Eric Coissac
5c1584967f
The command now supports reopening existing indexes instead of failing when the output file exists. Control flow branches between opening an existing index and constructing a new one, moving configuration setup exclusively to the creation path. Directory existence is enforced upfront with proper I/O error propagation. The --force flag retains its original semantics by removing the target directory before proceeding with a fresh build.
1681 lines
30 KiB
HTML
1681 lines
30 KiB
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DNA encoding
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Partitioning architecture
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Central-position SNP distance (discussion)
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SuperKmer
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Kmer
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Chunk reader
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obipipeline library
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Evidence elimination (discussion)
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obikindex layer tier
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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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<span class="md-ellipsis">
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Kmer filtering
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Select command
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<span class="md-ellipsis">
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obitaxonomy crate
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</span>
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<span class="md-ellipsis">
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Benchmark: query-path testing
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</a>
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Partition and layer caching (discussion)
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NUMA-aware worker pools
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NUMA-aware partition runner
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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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<a href="#macos" class="md-nav__link">
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macOS
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Building
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<span class="md-ellipsis">
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Building on HPC clusters (network filesystems)
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</a>
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</li>
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</ul>
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<li class="md-nav__item">
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<a href="#numa-support" class="md-nav__link">
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<span class="md-ellipsis">
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NUMA support
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="#verifying-the-installation" class="md-nav__link">
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<span class="md-ellipsis">
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Verifying the installation
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</a>
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</li>
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</ul>
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</nav>
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</div>
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</div>
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</div>
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<div class="md-content" data-md-component="content">
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<article class="md-content__inner md-typeset">
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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
|
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rustup<span class="w"> </span>update<span class="w"> </span>stable
|
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</code></pre></div>
|
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<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>
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<h4 id="linux-debianubuntu">Linux (Debian/Ubuntu)</h4>
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<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
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</code></pre></div>
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<h4 id="linux-rhelrockyalmalinux">Linux (RHEL/Rocky/AlmaLinux)</h4>
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<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>
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<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>
|
|
<ul>
|
|
<li>macOS (Apple Silicon, unified memory)</li>
|
|
<li>single-socket Linux machines</li>
|
|
<li>any system where hwloc reports only one NUMA node</li>
|
|
</ul>
|
|
<h2 id="verifying-the-installation">Verifying the installation</h2>
|
|
<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>--help
|
|
</code></pre></div>
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