talks: Add talk for DFN IT sysadmins.
* talks/2023-dfn: New directory.
This commit is contained in:
Ricardo Wurmus
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*.pdf
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SLIDES=\
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title \
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rekado \
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title2 \
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reproducibility \
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reproducibility2 \
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reproducibility \
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reproducible-4 \
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reproducible-2 \
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reproducible-3 \
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big-graph-fixed \
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hpc \
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conda1 \
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conda2 \
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containers \
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kernel \
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containers-details \
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smoothie \
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dockerfile \
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giraffe \
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functional-thesis \
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functional1a functional1b functional1c \
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guix-features \
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31-guix2 31-guix3 31-guix4 31-guix5 \
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demo \
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env \
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manifest time-travel describe \
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docker-pack \
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summary \
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end
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# Extra slides for which there is no time:
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BONUS= bonus \
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guix-architecture \
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profile-0 profile-1 rollback profile-1 \
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gc-1 gc-2 gc-3
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GS = gs
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slides.pdf: $(addsuffix .pdf, ${SLIDES} ${BONUS})
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${GS} -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=$@ $(addsuffix .pdf, ${SLIDES}) $(addsuffix .pdf, ${BONUS})
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%.pdf: %.svg
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rsvg-convert -f pdf $< > $@
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#+title: Reproducible software deployment in scientific computing
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#+author: Ricardo Wurmus
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presented on <2023-09-19 二>
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* Abstract
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Support teams of HPC systems often find themselves faced with an
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impossible task: operate complex systems conservatively, but also
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support scientists in deploying and running bleeding-edge scientific
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software. Their unique position of power in an otherwise restrictive
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environment gives them an often underappreciated role in the
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collaborative effort of truly reproducible computational science.
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In this talk we address the need for reproducibility and how it
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relates to software deployment, inspect tradeoffs of existing
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approaches, and lay out implications and recommendations for system
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administrators. We will demystify containers and introduce a
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declarative functional approach to reproducible and portable software
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environments using GNU Guix, and demonstrate possible integrations
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with scientific workflows.
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* Building the slides
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#+begin_src sh
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guix shell -m manifest.scm -- make
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#+end_src
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* How to present with notes
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#+begin_src sh
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guix shell pdfpc -- pdfpc slides.pdf -R script.pdfpc
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#+end_src
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@ -0,0 +1,24 @@
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#+title: Reproducible software deployment in scientific computing
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* Abstract
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Support teams of HPC systems often find themselves faced with an
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impossible task: operate complex systems conservatively, but also
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support scientists in deploying and running bleeding-edge scientific
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software. Their unique position of power in an otherwise restrictive
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environment gives them an often underappreciated role in the
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collaborative effort of truly reproducible computational science.
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In this talk we address the need for reproducibility and how it
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relates to software deployment, inspect tradeoffs of existing
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approaches, and lay out implications and recommendations for system
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administrators. We will demystify containers and introduce a
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declarative functional approach to reproducible and portable software
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environments using GNU Guix, and demonstrate possible integrations
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with scientific workflows.
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* Present
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#+begin_src sh
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guix shell pdfpc -- pdfpc slides.pdf -R script.pdfpc
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#+end_src
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diff -ru hello-2.12.1.original/src/hello.c hello-2.12.1/src/hello.c
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--- hello-2.12.1.original/src/hello.c 2020-03-07 19:53:27.000000000 +0100
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#endif
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diff -ru hello-2.12.1.original/tests/hello-1 hello-2.12.1/tests/hello-1
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--- hello-2.12.1.original/tests/hello-1 2020-03-07 19:53:27.000000000 +0100
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tmpfiles="hello-test1.ok"
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-Hello, world!
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/gnu/store/5mqwac3zshjjn1ig82s12rbi7whqm4n8-hello-2.12.1
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+ establish trust, and
|
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+ facilitate further experimentation.
|
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Konrad Hinsen, a researcher at the French CNRS, has written
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[T]here is no point in repeating a computation identically. The
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|
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|
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The point of computational reproducibility is to dispel those
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|
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|
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deliberately changed.
|
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|
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So we are in need of a system with strong reproducibility guarantees
|
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|
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"note": "
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Examples include:
|
||||
|
||||
+ a researcher resumes a project after a few months on the same
|
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computer
|
||||
|
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|
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|
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|
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|
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|
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|
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the project
|
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|
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|
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|
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All of these scenarios are fundamentally the same. It’s just bits on
|
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|
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|
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|
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Turns out that the scale of the problem is often much larger than
|
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|
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|
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What you see here are dozens of interconnected software packages. A
|
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|
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|
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|
||||
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|
||||
|
||||
Only *one* of these nodes corresponds to the code of the application
|
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|
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|
||||
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|
||||
|
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On the other hand, a user who receives a comprehensive book full of
|
||||
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|
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|
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|
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* What options do we have?
|
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|
||||
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|
||||
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|
||||
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|
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|
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|
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|
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|
||||
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|
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|
||||
|
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These systems are heavily dependent on system administrators who
|
||||
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|
||||
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|
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|
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* Example: Conda
|
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|
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|
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|
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|
||||
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|
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},
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"idx": 12,
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"label": "13",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
And yet Conda is know to have repeatedly failed to recreate
|
||||
environments. Conda lets users impose version constraints for their
|
||||
software environments. A SAT solver then finds an actual environment
|
||||
that satisfies these constraints. Since the result of the solver
|
||||
depends on the state of the Conda binary repositories the result of
|
||||
the solver can vary with time.
|
||||
|
||||
An even more common problem: Conda binaries often contain references
|
||||
to system libraries such as symbols in the GNU C library which may
|
||||
only be satisfied by *some* GNU+Linux distributions (say a recent
|
||||
Ubuntu) and not others (a dusty RHEL). Conda environments are
|
||||
incomplete and lossy.
|
||||
|
||||
In recent years, steps have been taken to refine the constraints to
|
||||
allow for a longer shelf-life of exported environments, but it is hard
|
||||
to predict when old environment files will stop working again due to
|
||||
the lack of a rigorous method of capturing all ingredients.
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 13,
|
||||
"label": "14",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
* Containers and reproducibility
|
||||
|
||||
Another popular attempt to bundle up software environments is to use
|
||||
container tools such as Docker. Docker and tools like it made the
|
||||
fiddly Linux kernel features of process isolation and file system
|
||||
virtualization easily accessible.
|
||||
|
||||
Let's take a quick look at what the kernel does.
|
||||
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 14,
|
||||
"label": "15",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
|
||||
The kernel Linux presents a number of interfaces to the C library and
|
||||
low level applications. Your code --- sometimes through many
|
||||
intermediaries --- talks to the kernel either via the C library or
|
||||
less commonly via system calls.
|
||||
|
||||
These kernel interfaces together provide processes with the familiar
|
||||
Unix persona.
|
||||
|
||||
When the kernel prepares to launch a process it creates a view on the
|
||||
slice of the system hardware that is relevant to the process: the
|
||||
process appears to have exclusive access to the CPU and memory, while
|
||||
the kernel actually just virtualizes these resources.
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 15,
|
||||
"label": "16",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
The kernel can *also* virtualize other resources that make up the Unix
|
||||
interface. It can present independent namespaces for different
|
||||
subsystems to a process. These namespaces include the process table,
|
||||
network devices, facilities for inter-process communication, the file
|
||||
system, user ids, and virtual time.
|
||||
|
||||
Give a process an empty mount namespace and it cannot see the host
|
||||
system's files any more. Give it a separate user namespace and it
|
||||
will think that it is the only user on the system, and also has root
|
||||
access.
|
||||
|
||||
In the common case of Docker (or Singularity/Apptainer), people run a
|
||||
process in a separate mount namespace, so that it cannot access the
|
||||
root file system (and all the globally installed software) and instead
|
||||
uses a provided binary bundle as the root file system.
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 16,
|
||||
"label": "17",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
This makes it much easier to *install* an application, but there is no
|
||||
way to *recreate* the bundled root file system independently, exactly,
|
||||
or with deliberate fine-grain modifications. This fine-grain control
|
||||
is a necessary requirement for the interactive exploratory process of
|
||||
computational science.
|
||||
|
||||
We don’t only want to clone an environment, but we may want to have
|
||||
the option of making *specific* changes without having anything else in
|
||||
the environment change.
|
||||
|
||||
Containers lack transparency. Looking at the binary image you cannot
|
||||
tell what ingredients really went into it. You have no guarantee that
|
||||
the binary you *received* really corresponds to the source code you
|
||||
*reviewed*.
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 17,
|
||||
"label": "18",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
|
||||
When container images are built, they modify or extend existing
|
||||
third-party images by fetching network resources that are not
|
||||
guaranteed to be immutable as time passes. Dockerfiles are imperative
|
||||
and execute traditional package management commands or perform
|
||||
downloads and successively mutate the new root file system. We end up
|
||||
with the raw bits of a new root file system and sacrifice any higher
|
||||
order abstractions.
|
||||
|
||||
When building a container image from a Dockerfile on one day and again
|
||||
a month later it is not unusual to get two very different containers.
|
||||
The secret ingredient in even the most transparent container smoothie
|
||||
is the current state of the internet.
|
||||
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 18,
|
||||
"label": "19",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
|
||||
So far we looked at software management approaches that are derived
|
||||
from the traditional approach of mutating shared storage. Even with
|
||||
modern containers we still work with a single blob of a shared root
|
||||
file system; we just ignore the existing system’s file system.
|
||||
|
||||
Computing practices are not so different from biological evolution.
|
||||
Evolution is descent with modification. All modification is subject
|
||||
to the cumulative constraints of past modifications; this means that
|
||||
backtracking is often prohibitively expensive. Giraffes, for example,
|
||||
are stuck with their ridiculously long laryngeal nerve that takes a
|
||||
detour from the head down the neck, around the aortic arch, all the
|
||||
way back up to the head.
|
||||
|
||||
Software deployment practices likewise are limited by the burden of
|
||||
decisions in the past that continue to influence the trajectory of our
|
||||
projects. What if we didn’t try to tack on reproducibility onto
|
||||
legacy methods of software installation but instead built a system
|
||||
from reproducible primitives?
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 19,
|
||||
"label": "20",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
* The functional approach
|
||||
|
||||
In 2006 Eelco Dolstra published his PhD thesis entitled “The Purely
|
||||
Functional Software Deployment Model”. The core idea is simple: treat
|
||||
the transformation from source code and tools to executable files as a
|
||||
pure function. The output of a function is fully determined by its
|
||||
inputs and nothing else.
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 20,
|
||||
"label": "21",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
* The functional approach
|
||||
|
||||
In 2006 Eelco Dolstra published his PhD thesis entitled “The Purely
|
||||
Functional Software Deployment Model”. The core idea is simple: treat
|
||||
the transformation from source code and tools to executable files as a
|
||||
pure function. The output of a function is fully determined by its
|
||||
inputs and nothing else.
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 21,
|
||||
"label": "22",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
|
||||
Inputs are source code files,
|
||||
any tools that run to translate the code to a binary,
|
||||
any libraries needed by these tools,
|
||||
any libraries that the software needs to link with, etc.
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 22,
|
||||
"label": "23",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
The output is a tree of files, some executable some not."
|
||||
},
|
||||
{
|
||||
"idx": 23,
|
||||
"label": "24",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
|
||||
GNU Guix is one implementation of this functional idea.
|
||||
|
||||
Guix comes with a very large collection of about 28000 package
|
||||
recipes that are each built in complete isolation (no internet, no
|
||||
root file system, no /bin, no /lib). This is enforced by a daemon
|
||||
that spawns jails where dedicated unprivileged user accounts build
|
||||
software. When compiling these packages only declared inputs are
|
||||
available, nothing else. The resulting files are stored in a unique
|
||||
output directory that is derived from the set of all inputs. Any
|
||||
change to any of the inputs results in a new output directory.
|
||||
|
||||
This simple property ensures that countless variants of applications
|
||||
and libraries can be installed on the same system without conflicts.
|
||||
Existing software doesn’t affect new software, and new software cannot
|
||||
affect existing software.
|
||||
|
||||
A Guix package is unambiguously described by its complete dependency
|
||||
graph; this includes all libraries it needs, any tools that are used
|
||||
to create it, any source code, and any configurations.
|
||||
|
||||
Building the same package twice on different machines will (in the
|
||||
absence of bugs) result in the exact same files. It doesn’t matter
|
||||
whether you are using Ubuntu or RHEL, or whether you are doing
|
||||
this in 2020 or 2024.
|
||||
|
||||
Guix heavily caches builds and deduplicates identical files, so the
|
||||
overall space consumption is lower than one would expect.
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 24,
|
||||
"label": "25",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
|
||||
This same simple idea is easily extended from individual packages to
|
||||
groups of packages in the same environment...
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 25,
|
||||
"label": "26",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
|
||||
...or to lightweight
|
||||
containers *without* the need to replace the root file system...
|
||||
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 26,
|
||||
"label": "27",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
...or even to full blown GNU+Linux systems...
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 27,
|
||||
"label": "28",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
|
||||
...whether that be system
|
||||
containers, virtual machines, or bare-metal installations.
|
||||
|
||||
Let us next look at the simplest features and work our way up.
|
||||
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 28,
|
||||
"label": "29",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
|
||||
As mentioned earlier, version numbers fail to describe software
|
||||
completely.
|
||||
|
||||
Let me show you an example with the humble “hello” package. [...]
|
||||
|
||||
All of these applications are “hello” version 2 point 12 point one, but
|
||||
some have patches, others use GCC 11, and yet others use different
|
||||
configuration flags. With Guix these are all distinct.
|
||||
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 29,
|
||||
"label": "30",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
|
||||
“guix build” is a low-level command. Users don’t need to care about
|
||||
all these /gnu/store locations. They would instead use Guix like a
|
||||
traditional package manager or like a shell.
|
||||
|
||||
[demo]
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 30,
|
||||
"label": "31",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
|
||||
Guix can be used declaratively. A manifest file declares what
|
||||
software the environment should contain, and Guix can instantiate an
|
||||
environment according to these specifications.
|
||||
|
||||
Previously I said that recreating environments is just a necessary
|
||||
step to facilitate further experimentation. Guix has a number of
|
||||
built-in transformations to modify selected parts of the massive
|
||||
dependency graph. Libraries can be replaced with variants that are
|
||||
optimized for specific CPUs, recursively for any package that uses
|
||||
them. Or a patch can be applied to a selected package, keeping the
|
||||
rest of the stack unaltered.
|
||||
|
||||
Beyond these transformation presets Guix is fully programmable in
|
||||
Scheme and packages can be rewritten with the flexibility of a modern
|
||||
general purpose programming language.
|
||||
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 31,
|
||||
"label": "32",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
|
||||
All the information about all dependencies of any package
|
||||
available through Guix is part of Guix itself. So by changing the
|
||||
version of Guix we can move backwards and forwards in time to
|
||||
install software as it was available when that particular version
|
||||
of Guix was current.
|
||||
|
||||
This means that for fully reproducible environments we only need two
|
||||
pieces of information:
|
||||
|
||||
+ the exact version of Guix we used at the time, and
|
||||
+ the name(s) of the package(s)
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 32,
|
||||
"label": "33",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
We can let Guix describe itself in a way that it can understand.
|
||||
|
||||
guix describe -f channels > channels.scm
|
||||
|
||||
You can think of the output as a complete snapshot of all the software
|
||||
known to Guix (including all the relationships between libraries,
|
||||
configurations, and tools) at this time.
|
||||
"
|
||||
},
|
||||
{
|
||||
"idx": 33,
|
||||
"label": "34",
|
||||
"overlay": 0,
|
||||
"note": "
|
||||
|
||||
Given that Guix knows exactly what relationships there are between
|
||||
applications and their dependencies it can also export all the bits in
|
||||
whatever format you want. GUIX PACK is a way to generate application
|
||||
bundles --- in docker format, singularity, or just as a plain tarball.
|
||||
|
||||
This lets you share the bits with people who are not (yet) using Guix.
|
||||
But remember that the resulting blob is an OUTPUT. By dumping all the
|
||||
bits into an file system image we lose all the higher level
|
||||
abstractions that enable us to perform controlled computational
|
||||
experiments.
|
||||
|
||||
"
|
||||
}
|
||||
]
|
||||
}
|
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Reference in New Issue