obikmer/docmd/installation.md

# Installation

## Prerequisites

### Rust toolchain

`obikmer` requires **Rust 1.85 or later** (edition 2024). Install or update via [rustup](https://rustup.rs):

```bash
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
rustup update stable
```

### C build environment (required for hwloc)

`obikmer` embeds [hwloc](https://www.open-mpi.org/projects/hwloc/) (Hardware Locality) for NUMA-aware thread placement on multi-socket machines. hwloc is built from source at compile time via the `vendored` feature of the `hwlocality` crate. This requires a standard C build environment.

#### Linux (Debian/Ubuntu)

```bash
apt install build-essential automake libtool autoconf pkg-config
```

#### Linux (RHEL/Rocky/AlmaLinux)

```bash
dnf install gcc make automake libtool autoconf pkgconfig
```

#### HPC clusters

Most HPC clusters provide these tools via the module system:

```bash
module load gcc automake libtool autoconf
```

If in doubt, check whether `autoreconf --version` and `libtool --version` return successfully.

#### macOS

```bash
brew install automake libtool autoconf pkg-config
```

## Building

```bash
git clone <repository-url>
cd obikmer/src
cargo build --release
```

The compiled binary is at `target/release/obikmer`.

### Building on HPC clusters (network filesystems)

HPC home directories are typically on a network filesystem (Lustre, NFS) optimised for large sequential reads — not for the thousands of small file operations that Cargo generates during compilation. Building directly on such a filesystem can be extremely slow (0.1% CPU utilisation, tens of minutes for what should take seconds).

**Always redirect the build directory to a local scratch disk:**

```bash
CARGO_TARGET_DIR=/scratch/$USER/cargo-target cargo build --release
```

Adapt the path to the local scratch available on your cluster (`/var/tmp`, `/tmp`, `/scratch/local`, etc.). Once built, copy the binary to a permanent location:

```bash
cp /scratch/$USER/cargo-target/release/obikmer ~/bin/
```

## NUMA support

NUMA-aware thread placement is active automatically on multi-socket Linux machines (detected at runtime via hwloc). No special build flag is required — the detection is built in and falls back gracefully to the single-pool adaptive strategy on:

- macOS (Apple Silicon, unified memory)
- single-socket Linux machines
- any system where hwloc reports only one NUMA node

## Verifying the installation

```bash
obikmer --help
```