mmml health-check¶
Validate MMML/PyCHARMM/JAX interface health.
Usage¶
mmml health-check --help
Options¶
usage: mmml health-check [-h] [--only CHECK [CHECK ...]]
[--skip CHECK [CHECK ...]] [--live]
[--checkpoint CHECKPOINT] [--live-residue LIVE_RESIDUE]
[--live-n-molecules LIVE_N_MOLECULES] [--require-gpu]
[--json] [--strict] [--prelaunch] [--tier2]
Validate MMML interface health before PyCHARMM / MLpot jobs: imports, JAX
devices, libcharmm, MLpot symbols, Packmol, checkpoint, MPI.
Input & configuration:
--checkpoint CHECKPOINT
PhysNet checkpoint (default: MMML_CKPT).
--live-residue LIVE_RESIDUE
Residue for --live smoke (default: DCM).
Output & artifacts:
--json Emit machine-readable JSON.
Diagnostics & safety:
-h, --help show this help message and exit
--strict Treat warnings as errors.
Other options:
--only CHECK [CHECK ...]
Run subset of: core, jax, charmm, mlpot, packmol,
checkpoint, mpi, live
--skip CHECK [CHECK ...]
Skip checks from the default set.
--live Run live MLpot registration + CHARMM energy (implies
charmm + checkpoint).
--live-n-molecules LIVE_N_MOLECULES
Monomer count for --live smoke (default: 2).
--require-gpu Fail if JAX does not see a CUDA device.
--prelaunch Relax MPI prelaunch warnings (serial health-check before
mpirun).
--tier2 Also run spatial-MPI GPU checks inside the mpi section.
Examples: # Fast preflight on a GPU node (no CHARMM energy eval): mmml health-
check --require-gpu # Under the MPI launcher (recommended on MPI-linked
libcharmm): MMML_MPI_NP=1 ./scripts/mmml-charmm-mpirun.sh health-check
--require-gpu --strict # Include live MLpot registration + CHARMM ENER on DCM:2:
MMML_MPI_NP=1 ./scripts/mmml-charmm-mpirun.sh health-check --live --checkpoint
"$MMML_CKPT" # Smallest liquid-DCM density smoke (after modules + CHARMM build):
mmml liquid-box --composition DCM:20 --target-density-g-cm3 1.326 \ --profile
standard -o boxes/dcm20 --charmm-sd-steps 50 --charmm-abnr-steps 50
MMML_MPI_NP=1 ./scripts/mmml-charmm-mpirun.sh md-system \ --from-psf
boxes/dcm20/model.psf --from-crd boxes/dcm20/model.crd \ --checkpoint
"$MMML_CKPT" --md-stages mini --mini-nstep 20 --no-echeck --quiet Checks: core,
jax, charmm, mlpot, packmol, checkpoint, mpi (+ live with --live).