compat-lib

README

Compat Lib

This is a library that provides tools for compatibility and understanding of filesystem events. There are several tools packaged here:

• fs-record: records events (paths and timestamps) that occur when you run an application. Since this is run with fuse (in user space) it can work on a local machine (a binary directly) or via a container! This was the third project I created here that I ultimately find the most interesting.
• compat-gen: is a tool that records library (or generally software) loading when you run a binary, and generates a compatibility artifact.
• spindle and spindle-server: are a library discovery wrapper and server to distribute the cache across nodes, respectively. It was the original prototype that I created to emulate spindle and I need to have discussion with the spindle developers about what they would like to do next! It was paramount for me to learn how to use fuse to write custom events (and further understand the SOCI snapshotter).

Usage

For all examples below, build first.

make

To make the proto (or re-generate, if necessary):

make proto

Tools

1. Application Recorder

fs-record to record filesystem events using a custom Fuse filesystem (works in a container too)!

This tool does the following:

1. Record the file access of running some HPC application (in a container or not) meaning paths and timestamps since start.
2. Record file access of a set of "the same" app over time to assess differences.

./bin/fs-record /home/vanessa/Desktop/Code/spack/opt/spack/linux-ubuntu24.04-zen4/gcc-13.2.0/xz-5.4.6-klise22d77jjaoejkucrczlkvnm6f4au/bin/xz --help

Here is how to customize the output file name:

./bin/fs-record --out ./example/compat/xz-libs.txt /home/vanessa/Desktop/Code/spack/opt/spack/linux-ubuntu24.04-zen4/gcc-13.2.0/xz-5.4.6-klise22d77jjaoejkucrczlkvnm6f4au/bin/xz

Test running in a container, and binding the binary!

# Test running lammps first
docker run -it ghcr.io/converged-computing/lammps-time:stable_29Aug2024_update1 lmp -v x 2 -v y 2 -v z 2 -in ./in.reaxff.hns -nocite

# Now record!
docker run -v $PWD/bin:/compat --security-opt apparmor:unconfined --device /dev/fuse --cap-add SYS_ADMIN -it ghcr.io/converged-computing/lammps-time-fuse:stable_29Aug2024_update1 /compat/fs-record --out /compat/lammps-run-1.out lmp -v x 2 -v y 2 -v z 2 -in ./in.reaxff.hns -nocite

# With a temporary file in the PWD
docker run -v $PWD/bin:/compat --security-opt apparmor:unconfined --device /dev/fuse --cap-add SYS_ADMIN -it ghcr.io/converged-computing/lammps-time-fuse:stable_29Aug2024_update1 /compat/fs-record --out-dir /compat lmp -v x 2 -v y 2 -v z 2 -in ./in.reaxff.hns -nocite

We provide functions in Python under python/compatlib for parsing and generating models for the event files. You can see using the library here, and early work in the lammps-time repository to do this that has since been turned into the library here. The next stage of work for that project will use the library here.

2. Compatibility Wrapper

compat-gen to generate compatibility artifacts

This idea was suited for the use case of compatibility, but I'm not sure it has captured enough interest yet to continue working on. The general idea is the following:

1. Generate compatibility artifacts that describe applications (or containers) of interest
2. They can live in a local cache or a registry
3. A service (like a daemon) runs on a node and can evaluate if the node is compatible with the application.

To start, I wanted to look at software. I generated an example artifact that described a binary and the libraries that are needed. The next step was to run the service that will discover the paths provided on the host (exposed via ldd) and be able to quickly answer if this is compatible or not. Ironically, as I was exploring this space I realized it was an easy way to cache library locations based on soname, which could be used akin to a tool like spindle. I started testing that (see the first idea) but ultimately returned to the compatibility use case because I find it more interesting.

Too long, didn't read

For this idea, I'll have one entrypoint that can generate a compatibility artifact for some binary. This will just be the .so libraries that are needed for the binary (along with the binary). Then I'll have a grpc server / service (or could also be a database) that you run to discover the paths on the node, and you can pull the artifact in advance to check if its compatible. Let's do a dummy case. First, generate the artifact.

./bin/compat-gen /home/vanessa/Desktop/Code/spack/opt/spack/linux-ubuntu24.04-zen4/gcc-13.2.0/xz-5.4.6-klise22d77jjaoejkucrczlkvnm6f4au/bin/xz

⭐️ Compatibility Library Generator (clib-gen)
Preparing to find shared libraries needed for [/home/vanessa/Desktop/Code/spack/opt/spack/linux-ubuntu24.04-zen4/gcc-13.2.0/xz-5.4.6-klise22d77jjaoejkucrczlkvnm6f4au/bin/xz]
{
  "version": "0.0.1",
  "attributes": {
    "llnl.compatlib.executable-name": "xz",
    "llnl.compatlib.library-name.0": "ld-linux-x86-64.so.2",
    "llnl.compatlib.library-name.1": "liblzma.so.5",
    "llnl.compatlib.library-name.2": "libc.so.6"
  }
}

Now let's save that to file.

./bin/compat-gen --out ./example/compat/xz-libs.json /home/vanessa/Desktop/Code/spack/opt/spack/linux-ubuntu24.04-zen4/gcc-13.2.0/xz-5.4.6-klise22d77jjaoejkucrczlkvnm6f4au/bin/xz

We could now push that to a registry with ORAS, but we are first going to test with a server. The following should happen:

1. The server starts and is oriented to a mode to parse libraries on the host.
2. The client is run to request a compatibility check of the artifact against that node (comparing libraries needed)
3. If all paths can be satisfied, we get an affirmative response, otherwise nope.

To run the server:

./bin/compat-server

2024/10/13 17:58:41 🧩 starting compatibility server: compatServer v0.0.1
2024/10/13 17:58:41 server listening: [::]:50051

3. Library Discovery Wrapper (spindle)

spindle to figure out what shared libraries are needed via an open intercept, and spindle-server to distribute the cache across nodes.

This was the experiment to generate something akin to spindle. I am still learning about fuse and the best way to go about this. So far, what I do:

1. The user provides a mount point root for a root (fuse) filesystem and cache, which will be located at /tmp/spindlexxxx.

• The location of this point is important, as the cache reads will happen here and (I think) help with the optimization.
• The fuse loopback filesystem (meaning it redirects to the root at / for all calls) is created at /tmp/spindlexxxx/root
• A cache to copy files (that will be opened) is created at /tmp/spindlexxxx/cache

1. Each Open call is intercepted, and the actual filesystem path moved to the cache, and the Open call uses the cache instead
2. The command is run with "proot" directed at the /tmp/spindlexxxx/root so all calls are intercepted here

• I do this because when I don't use proot, I don't see the libraries trying to be loaded.
• This will lead to problems because it means we don't have write at the moment
• We need a strategy that can direct all Open calls here (to redirect to the cache) but can return to the actual FS for write, etc.

1. I don't see "Close" (Flush) - that either means we are leaving files open, or the fuse root is not monitoring the /tmp/spindlexxxx/cache

In my testing environment, given that spindle and proot are on the path, we can do:

cd /opt/lammps/examples/reaxff/HNS/
spindle lmp -v x 1 -v y 1 -v z 1 -in ./in.reaxff.hns -nocite

I added options to help with debugging (e.g., an output file for events, verbose mode for proot, and the option to --wait to keep it running):

$ ./bin/spindle --help
🧵 Filesystem Cache (spindle)
Usage of ./bin/spindle:
  -mount-path string
        Mount path for fuse root and cache (created in /tmp/spindleXXXXX if does not exist)
  -out string
        Output file to write events (unset will not write anything anywhere)
  -read-only
        Read only mode (on by default, as the layer to intercept does not need write) (default true)
  -v    Run proot in verbose mode (off by default)
  -wait
        Wait (and do not unmount) at the end (off by default)
  -workdir string
        Working directory (defaults to pwd)

License

HPCIC DevTools is distributed under the terms of the MIT license. All new contributions must be made under this license.

See LICENSE, COPYRIGHT, and NOTICE for details.

SPDX-License-Identifier: (MIT)

LLNL-CODE- 842614