Issues

• Generated models (#1306): a floor/round/trunc law's answer depends on the output grid at rtol 1e-8, by up to 1e3x the tolerance; one fails at rtol 1e-12

  lanl/bngsim#1342 · Filter by author Montana opened on Oct 27, 2026

• sbml: reversing listOfSpecies makes MODEL1812040005 fail (P below 0, a*P^z NaN) where the order written runs; RoadRunner runs both

  lanl/bngsim#1340 · Filter by author Montana opened on Oct 27, 2026

• A step across a pole of the right-hand side returns a trajectory where no solution exists

  correctness concern
  lanl/bngsim#1339 · Filter by author wshlavacek opened on Oct 27, 2026

• Tests: KINSOL's and the steady-state march's difference quotients on a jump, and SUNDIALS other than 7.2, are not covered

  family: steady statetesting
  lanl/bngsim#1335 · Filter by author wshlavacek opened on Oct 27, 2026

• Performance: the step of the solvers' own difference quotients, and #1302's +4–36% wall on the fd path (Step 4 of #1002)

  family: steady stateperformance
  lanl/bngsim#1333 · Filter by author wshlavacek opened on Oct 27, 2026

• Forward sensitivity at a parameter that sits on a kink of a rate law returns one side's slope or neither (dX*/dq = 0 for ±47.6), with no error

  bugcorrectness concernfamily: sensitivity terms
  lanl/bngsim#1332 · Filter by author wshlavacek opened on Oct 27, 2026

• A run that slides along a moving threshold is wrong with no error on a differenced Jacobian (X(40) = 19.7 for 25), and times out on the closed form

  bugcorrectness concern
  lanl/bngsim#1331 · Filter by author wshlavacek opened on Oct 27, 2026

• A differenced Jacobian can be wrong at every step a check takes: take exact derivatives where there is no closed form (Step 3 of #1002)

  bugcorrectness concernfamily: steady state
  lanl/bngsim#1330 · Filter by author wshlavacek opened on Oct 27, 2026
  1

• A failed NFsim load leaves the host process in the XML's directory: create_system() changes the cwd and an exception from initializeFromXML skips the restore. The stream swap and global RNG reseed also need to be explicit and contained

  bug
  lanl/bngsim#1314 · Filter by author wshlavacek opened on Oct 27, 2026

• Typed exceptions for "no sparse Jacobian for KLU" and "codegen declined this model"

  enhancement
  lanl/bngsim#1313 · Filter by author wshlavacek opened on Oct 27, 2026

• differential: NFsim (nf_reject) against RuleMonkey (nf_exact) in distribution

  enhancementgatedtesting
  lanl/bngsim#1312 · Filter by author wshlavacek opened on Oct 27, 2026

• differential: steady_state() against a long run to equilibrium

  enhancementgatedtesting
  lanl/bngsim#1311 · Filter by author wshlavacek opened on Oct 27, 2026

• differential: SSA with compiled propensities against interpreted ones, seed for seed

  enhancementgatedtesting
  lanl/bngsim#1310 · Filter by author wshlavacek opened on Oct 27, 2026

• differential: attribute a disagreement with a third arm, and flag answers that flip with the grid or tolerance

  enhancementgatedtesting
  lanl/bngsim#1309 · Filter by author wshlavacek opened on Oct 27, 2026

• differential: the analytic Jacobian's values against differences of the right-hand side, not only its pattern

  enhancementgatedtesting
  lanl/bngsim#1308 · Filter by author wshlavacek opened on Oct 27, 2026

• differential: state-leak checks: a restarted run, a reused Model or Simulator, and a batch against fresh serial runs

  enhancementgatedtesting
  lanl/bngsim#1307 · Filter by author wshlavacek opened on Oct 27, 2026

• differential: generate models (random networks and rate laws) and shrink each finding to a minimal reproducer

  enhancementgatedtesting
  lanl/bngsim#1306 · Filter by author wshlavacek opened on Oct 27, 2026

• differential: metamorphic transforms of the model, the check a shared loader cannot fail together

  enhancementgatedtesting
  lanl/bngsim#1305 · Filter by author wshlavacek opened on Oct 27, 2026

• BIOMD0000000338 and 339: KLU and the dense solver take different branches past a step-size collapse (Fg 311 on KLU, 0.73 on dense and libRoadRunner)

  bugcorrectness concern
  lanl/bngsim#1304 · Filter by author wshlavacek opened on Oct 27, 2026
  1

• sens: after a sensitivity-RHS refusal, the output loop reads the integrator outside its step (one read on a solver at t = 2.6e-312)

  lanl/bngsim#1301 · Filter by author Montana opened on Oct 27, 2026

• A sensitivity run's state departs from a converged plain run by 0.9% on MODEL2001200002 (no events), and does not converge onto it at 100x tighter tolerances

  lanl/bngsim#1298 · Filter by author Montana opened on Oct 26, 2026
  1

• BIOMD0000000810 asked for 8x the output points returns 5.3e7 of its trajectory's peak off the converged run, with no error

  lanl/bngsim#1297 · Filter by author Montana opened on Oct 26, 2026
  2

• jacobian="fd" alone is refused, telling the caller to drop force_sparse_linear_solver, which they never set: the automatic routing picked KLU, and the pattern has nothing to color

  lanl/bngsim#1296 · Filter by author Montana opened on Oct 26, 2026

• deps: move the uv.lock pins to antimony 3.2.1 and libroadrunner 2.11.0, after evaluating what each upgrade changes

  enhancementtesting
  lanl/bngsim#1288 · Filter by author wshlavacek opened on Oct 26, 2026

• A smooth narrow pulse (a Gaussian or sech² in a clock) is stepped over: Y = 0 for 2.212 at every tolerance, with no warning

  bugcorrectness concern
  lanl/bngsim#1286 · Filter by author wshlavacek opened on Oct 25, 2026
  1