Installation

Prerequisites

Rust toolchain

obikmer requires Rust 1.85 or later (edition 2024). Install or update via rustup:

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

C build environment (required for hwloc)

obikmer embeds hwloc (Hardware Locality) for NUMA-aware thread placement on multi-socket machines. hwloc is built from source at compile time, which requires a standard C build environment.

Linux (Debian/Ubuntu)

apt install build-essential automake libtool autoconf pkg-config

Linux (RHEL/Rocky/AlmaLinux)

dnf install gcc make automake libtool autoconf pkgconfig

HPC clusters

Most HPC clusters provide these tools via the module system:

module load gcc automake libtool autoconf

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

macOS

brew install automake libtool autoconf pkg-config

Building

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) optimized for large sequential reads, not for the many small file operations Cargo generates during compilation. Building directly on such a filesystem can be extremely slow.

Redirect the build directory to a local scratch disk:

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

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

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 build flag is required — it falls back gracefully to a single-pool strategy on:

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

Verifying the installation

obikmer --help