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Installation
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Prerequisites
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Rust toolchain
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C build environment (required for hwloc)
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Linux (Debian/Ubuntu)
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Linux (RHEL/Rocky/AlmaLinux)
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HPC clusters
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macOS
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Building
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Building on HPC clusters (network filesystems)
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NUMA support
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Verifying the installation
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Theory
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Theory
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Kmers and super-kmers
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DNA encoding
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Entropy filter
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Minimizer selection
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Partitioning architecture
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Central-position SNP distance (discussion)
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Implementation
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Implementation
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SuperKmer
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Kmer
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Chunk reader
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Construction pipeline
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obipipeline library
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On-disk storage
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MPHF selection
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Unitig evidence encoding
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Evidence elimination (discussion)
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obilayeredmap crate
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PersistentCompactIntVec
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PersistentBitVec
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Merge command
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Merge parallelism & memory
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Kmer filtering
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Select command
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obitaxonomy crate
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Architecture
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Architecture
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Sequences
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Kmer index
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Sibling annex (discussion)
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NUMA-aware worker pools
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NUMA-aware partition runner
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Prerequisites
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Rust toolchain
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< h1 id = "installation" > Installation</ h1 >
< h2 id = "prerequisites" > Prerequisites</ h2 >
< h3 id = "rust-toolchain" > Rust toolchain</ h3 >
< p >< code > obikmer</ code > requires < strong > Rust 1.85 or later</ strong > (edition 2024). Install or update via < a href = "https://rustup.rs" > rustup</ a > :</ p >
< div class = "highlight" >< pre >< span ></ span >< code > curl< span class = "w" > </ span > --proto< span class = "w" > </ span >< span class = "s1" > ' =https' </ span >< span class = "w" > </ span > --tlsv1.2< span class = "w" > </ span > -sSf< span class = "w" > </ span > https://sh.rustup.rs< span class = "w" > </ span >< span class = "p" > |</ span >< span class = "w" > </ span > sh
rustup< span class = "w" > </ span > update< span class = "w" > </ span > stable
</ code ></ pre ></ div >
< h3 id = "c-build-environment-required-for-hwloc" > C build environment (required for hwloc)</ h3 >
< p >< code > obikmer</ code > embeds < a href = "https://www.open-mpi.org/projects/hwloc/" > hwloc</ a > (Hardware Locality) for NUMA-aware thread placement on multi-socket machines. hwloc is built from source at compile time via the < code > vendored</ code > feature of the < code > hwlocality</ code > crate. This requires a standard C build environment.</ p >
< h4 id = "linux-debianubuntu" > Linux (Debian/Ubuntu)</ h4 >
< div class = "highlight" >< pre >< span ></ span >< code > apt< span class = "w" > </ span > install< span class = "w" > </ span > build-essential< span class = "w" > </ span > automake< span class = "w" > </ span > libtool< span class = "w" > </ span > autoconf< span class = "w" > </ span > pkg-config
</ code ></ pre ></ div >
< h4 id = "linux-rhelrockyalmalinux" > Linux (RHEL/Rocky/AlmaLinux)</ h4 >
< div class = "highlight" >< pre >< span ></ span >< code > dnf< span class = "w" > </ span > install< span class = "w" > </ span > gcc< span class = "w" > </ span > make< span class = "w" > </ span > automake< span class = "w" > </ span > libtool< span class = "w" > </ span > autoconf< span class = "w" > </ span > pkgconfig
</ code ></ pre ></ div >
< h4 id = "hpc-clusters" > HPC clusters</ h4 >
< p > Most HPC clusters provide these tools via the module system:</ p >
< div class = "highlight" >< pre >< span ></ span >< code > module< span class = "w" > </ span > load< span class = "w" > </ span > gcc< span class = "w" > </ span > automake< span class = "w" > </ span > libtool< span class = "w" > </ span > autoconf
</ code ></ pre ></ div >
< p > If in doubt, check whether < code > autoreconf --version</ code > and < code > libtool --version</ code > return successfully.</ p >
< h4 id = "macos" > macOS</ h4 >
< div class = "highlight" >< pre >< span ></ span >< code > brew< span class = "w" > </ span > install< span class = "w" > </ span > automake< span class = "w" > </ span > libtool< span class = "w" > </ span > autoconf< span class = "w" > </ span > pkg-config
</ code ></ pre ></ div >
< h2 id = "building" > Building</ h2 >
< div class = "highlight" >< pre >< span ></ span >< code > git< span class = "w" > </ span > clone< span class = "w" > </ span > < repository-url>
< span class = "nb" > cd</ span >< span class = "w" > </ span > obikmer/src
cargo< span class = "w" > </ span > build< span class = "w" > </ span > --release
</ code ></ pre ></ div >
< p > The compiled binary is at < code > target/release/obikmer</ code > .</ p >
< h3 id = "building-on-hpc-clusters-network-filesystems" > Building on HPC clusters (network filesystems)</ h3 >
< p > 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).</ p >
< p >< strong > Always redirect the build directory to a local scratch disk:</ strong ></ p >
< div class = "highlight" >< pre >< span ></ span >< code >< span class = "nv" > CARGO_TARGET_DIR</ span >< span class = "o" > =</ span > /scratch/< span class = "nv" > $USER</ span > /cargo-target< span class = "w" > </ span > cargo< span class = "w" > </ span > build< span class = "w" > </ span > --release
</ code ></ pre ></ div >
< p > Adapt the path to the local scratch available on your cluster (< code > /var/tmp</ code > , < code > /tmp</ code > , < code > /scratch/local</ code > , etc.). Once built, copy the binary to a permanent location:</ p >
< div class = "highlight" >< pre >< span ></ span >< code > cp< span class = "w" > </ span > /scratch/< span class = "nv" > $USER</ span > /cargo-target/release/obikmer< span class = "w" > </ span > ~/bin/
</ code ></ pre ></ div >
< h2 id = "numa-support" > NUMA support</ h2 >
< p > 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:</ p >
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< ul >
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< li > macOS (Apple Silicon, unified memory)</ li >
< li > single-socket Linux machines</ li >
< li > any system where hwloc reports only one NUMA node</ li >
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</ ul >
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< h2 id = "verifying-the-installation" > Verifying the installation</ h2 >
< div class = "highlight" >< pre >< span ></ span >< code > obikmer< span class = "w" > </ span > --help
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