Struct ExtMemOpts 

#[non_exhaustive]
pub struct ExtMemOpts {
    pub max_context: usize,
    pub subproblem_count: usize,
    pub work_dir: PathBuf,
    pub physical_file_count: usize,
    pub ordered_phase4_emit: bool,
    pub lcp_memoization: LcpMemoizationPolicy,
    /* private fields */
}

Tunable options for build_ext_mem.

This structure is non-exhaustive so future releases can add options without repeatedly breaking callers that use struct literals. Start from Self::default or Self::from_env and use the builder methods.

Fields (Non-exhaustive)

Non-exhaustive structs could have additional fields added in future. Therefore, non-exhaustive structs cannot be constructed in external crates using the traditional Struct { .. } syntax; cannot be matched against without a wildcard ..; and struct update syntax will not work.

max_context: usize

Bound on suffix-comparison context. Comparisons equal through this many symbols are resolved by LimitProvider::boundary_order, so usize::MAX (the default) is required for ordinary full lexicographic ordering unless the caller deliberately wants truncated contexts.

subproblem_count: usize

Number of subarrays (p in upstream CaPS-SA). 0 (default) targets roughly 65,536 selected positions per subarray, clamped to at least one subarray per Rayon worker and at most 8,192 (and never above n).

work_dir: PathBuf

Directory for temp files. Defaults to std::env::temp_dir.

physical_file_count: usize

Number of physical files backing the final partition buckets. 0 (default) picks rayon::current_num_threads() — the right answer in practice: one writable inode per worker keeps kernel-level write contention bounded.

The p logical buckets (typically thousands at genome scale) collapse onto this pool of anonymous tempfiles via bucket_id % physical_file_count. Larger values lower kernel write contention; smaller values are kinder to networked filesystems with high metadata cost. The CAPS_SA_N_PHYS env var overrides this for one-off benches.

ordered_phase4_emit: bool

Use the bounded ordered phase-4 emitter instead of the default chunk collect-then-emit path. This can reduce transient merged partition residency on skewed workloads, but is slower on the GRCh38 32-thread benchmark because of channel coordination and backpressure, so it is opt-in.

lcp_memoization: LcpMemoizationPolicy

Policy for reusing exact long-LCP intervals during phase-4 partition merges. Disabled by default; callers with long repeated contexts can opt into LcpMemoizationPolicy::Geometric.

Implementations

impl ExtMemOpts

pub fn with_work_dir(work_dir: impl AsRef<Path>) -> Self

Convenience constructor with the supplied work_dir and defaults for everything else.

pub fn from_env() -> Self

Defaults plus caps-sa environment overrides.

Recognised variables:

• CAPS_SA_WORK_DIR / CAPS_SA_TMPDIR: temp-file directory
• CAPS_SA_SUBPROBLEMS: subarray count (p)
• CAPS_SA_N_PHYS: physical backing-file count
• CAPS_SA_MAX_CONTEXT: LCP comparison cap
• CAPS_SA_ORDERED_PHASE4=1|true|yes|on: bounded ordered phase-4 emit
• CAPS_SA_GEOMETRIC_MEMO=1|true|yes|on: geometric LCP memoization
• CAPS_SA_MEMO_PROBE: ordinary symbols compared before table lookup
• CAPS_SA_MEMO_MIN_LCP: minimum exact LCP admitted to the table
• CAPS_SA_MEMO_ACTIVATE_ENTRIES: entries learned before table lookup
• CAPS_SA_MEMO_CAPACITY: maximum entries per partition table
• CAPS_SA_MEMO_STATS=1|true|yes|on: detailed memoization counters

Invalid and zero-valued numeric overrides are ignored, preserving the corresponding defaults. Memoization tuning variables take effect only when CAPS_SA_GEOMETRIC_MEMO enables the policy.

pub fn max_context(self, max_context: usize) -> Self

Builder-style setter for Self::max_context.

pub fn subproblem_count(self, subproblem_count: usize) -> Self

Builder-style setter for Self::subproblem_count.

pub fn work_dir(self, work_dir: impl AsRef<Path>) -> Self

Builder-style setter for Self::work_dir.

pub fn physical_file_count(self, physical_file_count: usize) -> Self

Builder-style setter for Self::physical_file_count.

pub fn ordered_phase4_emit(self, ordered_phase4_emit: bool) -> Self

Builder-style setter for Self::ordered_phase4_emit.

pub fn lcp_memoization( self, lcp_memoization: impl Into<LcpMemoizationPolicy>, ) -> Self

Builder-style setter for Self::lcp_memoization.

Trait Implementations

impl Clone for ExtMemOpts

fn clone(&self) -> ExtMemOpts

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for ExtMemOpts

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for ExtMemOpts

fn default() -> Self

Returns the “default value” for a type.