Christian Schwarz 8afb783708 feat: Direct IO for the pageserver write path (#11558)
# Problem

The Pageserver read path exclusively uses direct IO if
`virtual_file_io_mode=direct`.

The write path is half-finished. Here is what the various writing
components use:

|what|buffering|flags on <br/>`v_f_io_mode`<br/>=`buffered`|flags on
<br/>`virtual_file_io_mode`<br/>=`direct`|
|-|-|-|-|
|`DeltaLayerWriter`| BlobWriter<BUFFERED=true> | () | () |
|`ImageLayerWriter`| BlobWriter<BUFFERED=false> | () | () |
|`download_layer_file`|BufferedWriter|()|()|
|`InMemoryLayer`|BufferedWriter|()|O_DIRECT|


The vehicle towards direct IO support is `BufferedWriter` which
- largely takes care of O_DIRECT alignment & size-multiple requirements 
- double-buffering to mask latency

`DeltaLayerWriter`, `ImageLayerWriter` use `blob_io::BlobWriter` , which
has neither of these.

# Changes

## High-Level

At a high-level this PR makes the following primary changes:

- switch the two layer writer types to use `BufferedWriter` & make
sensitive to `virtual_file_io_mode` (via open_with_options_**v2**)
- make `download_layer_file` sensitive to `virtual_file_io_mode` (also
via open_with_options_**v2**)
- add `virtual_file_io_mode=direct-rw` as a feature gate
- we're hackish-ly piggybacking on OpenOptions's ask for write access
here
- this means with just `=direct` InMemoryLayer reads and writes no
longer uses O_DIRECT
- this is transitory and we'll remove the `direct-rw` variant once the
rollout is complete

(The `_v2` APIs for opening / creating VirtualFile are those that are
sensitive to `virtual_file_io_mode`)

The result is:

|what|uses <br/>`BufferedWriter`|flags on
<br/>`v_f_io_mode`<br/>=`buffered`|flags on
<br/>`v_f_io_mode`<br/>=`direct`|flags on
<br/>`v_f_io_mode`<br/>=`direct-rw`|
|-|-|-|-|-|
|`DeltaLayerWriter`| ~~Blob~~BufferedWriter | () | () |  O_DIRECT |
|`ImageLayerWriter`| ~~Blob~~BufferedWriter | () | () |  O_DIRECT |
|`download_layer_file`|BufferedWriter|()|()|O_DIRECT|
|`InMemoryLayer`|BufferedWriter|()|~~O_DIRECT~~()|O_DIRECT|


## Code-Level


The main change is:
- Switch `blob_io::BlobWriter` away from its own buffering method to use
`BufferedWriter`.

Additional prep for upholding `O_DIRECT` requirements:
- Layer writer `finish()` methods switched to use IoBufferMut for
guaranteed buffer address alignment. The size of the buffers is PAGE_SZ
and thereby implicitly assumed to fulfill O_DIRECT requirements.

For the hacky feature-gating via `=direct-rw`:
- Track `OpenOptions::write(true|false)` in a field; bunch of mechanical
churn.
- Consolidate the APIs in which we "open" or "create" VirtualFile for
better overview over which parts of the code use the `_v2` APIs.

Necessary refactorings & infra work:
- Add doc comments explaining how BufferedWriter ensures that writes are
compliant with O_DIRECT alignment & size constraints. This isn't new,
but should be spelled out.
- Add the concept of shutdown modes to `BufferedWriter::shutdown` to
make writer shutdown adhere to these constraints.
- The `PadThenTruncate` mode might not be necessary in practice because
I believe all layer files ever written are sized in multiples `PAGE_SZ`
and since `PAGE_SZ` is larger than the current alignment requirements
(512/4k depending on platform), it won't be necesary to pad.
- Some test (I believe `round_trip_test_compressed`?) required it though
- [ ] TODO: decide if we want to accept that complexity; if we do then
address TODO in the code to separate alignment requirement from buffer
capacity
- Add `set_len` (=`ftruncate`) VirtualFile operation to support the
above.
- Allow `BufferedWriter` to start at a non-zero offset (to make room for
the summary block).

Cleanups unlocked by this change:
- Remove non-positional APIs from VirtualFile (e.g. seek, write_full,
read_full)

Drive-by fixes:
- PR https://github.com/neondatabase/neon/pull/11585 aimed to run unit
tests for all `virtual_file_io_mode` combinations but didn't because of
a missing `_` in the env var.

# Performance

This section assesses this PR's impact on deployments with current
production setting (`=direct`) and anticipated impact of switching to
(`=direct-rw`).

For `DeltaLayerWriter`, `=direct` should remain unchanged to slightly
improved on throughput because the `BlobWriter`'s buffer had the same
size as the `BufferedWriter`'s buffer, but it didn't have the
double-buffering that `BufferedWriter` has.
The `=direct-rw` enables direct IO; throughput should not be suffering
because of double-buffering; benchmarks will show if this is true.

The `ImageLayerWriter` was previously not doing any buffering
(`BUFFERED=false`).
It went straight to issuing the IO operation to the underlying
VirtualFile and the buffering was done by the kernel.
The switch to `BufferedWriter` under `=direct` adds an additional memcpy
into the BufferedWriter's buffer.
We will win back that memcpy when enabling direct IO via `=direct-rw`.

A nice win from the switch to `BufferedWriter` is that ImageLayerWriter
performs >=16x fewer write operations to VirtualFile (the BlobWriter
performs one write per len field and one write per image value).
This should save low tens of microseconds of CPU overhead from doing all
these syscalls/io_uring operations, regardless of `=direct` or
`=direct-rw`.
Aside from problems with alignment, this write frequency without
double-buffering is prohibitive if we actually have to wait for the
disk, which is what will happen when we enable direct IO via
(`=direct-rw`).
Throughput should not be suffering because of BufferedWrite's
double-buffering; benchmarks will show if this is true.

`InMemoryLayer` at `=direct` will flip back to using buffered IO but
remain on BufferedWriter.
The buffered IO adds back one memcpy of CPU overhead.
Throughput should not suffer and will might improve on
not-memory-pressured Pageservers but let's remember that we're doing the
whole direct IO thing to eliminate global memory pressure as a source of
perf variability.

## bench_ingest

I reran `bench_ingest` on `im4gn.2xlarge` and `Hetzner AX102`.
Use `git diff` with `--word-diff` or similar to see the change.

General guidance on interpretation:
- immediate production impact of this PR without production config
change can be gauged by comparing the same `io_mode=Direct`
- end state of production switched over to `io_mode=DirectRw` can be
gauged by comparing old results' `io_mode=Direct` to new results'
`io_mode=DirectRw`

Given above guidance, on `im4gn.2xlarge`
- immediate impact is a significant improvement in all cases
- end state after switching has same significant improvements in all
cases
- ... except `ingest/io_mode=DirectRw volume_mib=128 key_size_bytes=8192
key_layout=Sequential write_delta=Yes` which only achieves `238 MiB/s`
instead of `253.43 MiB/s`
  - this is a 6% degradation
  - this workload is typical for image layer creation

# Refs
- epic https://github.com/neondatabase/neon/issues/9868
- stacked atop
  - preliminary refactor https://github.com/neondatabase/neon/pull/11549
- bench_ingest overhaul https://github.com/neondatabase/neon/pull/11667
- derived from https://github.com/neondatabase/neon/pull/10063

Co-authored-by: Yuchen Liang <yuchen@neon.tech>
2025-04-24 14:57:36 +00:00
2025-04-24 11:20:41 +00:00
2021-05-27 15:33:08 +03:00

Neon

Neon

Neon is a serverless open-source alternative to AWS Aurora Postgres. It separates storage and compute and substitutes the PostgreSQL storage layer by redistributing data across a cluster of nodes.

Quick start

Try the Neon Free Tier to create a serverless Postgres instance. Then connect to it with your preferred Postgres client (psql, dbeaver, etc) or use the online SQL Editor. See Connect from any application for connection instructions.

Alternatively, compile and run the project locally.

Architecture overview

A Neon installation consists of compute nodes and the Neon storage engine. Compute nodes are stateless PostgreSQL nodes backed by the Neon storage engine.

The Neon storage engine consists of two major components:

  • Pageserver: Scalable storage backend for the compute nodes.
  • Safekeepers: The safekeepers form a redundant WAL service that received WAL from the compute node, and stores it durably until it has been processed by the pageserver and uploaded to cloud storage.

See developer documentation in SUMMARY.md for more information.

Running a local development environment

Neon can be run on a workstation for small experiments and to test code changes, by following these instructions.

Installing dependencies on Linux

  1. Install build dependencies and other applicable packages
  • On Ubuntu or Debian, this set of packages should be sufficient to build the code:
apt install build-essential libtool libreadline-dev zlib1g-dev flex bison libseccomp-dev \
libssl-dev clang pkg-config libpq-dev cmake postgresql-client protobuf-compiler \
libprotobuf-dev libcurl4-openssl-dev openssl python3-poetry lsof libicu-dev
  • On Fedora, these packages are needed:
dnf install flex bison readline-devel zlib-devel openssl-devel \
  libseccomp-devel perl clang cmake postgresql postgresql-contrib protobuf-compiler \
  protobuf-devel libcurl-devel openssl poetry lsof libicu-devel libpq-devel python3-devel \
  libffi-devel
  • On Arch based systems, these packages are needed:
pacman -S base-devel readline zlib libseccomp openssl clang \
postgresql-libs cmake postgresql protobuf curl lsof

Building Neon requires 3.15+ version of protoc (protobuf-compiler). If your distribution provides an older version, you can install a newer version from here.

  1. Install Rust
# recommended approach from https://www.rust-lang.org/tools/install
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

Installing dependencies on macOS (12.3.1)

  1. Install XCode and dependencies
xcode-select --install
brew install protobuf openssl flex bison icu4c pkg-config m4

# add openssl to PATH, required for ed25519 keys generation in neon_local
echo 'export PATH="$(brew --prefix openssl)/bin:$PATH"' >> ~/.zshrc

If you get errors about missing m4 you may have to install it manually:

brew install m4
brew link --force m4
  1. Install Rust
# recommended approach from https://www.rust-lang.org/tools/install
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
  1. Install PostgreSQL Client
# from https://stackoverflow.com/questions/44654216/correct-way-to-install-psql-without-full-postgres-on-macos
brew install libpq
brew link --force libpq

Rustc version

The project uses rust toolchain file to define the version it's built with in CI for testing and local builds.

This file is automatically picked up by rustup that installs (if absent) and uses the toolchain version pinned in the file.

rustup users who want to build with another toolchain can use the rustup override command to set a specific toolchain for the project's directory.

non-rustup users most probably are not getting the same toolchain automatically from the file, so are responsible to manually verify that their toolchain matches the version in the file. Newer rustc versions most probably will work fine, yet older ones might not be supported due to some new features used by the project or the crates.

Building on Linux

  1. Build neon and patched postgres
# Note: The path to the neon sources can not contain a space.

git clone --recursive https://github.com/neondatabase/neon.git
cd neon

# The preferred and default is to make a debug build. This will create a
# demonstrably slower build than a release build. For a release build,
# use "BUILD_TYPE=release make -j`nproc` -s"
# Remove -s for the verbose build log

make -j`nproc` -s

Building on OSX

  1. Build neon and patched postgres
# Note: The path to the neon sources can not contain a space.

git clone --recursive https://github.com/neondatabase/neon.git
cd neon

# The preferred and default is to make a debug build. This will create a
# demonstrably slower build than a release build. For a release build,
# use "BUILD_TYPE=release make -j`sysctl -n hw.logicalcpu` -s"
# Remove -s for the verbose build log

make -j`sysctl -n hw.logicalcpu` -s

Dependency installation notes

To run the psql client, install the postgresql-client package or modify PATH and LD_LIBRARY_PATH to include pg_install/bin and pg_install/lib, respectively.

To run the integration tests or Python scripts (not required to use the code), install Python (3.11 or higher), and install the python3 packages using ./scripts/pysync (requires poetry>=1.8) in the project directory.

Running neon database

  1. Start pageserver and postgres on top of it (should be called from repo root):
# Create repository in .neon with proper paths to binaries and data
# Later that would be responsibility of a package install script
> cargo neon init
Initializing pageserver node 1 at '127.0.0.1:64000' in ".neon"

# start pageserver, safekeeper, and broker for their intercommunication
> cargo neon start
Starting neon broker at 127.0.0.1:50051.
storage_broker started, pid: 2918372
Starting pageserver node 1 at '127.0.0.1:64000' in ".neon".
pageserver started, pid: 2918386
Starting safekeeper at '127.0.0.1:5454' in '.neon/safekeepers/sk1'.
safekeeper 1 started, pid: 2918437

# create initial tenant and use it as a default for every future neon_local invocation
> cargo neon tenant create --set-default
tenant 9ef87a5bf0d92544f6fafeeb3239695c successfully created on the pageserver
Created an initial timeline 'de200bd42b49cc1814412c7e592dd6e9' at Lsn 0/16B5A50 for tenant: 9ef87a5bf0d92544f6fafeeb3239695c
Setting tenant 9ef87a5bf0d92544f6fafeeb3239695c as a default one

# create postgres compute node
> cargo neon endpoint create main

# start postgres compute node
> cargo neon endpoint start main
Starting new endpoint main (PostgreSQL v14) on timeline de200bd42b49cc1814412c7e592dd6e9 ...
Starting postgres at 'postgresql://cloud_admin@127.0.0.1:55432/postgres'

# check list of running postgres instances
> cargo neon endpoint list
 ENDPOINT  ADDRESS          TIMELINE                          BRANCH NAME  LSN        STATUS
 main      127.0.0.1:55432  de200bd42b49cc1814412c7e592dd6e9  main         0/16B5BA8  running
  1. Now, it is possible to connect to postgres and run some queries:
> psql -p 55432 -h 127.0.0.1 -U cloud_admin postgres
postgres=# CREATE TABLE t(key int primary key, value text);
CREATE TABLE
postgres=# insert into t values(1,1);
INSERT 0 1
postgres=# select * from t;
 key | value
-----+-------
   1 | 1
(1 row)
  1. And create branches and run postgres on them:
# create branch named migration_check
> cargo neon timeline branch --branch-name migration_check
Created timeline 'b3b863fa45fa9e57e615f9f2d944e601' at Lsn 0/16F9A00 for tenant: 9ef87a5bf0d92544f6fafeeb3239695c. Ancestor timeline: 'main'

# check branches tree
> cargo neon timeline list
(L) main [de200bd42b49cc1814412c7e592dd6e9]
(L) ┗━ @0/16F9A00: migration_check [b3b863fa45fa9e57e615f9f2d944e601]

# create postgres on that branch
> cargo neon endpoint create migration_check --branch-name migration_check

# start postgres on that branch
> cargo neon endpoint start migration_check
Starting new endpoint migration_check (PostgreSQL v14) on timeline b3b863fa45fa9e57e615f9f2d944e601 ...
Starting postgres at 'postgresql://cloud_admin@127.0.0.1:55434/postgres'

# check the new list of running postgres instances
> cargo neon endpoint list
 ENDPOINT         ADDRESS          TIMELINE                          BRANCH NAME      LSN        STATUS
 main             127.0.0.1:55432  de200bd42b49cc1814412c7e592dd6e9  main             0/16F9A38  running
 migration_check  127.0.0.1:55434  b3b863fa45fa9e57e615f9f2d944e601  migration_check  0/16F9A70  running

# this new postgres instance will have all the data from 'main' postgres,
# but all modifications would not affect data in original postgres
> psql -p 55434 -h 127.0.0.1 -U cloud_admin postgres
postgres=# select * from t;
 key | value
-----+-------
   1 | 1
(1 row)

postgres=# insert into t values(2,2);
INSERT 0 1

# check that the new change doesn't affect the 'main' postgres
> psql -p 55432 -h 127.0.0.1 -U cloud_admin postgres
postgres=# select * from t;
 key | value
-----+-------
   1 | 1
(1 row)
  1. If you want to run tests afterwards (see below), you must stop all the running pageserver, safekeeper, and postgres instances you have just started. You can terminate them all with one command:
> cargo neon stop

More advanced usages can be found at Local Development Control Plane (neon_local)).

Handling build failures

If you encounter errors during setting up the initial tenant, it's best to stop everything (cargo neon stop) and remove the .neon directory. Then fix the problems, and start the setup again.

Running tests

Rust unit tests

We are using cargo-nextest to run the tests in Github Workflows. Some crates do not support running plain cargo test anymore, prefer cargo nextest run instead. You can install cargo-nextest with cargo install cargo-nextest.

Integration tests

Ensure your dependencies are installed as described here.

git clone --recursive https://github.com/neondatabase/neon.git

CARGO_BUILD_FLAGS="--features=testing" make

./scripts/pytest

By default, this runs both debug and release modes, and all supported postgres versions. When testing locally, it is convenient to run just one set of permutations, like this:

DEFAULT_PG_VERSION=17 BUILD_TYPE=release ./scripts/pytest

Flamegraphs

You may find yourself in need of flamegraphs for software in this repository. You can use flamegraph-rs or the original flamegraph.pl. Your choice!

Important

If you're using lld or mold, you need the --no-rosegment linker argument. It's a general thing with Rust / lld / mold, not specific to this repository. See this PR for further instructions.

Cleanup

For cleaning up the source tree from build artifacts, run make clean in the source directory.

For removing every artifact from build and configure steps, run make distclean, and also consider removing the cargo binaries in the target directory, as well as the database in the .neon directory. Note that removing the .neon directory will remove your database, with all data in it. You have been warned!

Documentation

docs Contains a top-level overview of all available markdown documentation.

To view your rustdoc documentation in a browser, try running cargo doc --no-deps --open

See also README files in some source directories, and rustdoc style documentation comments.

Other resources:

Postgres-specific terms

Due to Neon's very close relation with PostgreSQL internals, numerous specific terms are used. The same applies to certain spelling: i.e. we use MB to denote 1024 * 1024 bytes, while MiB would be technically more correct, it's inconsistent with what PostgreSQL code and its documentation use.

To get more familiar with this aspect, refer to:

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