Environment variables¶
| Variable | Effect |
|---|---|
FIBERHMM_NO_UPDATE_CHECK |
Any non-empty value turns off the update reminder. Otherwise each command (except fiberhmm-consensus, fiberhmm-transfer and fiberhmm-nfr, which never check) looks up the latest release on PyPI at most once a day (1.5 s timeout, cached in $XDG_CACHE_HOME/fiberhmm/update_check.json, default ~/.cache/…) and prints a one-line reminder on stderr while a newer version exists. It never writes to stdout and never fails a run. |
FIBERHMM_MP_CONTEXT |
Worker start method: fork, spawn or forkserver. Default: spawn on Python ≥ 3.14, fork otherwise. Set spawn if workers crash with a segmentation fault. |
OPENBLAS_NUM_THREADS, MKL_NUM_THREADS, VECLIB_MAXIMUM_THREADS, OMP_NUM_THREADS |
BLAS threads. Consensus runs are reproducible to the last bit only with single-threaded BLAS; set OPENBLAS_NUM_THREADS=1 (or the equivalent for your BLAS) before starting. A run with multi-threaded BLAS warns and records the thread state in its manifest. |
NUMBA_CACHE_DIR |
Numba's own setting: where compiled kernels are cached. Useful when the installation directory is read-only or synchronized (Dropbox, network drives). Worker processes inherit it unchanged, so set it before starting a run to keep caches out of the installation; unset, numba caches beside the installed sources. |
PYTORCH_MPS_FAST_MATH |
With the [cuda] extra on Apple silicon, 1 disables the MPS backend of the staged engine's predictive kernels (fast math breaks their numerical check). |
XDG_CACHE_HOME |
Base directory of the update-check cache. |
FIBERHMM_DORADO |
fiberhmm-pipeline: the dorado program (or its install folder) when --dorado is not given. Searched before PATH and the usual install locations. |
FIBERHMM_DORADO_MODELS_DIR |
fiberhmm-pipeline: where dorado keeps downloaded models when --dorado-models-dir is not given. Default ~/.fiberhmm/dorado_models. |
FIBERHMM_MINIMAP2_INDEX_DIR |
fiberhmm-pipeline: where minimap2 reference indexes are cached. Default ~/.fiberhmm/minimap2_index. |
FIBERHMM_DEBUG |
Any non-empty value shows the full traceback for input errors (a missing path, a file that is not a readable BAM) instead of the one-line error: message with exit status 2. |
Internal: FIBERHMM_DAF_RUN_MASK and FIBERHMM_DAF_RUN_POLICY carry the
--daf-mask-runs / --daf-run-policy setting to worker processes, and
FIBERHMM_DAF_MASK_UNALIGNED carries --daf-mask-unaligned /
--no-daf-mask-unaligned. The CLI sets them; do not set them yourself (an
inherited run-mask value is reported as a warning).
For a clean test run from a copied or synchronized source tree, use fresh cache directories: