version

bwa-mem3 version prints the release version, the compiler that built the binary, the build’s compiled-in SIMD floor, the SIMD tier resolved at runtime, and (when mimalloc is compiled in) the mimalloc version. It is the canonical way to confirm which build is on PATH, what toolchain produced it, what host class it requires, and what kernel path it will dispatch to.

bwa-mem3 version always exits 0 — even on a host below the build’s SIMD floor — so operators can introspect a binary on a host that cannot actually run alignment. bwa-mem3 <subcommand> --help and -h share the same property.

Synopsis

v<MAJOR.MINOR>-<N>-g<COMMIT>
Compiler: <TOOLCHAIN> <VERSION>
SIMD floor: <FLOOR-TIER> (<HOST-CLASS>); kernels: <KERNEL-LIST>
SIMD runtime: <RUNTIME-TIER> (<FORCE-TIER-STATE>)
mimalloc 3.3.0 (active)

Common usage

Confirm the installed version, SIMD floor, and resolved tier:

./bwa-mem3 version

A typical run on an AVX-512BW host with the default BASELINE_ARCH=avx2 build prints (every line below goes to stdout; only the host-below-floor warning described further down goes to stderr):

v0.3.0-12-gabcdef1
Compiler: clang 19.1.7
SIMD floor: avx2 (x86-64-v3, Haswell 2013+); kernels: sse41 sse42 avx avx2 avx512bw
SIMD runtime: avx512bw (BWAMEM3_FORCE_TIER unset)
mimalloc 3.3.0 (active)

• version line — bwa-mem3’s release string, derived from git describe at build time and stored as PACKAGE_VERSION in the binary. When building from a tarball without git history, the fallback value is set via FG_LABS_VERSION_FALLBACK at compile time.
• Compiler: — the toolchain that compiled the binary, reported from the compiler’s own preprocessor macros: clang, gcc, icpx (Intel oneAPI), or icpc (Intel Classic). bwa-mem3 runs ~5–10% faster on x86 built with clang than with g++, so this line is how you confirm a production binary came from the recommended toolchain — see Best Practices → Build.
• SIMD floor: — the compile-time minimum the binary requires. Set by BASELINE_ARCH (default avx2) and listed alongside the per-tier kernel set the binary carries.
• SIMD runtime: — the tier resolved at startup by __builtin_cpu_supports (or BWAMEM3_FORCE_TIER if set in the environment). On arm64 this is always neon.
• mimalloc line — present only when USE_MIMALLOC=1 (the default). The parenthetical reports whether mimalloc is actually intercepting malloc/free — (active) when it is, (linked but NOT overriding malloc) when the binary merely links a libmimalloc that exports the mi_* API without installing the allocator override.

On a host below the SIMD floor, version also writes a [W::bwa-mem3] warning on stderr identifying the gap (and the alignment subcommands will refuse to run with exit code 2 — see Host requirements for the exit-2 message format and rebuild instructions).

Notes / Gotchas

Tip — version | grep is safe in CI

The whole banner — the version, Compiler:, SIMD floor:, SIMD runtime:, and mimalloc lines — goes to stdout; only the host-below-floor [W::bwa-mem3] warning goes to stderr. So bwa-mem3 version | grep '^SIMD' (or grep '^Compiler:' to assert the toolchain, grep '^mimalloc' to assert the allocator) works in CI scripts even on hosts that cannot run alignment. Use 2>/dev/null to suppress the warning line if you want stdout only.

Tip — No mimalloc line means USE_MIMALLOC=0

If no mimalloc line appears, the binary was built without the bundled allocator (make USE_MIMALLOC=0). See User Guide — Memory allocator (mimalloc) for when this is appropriate.

See also: User Guide — Memory allocator (mimalloc) · Developer Guide — Release process · Getting Started — Installation · What’s Different — Build & infrastructure