-mimeinfo-perl libfont-afm-perl libfontconfig1 libfontenc1 libgcc-9-dev libgfortran-9-dev
  libgfortran5 libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libharfbuzz0b libhtml-form-perl libhtml-format-perl
  libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6
  libicu-dev libio-html-perl libio-socket-ssl-perl libio-stringy-perl libipc-system-simple-perl libisl22 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8
  libjpeg8-dev liblapack-dev liblapack3 libllvm12 liblsan0 liblwp-mediatypes-perl liblwp-protocol-https-perl liblzma-dev libmailtools-perl libmpc3 libmpfr6 libncurses-dev
  libncurses5-dev libnet-dbus-perl libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1
  libpciaccess0 libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpixman-1-0 libpng-dev libpng-tools libquadmath0
  libreadline-dev libsensors-config libsensors5 libsm6 libstdc++-9-dev libtcl8.6 libthai-data libthai0 libtie-ixhash-perl libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl
  libtsan0 libubsan1 liburi-perl libvulkan1 libwayland-client0 libwebp6 libwww-perl libwww-robotrules-perl libx11-protocol-perl libx11-xcb1 libxaw7 libxcb-dri2-0 libxcb-dri3-0
  libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 libxfixes3 libxft2 libxi6
  libxinerama1 libxkbfile1 libxml-parser-perl libxml-twig-perl libxml-xpathengine-perl libxmu6 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxv1
  libxxf86dga1 libxxf86vm1 make mesa-vulkan-drivers perl-openssl-defaults pkg-config r-base r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster
  r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival
  r-doc-html r-recommended unzip x11-common x11-utils x11-xserver-utils xdg-utils zip zlib1g-dev
0 upgraded, 202 newly installed, 0 to remove and 0 not upgraded.
Need to get 158 MB of archives.
After this operation, 914 MB of additional disk space will be used.
Do you want to continue? [Y/n]
```
:::


## Removing R

::: {.xsmall}
```shell
sudo apt remove r-base
```

```
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
  fontconfig fontconfig-config fonts-dejavu-core gfortran gfortran-9 icu-devtools libblas-dev libblas3 libbz2-dev libcairo2 libdatrie1 libdrm-amdgpu1 libdrm-intel1
  libdrm-nouveau2 libdrm-radeon1 libfile-basedir-perl libfile-desktopentry-perl libfile-mimeinfo-perl libfontconfig1 libfontenc1 libgfortran-9-dev libgfortran5 libgl1
  libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgraphite2-3 libharfbuzz0b libice6 libicu-dev libio-stringy-perl libipc-system-simple-perl libjbig0 libjpeg-dev
  libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libllvm12 liblzma-dev libncurses-dev libncurses5-dev libnet-dbus-perl libpango-1.0-0
  libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3
  libpcrecpp0v5 libpixman-1-0 libpng-dev libpng-tools libreadline-dev libsensors-config libsensors5 libsm6 libtcl8.6 libthai-data libthai0 libtie-ixhash-perl libtiff5 libtk8.6
  libvulkan1 libwayland-client0 libwebp6 libx11-protocol-perl libx11-xcb1 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0
  libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 libxfixes3 libxft2 libxi6 libxinerama1 libxkbfile1 libxml-parser-perl libxml-twig-perl
  libxml-xpathengine-perl libxmu6 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 mesa-vulkan-drivers pkg-config r-base-core
  r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
  r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended unzip x11-common x11-utils x11-xserver-utils xdg-utils zip zlib1g-dev
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED:
  r-base
0 upgraded, 0 newly installed, 1 to remove and 1 not upgraded.
After this operation, 62.5 kB disk space will be freed.
```
:::

## and all of its dependencies

::: {.xsmall}
```shell
sudo apt autoremove
```
```
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED:
  fontconfig fontconfig-config fonts-dejavu-core gfortran gfortran-9 icu-devtools libblas-dev libblas3 libbz2-dev libcairo2 libdatrie1 libdrm-amdgpu1 libdrm-intel1
  libdrm-nouveau2 libdrm-radeon1 libfile-basedir-perl libfile-desktopentry-perl libfile-mimeinfo-perl libfontconfig1 libfontenc1 libgfortran-9-dev libgfortran5 libgl1
  libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgraphite2-3 libharfbuzz0b libice6 libicu-dev libio-stringy-perl libipc-system-simple-perl libjbig0 libjpeg-dev
  libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libllvm12 liblzma-dev libncurses-dev libncurses5-dev libnet-dbus-perl libpango-1.0-0
  libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3
  libpcrecpp0v5 libpixman-1-0 libpng-dev libpng-tools libreadline-dev libsensors-config libsensors5 libsm6 libtcl8.6 libthai-data libthai0 libtie-ixhash-perl libtiff5 libtk8.6
  libvulkan1 libwayland-client0 libwebp6 libx11-protocol-perl libx11-xcb1 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0
  libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 libxfixes3 libxft2 libxi6 libxinerama1 libxkbfile1 libxml-parser-perl libxml-twig-perl
  libxml-xpathengine-perl libxmu6 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 mesa-vulkan-drivers pkg-config r-base-core
  r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
  r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended unzip x11-common x11-utils x11-xserver-utils xdg-utils zip zlib1g-dev
0 upgraded, 0 newly installed, 140 to remove and 1 not upgraded.
After this operation, 749 MB disk space will be freed.
Do you want to continue? [Y/n]
```
:::


## Updating & Upgrading

::: {.xsmall}
```shell
sudo apt update
```
```
Hit:1 http://archive.linux.duke.edu/ubuntu focal InRelease
Hit:2 http://archive.linux.duke.edu/ubuntu focal-updates InRelease
Hit:3 http://archive.linux.duke.edu/ubuntu focal-backports InRelease
Hit:4 http://archive.linux.duke.edu/ubuntu focal-security InRelease
Hit:5 https://falcon-dl.oit.duke.edu/ubuntu focal InRelease
Reading package lists... Done
Building dependency tree
Reading state information... Done
1 package can be upgraded. Run 'apt list --upgradable' to see it.
```
:::

. . .

::: {.xsmall}
```shell
sudo apt upgrade
```
```
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages will be upgraded:
  libfribidi0
1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1 standard security update
Need to get 24.2 kB of archives.
After this operation, 0 B of additional disk space will be used.
Do you want to continue? [Y/n]
```
:::


## Aside - Conflicts

::: {.xsmall}
```{.shell code-line-numbers="|9-18"}
...
update-initramfs: deferring update (trigger activated)
amd64-microcode: microcode will be updated at next boot
Setting up intel-microcode (3.20180807a.0ubuntu0.18.04.1) ...
update-initramfs: deferring update (trigger activated)
intel-microcode: microcode will be updated at next boot
Setting up kmod (24-1ubuntu3.1) ...

*Configuration file '/etc/modprobe.d/blacklist.conf'
* ==> Modified (by you or by a script) since installation.
* ==> Package distributor has shipped an updated version.
*   What would you like to do about it ?  Your options are:
*    Y or I  : install the package maintainer's version
*    N or O  : keep your currently-installed version
*      D     : show the differences between the versions
*      Z     : start a shell to examine the situation
* The default action is to keep your current version.
**** blacklist.conf (Y/I/N/O/D/Z) [default=N] ?
Setting up initramfs-tools-core (0.130ubuntu3.6) ...
Setting up linux-headers-4.15.0-43-generic (4.15.0-43.46) ...
Setting up initramfs-tools (0.130ubuntu3.6) ...

...
```
:::


## Package Details

::: {.xsmall}
```shell
apt show r-base
```
```
Package: r-base
Version: 4.3.3-2build2
Priority: optional
Section: universe/math
Origin: Ubuntu
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Original-Maintainer: Dirk Eddelbuettel <edd@debian.org>
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 33.8 kB
Depends: r-base-core (>= 4.3.3-2build2), r-recommended (= 4.3.3-2build2)
Recommends: r-base-html, r-doc-html
Suggests: elpa-ess, r-doc-info | r-doc-pdf
Homepage: http://www.r-project.org/
Download-Size: 9,304 B
APT-Sources: http://archive.linux.duke.edu/ubuntu noble/universe amd64 Packages
Description: GNU R statistical computation and graphics system
 R is a system for statistical computation and graphics.  It consists
 of a language plus a run-time environment with graphics, a debugger,
 access to certain system functions, and the ability to run programs
 stored in script files.
...
```
:::

## Package Contents

To list the files installed by a package,

::: {.xsmall}
```shell
dpkg -L r-base
```
```
/.
/usr
/usr/share
/usr/share/doc
/usr/share/doc/r-base
/usr/share/doc/r-base/README.Debian
/usr/share/doc/r-base/copyright
/usr/share/doc/r-base/changelog.Debian.gz
```
:::

<br class=class/>
or if you want to find which package created a file,

::: {.xsmall}
```shell
dpkg -S /usr/bin/R
```
```
r-base-core: /usr/bin/R
```
:::




## Package Manager Comparison

::: {.xsmall}

|                       | Ubuntu / Debian                        | RHEL / Fedora                              | Requires root  |
|:----------------------|:---------------------------------------|:-------------------------------------------|:---------------|
| Install               | `apt install`                          | `dnf install`                              | Yes            |
| Install Local         | `dpkg -i pkg.deb`                      | `dnf install pkg.rpm`                      | Yes            |
| Remove                | `apt remove`                           | `dnf remove`                               | Yes            |
| Update                | `apt update`                           | `dnf check-update`                         | Yes            |
| Upgrade               | `apt upgrade` <br/> `apt full-upgrade` | `dnf upgrade`                              | Yes            |
| Clean Deps.           | `apt autoremove`                       | `dnf autoremove`                           | Yes            |
| Reinstall             | `apt install --reinstall`              | `dnf reinstall`                            | Yes            |
| Details.              | `apt show`                             | `dnf info`                                 | No             |
| Dependencies          | `apt show`                             | `dnf repoquery --requires`                 | No             |
| Pkg -> Files          | `dpkg -L`                              | `rpm -ql` or <br/> `dnf repoquery -l`      | No             |
| Files -> Pkg          | `dpkg -S`                              | `rpm -qf`                                  | No             |

:::




# A bit about libraries

## System libraries

These are shared common components that are used by a variety of software on a Linux system. For the most part they are a collection of compiled code (typically C / C++) that are stored in a single file.

* Allows for code reuse

* Allows for multiple (concurrent) versions

* Avoids reinventing and/or duplicating the wheel

* Installed in `/lib`, `/usr/lib`, `/usr/local/lib`, etc.

* Two flavors: static (`.a`) and dynamic / shared (`.so`)

## `libcurl`

::: {.xxsmall}
```shell
ls -la /usr/lib/x86_64-linux-gnu/libcurl*
```

```
-rw-r--r-- 1 root root 1057632 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl.a
lrwxrwxrwx 1 root root      19 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl-gnutls.so.3 -> libcurl-gnutls.so.4
lrwxrwxrwx 1 root root      23 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl-gnutls.so.4 -> libcurl-gnutls.so.4.5.0
-rw-r--r-- 1 root root  510408 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl-gnutls.so.4.5.0
-rw-r--r-- 1 root root     951 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl.la
lrwxrwxrwx 1 root root      16 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl.so -> libcurl.so.4.5.0
lrwxrwxrwx 1 root root      16 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl.so.4 -> libcurl.so.4.5.0
-rw-r--r-- 1 root root  518600 Oct 29 08:10 /usr/lib/x86_64-linux-gnu/libcurl.so.4.5.0
```
:::


## Getting what you want

The following is a basic heuristic of library package naming schemes for the two primary distro families; there are exceptions and edge cases.

These are the names that would then be used with something like `apt install` or `dnf install` respectively.

<br/>

|                       | Debian          | Redhat          |
|-----------------------|-----------------|-----------------|
| Dynamic library (.so) | `lib{name}`     | `{name}`        |
| Headers               | `lib{name}-dev` | `{name}-devel`  |
| Static library (.a)   | `lib{name}-dev` | `{name}-static` |
| Documentation         | `lib{name}-doc` | `{name}-devel`  | 


## Troubleshooting dynamic libraries

::: {.xxsmall}
```shell
ldd /usr/lib/x86_64-linux-gnu/libcurl.so
```

```
	linux-vdso.so.1 (0x00007ffd98176000)
	libnghttp2.so.14 => /usr/lib/x86_64-linux-gnu/libnghttp2.so.14 (0x00007f1e3dc60000)
	libidn2.so.0 => /usr/lib/x86_64-linux-gnu/libidn2.so.0 (0x00007f1e3da43000)
	librtmp.so.1 => /usr/lib/x86_64-linux-gnu/librtmp.so.1 (0x00007f1e3d827000)
	libpsl.so.5 => /usr/lib/x86_64-linux-gnu/libpsl.so.5 (0x00007f1e3d619000)
	libssl.so.1.1 => /usr/lib/x86_64-linux-gnu/libssl.so.1.1 (0x00007f1e3d3af000)
	libcrypto.so.1.1 => /usr/lib/x86_64-linux-gnu/libcrypto.so.1.1 (0x00007f1e3cf37000)
	libgssapi_krb5.so.2 => /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2 (0x00007f1e3ccec000)
	libldap_r-2.4.so.2 => /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2 (0x00007f1e3ca9a000)
	liblber-2.4.so.2 => /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2 (0x00007f1e3c88c000)
	libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f1e3c66f000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f1e3c450000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f1e3c05f000)
	libunistring.so.2 => /usr/lib/x86_64-linux-gnu/libunistring.so.2 (0x00007f1e3bce1000)
	libgnutls.so.30 => /usr/lib/x86_64-linux-gnu/libgnutls.so.30 (0x00007f1e3b97c000)
	libhogweed.so.4 => /usr/lib/x86_64-linux-gnu/libhogweed.so.4 (0x00007f1e3b748000)
	libnettle.so.6 => /usr/lib/x86_64-linux-gnu/libnettle.so.6 (0x00007f1e3b512000)
	libgmp.so.10 => /usr/lib/x86_64-linux-gnu/libgmp.so.10 (0x00007f1e3b291000)
	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f1e3b08d000)
	libkrb5.so.3 => /usr/lib/x86_64-linux-gnu/libkrb5.so.3 (0x00007f1e3adb7000)
	libk5crypto.so.3 => /usr/lib/x86_64-linux-gnu/libk5crypto.so.3 (0x00007f1e3ab85000)
	libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2 (0x00007f1e3a981000)
	libkrb5support.so.0 => /usr/lib/x86_64-linux-gnu/libkrb5support.so.0 (0x00007f1e3a776000)
	libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007f1e3a55b000)
	libsasl2.so.2 => /usr/lib/x86_64-linux-gnu/libsasl2.so.2 (0x00007f1e3a340000)
	libgssapi.so.3 => /usr/lib/x86_64-linux-gnu/libgssapi.so.3 (0x00007f1e3a0ff000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f1e3e104000)
	libp11-kit.so.0 => /usr/lib/x86_64-linux-gnu/libp11-kit.so.0 (0x00007f1e39dd0000)
	libtasn1.so.6 => /usr/lib/x86_64-linux-gnu/libtasn1.so.6 (0x00007f1e39bbd000)
	libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1 (0x00007f1e399b9000)
	libheimntlm.so.0 => /usr/lib/x86_64-linux-gnu/libheimntlm.so.0 (0x00007f1e397b0000)
	libkrb5.so.26 => /usr/lib/x86_64-linux-gnu/libkrb5.so.26 (0x00007f1e39523000)
	libasn1.so.8 => /usr/lib/x86_64-linux-gnu/libasn1.so.8 (0x00007f1e39281000)
	libhcrypto.so.4 => /usr/lib/x86_64-linux-gnu/libhcrypto.so.4 (0x00007f1e3904b000)
	libroken.so.18 => /usr/lib/x86_64-linux-gnu/libroken.so.18 (0x00007f1e38e35000)
	libffi.so.6 => /usr/lib/x86_64-linux-gnu/libffi.so.6 (0x00007f1e38c2d000)
	libwind.so.0 => /usr/lib/x86_64-linux-gnu/libwind.so.0 (0x00007f1e38a04000)
	libheimbase.so.1 => /usr/lib/x86_64-linux-gnu/libheimbase.so.1 (0x00007f1e387f5000)
	libhx509.so.5 => /usr/lib/x86_64-linux-gnu/libhx509.so.5 (0x00007f1e385ab000)
	libsqlite3.so.0 => /usr/lib/x86_64-linux-gnu/libsqlite3.so.0 (0x00007f1e382a2000)
	libcrypt.so.1 => /lib/x86_64-linux-gnu/libcrypt.so.1 (0x00007f1e3806a000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f1e37ccc000)
```
:::


## Python management

::: {.xsmall}
```shell
pip install torch
```
```
Command 'pip' not found, but can be installed with:

apt install python3-pip
Please ask your administrator.
```
:::

. . .

::: {.xsmall}
```shell
sudo apt install python3-pip
```
```
[sudo] password for cr173:
```
```
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
The following additional packages will be installed:
  build-essential bzip2 cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu dpkg-dev fakeroot g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-13 gcc-13-base
  gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu javascript-common libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl libasan8 libatomic1 libcc1-0 libdpkg-perl
  libexpat1-dev libfakeroot libfile-fcntllock-perl libgcc-13-dev libgomp1 libhwasan0 libisl23 libitm1 libjs-jquery libjs-sphinxdoc libjs-underscore liblsan0 libmpc3 libpython3-dev
  libpython3.12-dev libquadmath0 libstdc++-13-dev libtsan2 libubsan1 lto-disabled-list make python3-dev python3-wheel python3.12-dev zlib1g-dev
Suggested packages:
  bzip2-doc cpp-doc gcc-13-locales cpp-13-doc debian-keyring g++-multilib g++-13-multilib gcc-13-doc gcc-multilib autoconf automake libtool flex bison gdb gcc-doc gcc-13-multilib
  gdb-x86-64-linux-gnu apache2 | lighttpd | httpd bzr libstdc++-13-doc make-doc
The following NEW packages will be installed:
  build-essential bzip2 cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu dpkg-dev fakeroot g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-13 gcc-13-base
  gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu javascript-common libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl libasan8 libatomic1 libcc1-0 libdpkg-perl
  libexpat1-dev libfakeroot libfile-fcntllock-perl libgcc-13-dev libgomp1 libhwasan0 libisl23 libitm1 libjs-jquery libjs-sphinxdoc libjs-underscore liblsan0 libmpc3 libpython3-dev
  libpython3.12-dev libquadmath0 libstdc++-13-dev libtsan2 libubsan1 lto-disabled-list make python3-dev python3-pip python3-wheel python3.12-dev zlib1g-dev
0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded.
Need to get 72.6 MB of archives.
After this operation, 251 MB of additional disk space will be used.
Do you want to continue? [Y/n]
```
:::


## Package manager vs pip

::: {.xsmall}
```shell
sudo apt install python3-numpy
```
```
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
The following additional packages will be installed:
  libblas3 libgfortran5 liblapack3
Suggested packages:
  gfortran python3-pytest
The following NEW packages will be installed:
  libblas3 libgfortran5 liblapack3 python3-numpy
0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
Need to get 8,238 kB of archives.
After this operation, 35.2 MB of additional disk space will be used.
Do you want to continue? [Y/n] 
```


```shell
python3
```
```
Python 3.12.3 (main, Jan 22 2026, 20:57:42) [GCC 13.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> np.__version__
'1.26.4'
```
:::



## pip install & PEP 668

::: {.panel-tabset}

### pip

::: {.xsmall}
```shell
sudo pip install numpy --upgrade
```

```
sudo pip install numpy --upgrade
error: externally-managed-environment

× This environment is externally managed
╰─> To install Python packages system-wide, try apt install
    python3-xyz, where xyz is the package you are trying to
    install.
    
    If you wish to install a non-Debian-packaged Python package,
    create a virtual environment using python3 -m venv path/to/venv.
    Then use path/to/venv/bin/python and path/to/venv/bin/pip. Make
    sure you have python3-full installed.
    
    If you wish to install a non-Debian packaged Python application,
    it may be easiest to use pipx install xyz, which will manage a
    virtual environment for you. Make sure you have pipx installed.
    
    See /usr/share/doc/python3.12/README.venv for more information.

note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages.
hint: See PEP 668 for the detailed specification.
```
:::

### uv

::: {.xsmall}
```shell
sudo apt install python3-uv
```
```
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
E: Unable to locate package python3-uv
```

::: {.fragment}
```shell
curl -LsSf https://astral.sh/uv/install.sh | sh
```

```
downloading uv 0.10.6 x86_64-unknown-linux-gnu
no checksums to verify
installing to /home/cr173/.local/bin
  uv
  uvx
everything's installed!

To add $HOME/.local/bin to your PATH, either restart your shell or run:

    source $HOME/.local/bin/env (sh, bash, zsh)
    source $HOME/.local/bin/env.fish (fish)
```

```shell
.local/bin/uv self version
```
```
uv 0.10.6
```
:::
:::

:::



# Docker

## Docker

::: {.xsmall}
> Docker can package an application and its dependencies in a virtual container that can run on any Linux, Windows, or macOS computer. This enables the application to run in a variety of locations, such as on-premises, in the public or private cloud. When running on Linux, Docker uses the resource isolation features of the Linux kernel (such as cgroups and kernel namespaces) and a union-capable file system to allow containers to run within a single Linux instance, avoiding the overhead of starting and maintaining virtual machines. 
>
>From [Wikipedia](https://en.wikipedia.org/wiki/Docker_%28software%29)
:::

:::: {.columns}
::: {.column width='50%'}
![](imgs/Docker/docker2.webp){fig-align="center" width="75%"}
:::

::: {.column width='50%'}
![](imgs/Docker/docker1.webp){fig-align="center" width="75%"}
:::
::::


## Installation - Ubuntu / Debian {.scrollable}

See official Docker install [docs](https://docs.docker.com/engine/install/ubuntu/) - below is the yolo method.

::: {.xxsmall}
```shell
curl -fsSL https://get.docker.com -o get-docker.sh
sudo sh get-docker.sh
```

```
# Executing docker install script, commit: f381ee68b32e515bb4dc034b339266aff1fbc460
+ sh -c apt-get -qq update >/dev/null
+ sh -c DEBIAN_FRONTEND=noninteractive apt-get -y -qq install ca-certificates curl >/dev/null
+ sh -c install -m 0755 -d /etc/apt/keyrings
+ sh -c curl -fsSL "https://download.docker.com/linux/ubuntu/gpg" -o /etc/apt/keyrings/docker.asc
+ sh -c chmod a+r /etc/apt/keyrings/docker.asc
+ sh -c echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu noble stable" > /etc/apt/sources.list.d/docker.list
+ sh -c apt-get -qq update >/dev/null
+ sh -c DEBIAN_FRONTEND=noninteractive apt-get -y -qq install docker-ce docker-ce-cli containerd.io docker-compose-plugin docker-ce-rootless-extras docker-buildx-plugin docker-model-plugin >/dev/null
Scanning processes...                                                                                                                                               
Scanning linux images...                                                                                                                                            
Using systemd to manage Docker service
+ sh -c systemctl enable --now docker.service

...

INFO: Docker daemon enabled and started

+ sh -c docker version
Client: Docker Engine - Community
 Version:           29.2.1
 API version:       1.53
 Go version:        go1.25.6
 Git commit:        a5c7197
 Built:             Mon Feb  2 17:17:26 2026
 OS/Arch:           linux/amd64
 Context:           default

Server: Docker Engine - Community
 Engine:
  Version:          29.2.1
  API version:      1.53 (minimum version 1.44)
  Go version:       go1.25.6
  Git commit:       6bc6209
  Built:            Mon Feb  2 17:17:26 2026
  OS/Arch:          linux/amd64
  Experimental:     false
 containerd:
  Version:          v2.2.1
  GitCommit:        dea7da592f5d1d2b7755e3a161be07f43fad8f75
 runc:
  Version:          1.3.4
  GitCommit:        v1.3.4-0-gd6d73eb8
 docker-init:
  Version:          0.19.0
  GitCommit:        de40ad0

...
```
:::
 

## Troubleshooting - daemon

::: {.xsmall}
```shell
sudo docker run hello-world
```
```
docker: Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?.
See 'docker run --help'.
```
:::

. . .

<br/>

This occurs when the docker daemon (service) is not running. This can be fixed by enabling and starting the docker service / daemon:

<br/>

::: {.xsmall}
```shell
sudo systemctl enable docker
```
```
Synchronizing state of docker.service with SysV service script with /usr/lib/systemd/systemd-sysv-install.
Executing: /usr/lib/systemd/systemd-sysv-install enable docker
```


```shell
sudo systemctl start docker
```
:::

## Success

::: {.xsmall}
```shell
sudo docker run hello-world
```
```
Unable to find image 'hello-world:latest' locally
latest: Pulling from library/hello-world
1b930d010525: Pull complete 
Digest: sha256:2557e3c07ed1e38f26e389462d03ed943586f744621577a99efb77324b0fe535
Status: Downloaded newer image for hello-world:latest

Hello from Docker!
This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:
 1. The Docker client contacted the Docker daemon.
 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
    (amd64)
 3. The Docker daemon created a new container from that image which runs the
    executable that produces the output you are currently reading.
 4. The Docker daemon streamed that output to the Docker client, which sent it
    to your terminal.

To try something more ambitious, you can run an Ubuntu container with:
 $ docker run -it ubuntu bash

Share images, automate workflows, and more with a free Docker ID:
 https://hub.docker.com/

For more examples and ideas, visit:
 https://docs.docker.com/get-started/
```
:::


## Troubleshooting - permissions

::: {.xsmall}
```shell
docker run hello-world
```

```
permission denied while trying to connect to the docker API at unix:///var/run/docker.sock
```
:::

. . .

You must either be root or be a member of the `docker` group to use most Docker commands. Currently, your VM may or may not have a docker group and your account is likely not a member. If you get tired of typing sudo + your password there is an easy fix,

. . .

<br class="small">

::: {.xsmall}
```shell
sudo groupadd docker
sudo usermod -aG docker $USER
groups
```
```
cr173 docker
```
:::

<br class="small">

If docker is not listed by `groups` - log out and log back in


## Success

::: {.xsmall}
```shell
docker run hello-world
```
```
Hello from Docker!
This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:
 1. The Docker client contacted the Docker daemon.
 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
    (amd64)
 3. The Docker daemon created a new container from that image which runs the
    executable that produces the output you are currently reading.
 4. The Docker daemon streamed that output to the Docker client, which sent it
    to your terminal.

To try something more ambitious, you can run an Ubuntu container with:
 $ docker run -it ubuntu bash

Share images, automate workflows, and more with a free Docker ID:
 https://hub.docker.com/

For more examples and ideas, visit:
 https://docs.docker.com/get-started/
```
:::



# Getting Started


## {background-image="imgs/Docker/docker_sketch.png" background-size=contain}

## Getting images

::: {.xsmall}
```shell
docker pull ubuntu
```

```
Using default tag: latest
latest: Pulling from library/ubuntu
5a7813e071bf: Pull complete 
Digest: sha256:72297848456d5d37d1262630108ab308d3e9ec7ed1c3286a32fe09856619a782
Status: Downloaded newer image for ubuntu:latest
docker.io/library/ubuntu:latest
```
:::

. . .

<br/>

::: {.xsmall}
```shell
docker images
```
```
IMAGE                                     ID             DISK USAGE   CONTENT SIZE   EXTRA
hello-world:latest                        ef54e839ef54       21.8kB         9.52kB        
ubuntu:latest                             d1e2e92c075e        117MB         31.7MB   
```
:::


## {background-image="imgs/Docker/dockerhub_ubuntu.png" background-size=contain}


## Tags (versions)

::: {.xsmall}
```shell
docker pull ubuntu:25.10
```
```
25.10: Pulling from library/ubuntu
16c195d4c5e9: Pull complete 
458996317100: Download complete 
Digest: sha256:4a9232cc47bf99defcc8860ef6222c99773330367fcecbf21ba2edb0b810a31e
Status: Downloaded newer image for ubuntu:25.10
docker.io/library/ubuntu:25.10
```

```shell
docker pull ubuntu:24.04
```
```
24.04: Pulling from library/ubuntu
Digest: sha256:72297848456d5d37d1262630108ab308d3e9ec7ed1c3286a32fe09856619a782
Status: Downloaded newer image for ubuntu:24.04
docker.io/library/ubuntu:24.04
```
:::

::: {.xsmall}
```shell
docker images
```
```
IMAGE                                     ID             DISK USAGE   CONTENT SIZE   EXTRA
hello-world:latest                        ef54e839ef54       21.8kB         9.52kB        
ubuntu:24.04                              d1e2e92c075e        117MB         31.7MB        
ubuntu:25.10                              4a9232cc47bf        134MB         36.6MB        
ubuntu:latest                             d1e2e92c075e        117MB         31.7MB    
```
:::


## Other sources

DockerHub is not the only source of images - there are many other possible hosts and all you need to provide is a URL along with the image name.

. . .


::: {.xxsmall}
```shell
docker pull ghcr.io/dukestatsci/r_gh_actions:latest
```
```
latest: Pulling from dukestatsci/r_gh_actions
4f4fb700ef54: Pull complete 
20043066d3d5: Pull complete 
a7f34fb66e20: Pull complete 
4eca9b252235: Pull complete 
def0e092fa23: Pull complete 
685ec124a2b4: Pull complete 
19147305769e: Pull complete 
600a4a837ad4: Pull complete 
644298603b9d: Pull complete 
d43d99a2c25f: Pull complete 
2adec7c973e0: Pull complete 
c0de31d8db54: Pull complete 
b66843124b28: Pull complete 
147156882b74: Pull complete 
83797ba50aaf: Pull complete 
7a7094a09d9b: Download complete 
Digest: sha256:0c15f386b4e0a0fe8ac18e4a513db49294a0f05558f92741beb4604f22109298
Status: Downloaded newer image for ghcr.io/dukestatsci/r_gh_actions:latest
ghcr.io/dukestatsci/r_gh_actions:latest
```
:::

::: {.aside}
See our image on GitHub [here](https://github.com/orgs/DukeStatSci/packages/container/package/r_gh_actions) and the underlying [repo](https://github.com/DukeStatSci/r_gh_actions)
:::

## 

::: {.xsmall}
```shell
docker images
```
```
IMAGE                                     ID             DISK USAGE   CONTENT SIZE   EXTRA
ghcr.io/dukestatsci/r_gh_actions:latest   0c15f386b4e0        3.5GB          888MB        
hello-world:latest                        ef54e839ef54       21.8kB         9.52kB        
ubuntu:24.04                              d1e2e92c075e        117MB         31.7MB        
ubuntu:25.10                              4a9232cc47bf        134MB         36.6MB        
ubuntu:latest                             d1e2e92c075e        117MB         31.7MB  
```
:::




## Running a container

:::: {.columns .xxsmall}
::: {.column width='50%'}
```shell
docker run --rm ubuntu cat /etc/os-release
```

```
PRETTY_NAME="Ubuntu 24.04.1 LTS"
NAME="Ubuntu"
VERSION_ID="24.04"
VERSION="24.04.1 LTS (Noble Numbat)"
VERSION_CODENAME=noble
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=noble
LOGO=ubuntu-logo
```
:::

::: {.column width='50%' .fragment}
```shell
docker run --rm ubuntu:25.10 cat /etc/os-release
```
```
PRETTY_NAME="Ubuntu 25.10"
NAME="Ubuntu"
VERSION_ID="25.10"
VERSION="25.10 (Questing Quokka)"
VERSION_CODENAME=questing
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=questing
LOGO=ubuntu-logo
```
:::
::::

## 

::: {.xxsmall}
```shell
docker run --rm fedora:latest cat /etc/os-release
```
```
Unable to find image 'fedora:latest' locally
latest: Pulling from library/fedora
0c5a86865c5d: Pull complete 
Digest: sha256:3ec60eb34fa1a095c0c34dd37cead9fd38afb62612d43892fcf1d3425c32bc1e
Status: Downloaded newer image for fedora:latest
NAME="Fedora Linux"
VERSION="41 (Container Image)"
RELEASE_TYPE=stable
ID=fedora
VERSION_ID=41
VERSION_CODENAME=""
PLATFORM_ID="platform:f41"
PRETTY_NAME="Fedora Linux 41 (Container Image)"
ANSI_COLOR="0;38;2;60;110;180"
LOGO=fedora-logo-icon
CPE_NAME="cpe:/o:fedoraproject:fedora:41"
DEFAULT_HOSTNAME="fedora"
HOME_URL="https://fedoraproject.org/"
DOCUMENTATION_URL="https://docs.fedoraproject.org/en-US/fedora/f41/system-administrators-guide/"
SUPPORT_URL="https://ask.fedoraproject.org/"
BUG_REPORT_URL="https://bugzilla.redhat.com/"
REDHAT_BUGZILLA_PRODUCT="Fedora"
REDHAT_BUGZILLA_PRODUCT_VERSION=41
REDHAT_SUPPORT_PRODUCT="Fedora"
REDHAT_SUPPORT_PRODUCT_VERSION=41
SUPPORT_END=2025-05-13
VARIANT="Container Image"
VARIANT_ID=container
```
:::



## docker run common options

<br/>
```
docker run [OPTIONS] IMAGE[:TAG|@DIGEST] [COMMAND] [ARG...]
```

<br/>

::: {.medium}

| Option         | Description                                                      |
|----------------|:-----------------------------------------------------------------|
| `--name`       | Give your container a name                                       |
| `--rm`         | Automatically remove the container when it exits                 |
| `-i -t`        | Allow for interaction with container (STDIN & tty specifically)  |
| `-p host:cont` | Publish a container's port                                       |
| `-v host:cont` | Share filesystems                                                |
| `-e "VAR=VAL"` | Define environmental variables                                   |
:::

::: {.aside}
See <https://docs.docker.com/engine/reference/run/> for more details
:::

## Other useful commands

::: {.medium}

| command                                 | Description                                  |
|-----------------------------------------|:---------------------------------------------|
| `docker pull NAME[:TAG]`                | Pull docker image (usually from DockerHub)   |
| `docker images`                         | List docker images                           |
| `docker rmi IMAGE`                      | Remove an image                              |
| `docker container ls [--all]`           | List (all) docker containers                 |
| `docker rm CONTAINER`                   | Remove a container                           |
| `docker stop CONTAINER`                 | Stop a running container                     |
| `docker start CONTAINER`                | Start a stopped container                    |
| `docker attach CONTAINER`               | Attach to a running container                |
| `docker exec CONTAINER CMD`             | Runs a new command in a running container    |
| `docker commit CONTAINER REPO[:TAG]`    | Create an image from a container             |
| `docker rename CONTAINER NAME`          | Rename a container                           |

:::

## rocker

::: {.center .giant}
  `r fontawesome::fa("docker")` + `r fontawesome::fa("r-project")` = [Rocker](https://www.rocker-project.org/)
:::

::: {.small}
> The rocker project provides a collection of containers suited for different needs. find a base image to extend or images with popular software and optimized libraries pre-installed. Get the latest version or a reproducibly fixed environment.
:::

. . .

:::: {.columns}
::: {.column width='50%'}
![](imgs/Docker/rocker1.png){fig-align="center" width="100%"}

:::

::: {.column width='50%'}
![](imgs/Docker/rocker2.png){fig-align="center" width="100%"}

:::
::::


## {background-image="imgs/Docker/rocker_ver_sketch.png" background-size=contain}


## {background-image="imgs/Docker/Docker_python.png" background-size=contain}

## Docker + Python

::: {.xsmall}
```shell
docker pull python:latest
```

```
latest: Pulling from library/python
7cd785773db4: Pull complete 
091eb8249475: Pull complete 
255774e0027b: Pull complete 
353e14e5cc47: Pull complete 
70847531e23d: Pull complete 
af0b544b1a82: Pull complete 
379f06e37dbb: Pull complete 
Digest: sha256:8c55c44b9e81d537f8404d0000b7331863d134db87c1385dd0ec7fefff656495
Status: Downloaded newer image for python:latest
docker.io/library/python:latest
```
:::

. . .

::: {.xsmall}
```shell
docker run --rm python:latest python -V
```

```
Python 3.14.3
```
:::

. . .

::: {.xsmall}
```shell
docker run --rm python:latest pip install numpy
```

```
Collecting numpy
  Downloading numpy-2.2.4-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
Downloading numpy-2.2.4-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.1/16.1 MB 77.0 MB/s eta 0:00:00
Installing collected packages: numpy
Successfully installed numpy-2.2.4
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.

[notice] A new release of pip is available: 24.3.1 -> 25.0.1
[notice] To update, run: pip install --upgrade pip
```
:::

##

::: {.xsmall}
```shell
docker run --rm python:latest cat /etc/os-release
```
```
PRETTY_NAME="Debian GNU/Linux 13 (trixie)"
NAME="Debian GNU/Linux"
VERSION_ID="13"
VERSION="13 (trixie)"
VERSION_CODENAME=trixie
DEBIAN_VERSION_FULL=13.3
ID=debian
HOME_URL="https://www.debian.org/"
SUPPORT_URL="https://www.debian.org/support"
BUG_REPORT_URL="https://bugs.debian.org/"
```
:::


## Interactive usage

For interactive use we use the `-it` (or `-i -t`) flags,

::: {.xsmall}
```shell
docker run -it --rm python:latest
```

```
Python 3.14.3 (main, Mar 18 2025, 03:30:45) [GCC 12.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> 
```
:::

. . .

::: {.xsmall}
```shell
docker run -it --rm python:latest bash
```
```
root@0200ab573e93:/# 
```
:::

. . .

<br/>

::: {.xsmall}
```shell
docker ps
```
```
CONTAINER ID   IMAGE     COMMAND   CREATED   STATUS    PORTS     NAMES
```
:::

. . .

::: {.xsmall}
```shell
docker ps --all
```
```
CONTAINER ID   IMAGE           COMMAND     CREATED          STATUS                      PORTS     NAMES
fa52839a6bb0   python:latest   "bash"      4 seconds ago    Exited (0) 2 seconds ago              elated_pare
41de571bce2d   python:latest   "python3"   12 seconds ago   Exited (0) 10 seconds ago             zealous_knuth
```
:::

## Building a container interactively

::: {.xsmall}
```shell
docker run -it --name python-uv python:latest bash
```
```
root@b08cd30d4148:/# pip install uv
Collecting uv
  Downloading uv-0.10.6-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Downloading uv-0.10.6-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 23.2/23.2 MB 159.3 MB/s  0:00:00
Installing collected packages: uv
Successfully installed uv-0.10.6
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.

[notice] A new release of pip is available: 25.3 -> 26.0.1
[notice] To update, run: pip install --upgrade pip
root@b08cd30d4148:/# uv self version
uv 0.10.6
```
:::

## Container -> Image

::: {.xsmall}
```shell
docker ps --all
```
```
CONTAINER ID   IMAGE           COMMAND     CREATED              STATUS                     PORTS     NAMES
b08cd30d4148   python:latest   "bash"      About a minute ago   Exited (0) 4 seconds ago             python-uv
```
:::

. . .

::: {.xsmall}
```shell
docker commit python-uv python-uv:latest
```
```
sha256:7cc45fe8b0b7796015f3d796d2740403a52d75d9e157da7a2f792c72b0335980
```
:::

. . .

::: {.xsmall}
```shell
docker images
```
```
IMAGE                                     ID             DISK USAGE   CONTENT SIZE   EXTRA
fedora:latest                             781b7642e8bf        261MB         70.7MB        
ghcr.io/dukestatsci/r_gh_actions:latest   0c15f386b4e0        3.5GB          888MB        
hello-world:latest                        ef54e839ef54       21.8kB         9.52kB        
python-uv:latest                          7cc45fe8b0b7       1.74GB          465MB        
python:latest                             61346539f7b2       1.61GB          432MB    U   
ubuntu:24.04                              d1e2e92c075e        117MB         31.7MB        
ubuntu:25.10                              4a9232cc47bf        134MB         36.6MB        
ubuntu:latest                             d1e2e92c075e        117MB         31.7MB  
```
:::

## Using the image

::: {.xsmall}
```shell
docker run --rm -it python-uv:latest
```
```
root@7ea404da10d1:/# mkdir proj
root@7ea404da10d1:/# cd proj/
root@7ea404da10d1:/proj# uv init --bare
Initialized project `proj`
root@7ea404da10d1:/proj# uv add numpy scipy matplotlib
Using CPython 3.14.3 interpreter at: /usr/local/bin/python3
Creating virtual environment at: .venv
Resolved 13 packages in 336ms
Prepared 12 packages in 1.56s
Installed 12 packages in 1.44s
 + contourpy==1.3.3
 + cycler==0.12.1
 + fonttools==4.61.1
 + kiwisolver==1.4.9
 + matplotlib==3.10.8
 + numpy==2.4.2
 + packaging==26.0
 + pillow==12.1.1
 + pyparsing==3.3.2
 + python-dateutil==2.9.0.post0
 + scipy==1.17.1
 + six==1.17.0
root@7ea404da10d1:/proj# uv run python
Python 3.14.3 (main, Feb 24 2026, 21:41:39) [GCC 14.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> import numpy as np
>>> np.__version__
'2.4.2'
```
:::
