Modernize standalone BLaDE runtime, prefix sums, and large-system support#10
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stanislc wants to merge 47 commits into
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Modernize standalone BLaDE runtime, prefix sums, and large-system support#10stanislc wants to merge 47 commits into
stanislc wants to merge 47 commits into
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- Added nprint parameter for controlling MINI> output frequency (default: 50) - Fixed SD damping to halve first, then scale by 2.4 on energy decrease - Added NaN/Inf energy detection with fatal error for both SD and SDFD - Added dxRMS cap at 10x initial value to prevent unbounded step growth - Added MINI> output showing step, energy, deltaE, and RMS gradient - Wrapped debug output with verbose > 1 checks for cleaner output
…ONS DIHE compatibility Dihedral restraints (originally from ChrispyYeh/BLaDE, PR RyanLeeHayes#5): - Added WIDTH field to DiRestPotential for flat-bottom harmonic potential - Based on CHARMM CDIH reference (default width=0 = pure harmonic) - Fixed bug: block field was not being copied to GPU CHARMM CONS DIHE compatibility fixes: - Periodic: changed n*phi - phi0 to n*(phi - phi0) - Harmonic: E = K*(phi-phi0)^2 without 0.5 factor (matches CHARMM) - Verified against CHARMM CONS DIHE calculated values Build system modernization: - CMakeLists.txt: Updated to CMake 3.18+ with native CUDA support
Options: - --double: Use double precision (default: float) - --gromacs: Use NMPS/GROMACS units (default: AKMA/CHARMM) - -j N, --jobs N: Parallel build jobs - --install [PREFIX]: Build and install - --reconfigure: Force CMake reconfiguration - --clean: Remove build directory - -h, --help: Show usage
- Add EElec enum (efswitch, epme, efshift) and EVdw enum (evswitch, evfswitch, evshift) - Change template dispatch from bool to int for 9 method combinations (3 elec × 3 VDW) - FSHIFT: Force-shifted electrostatics E = kqq*(1/r - 2/roff + r/roff²) - VSHIFT: Potential-shifted VDW with smooth energy cutoff - Update nbdirect.cu and pair.cu kernels with new method dispatch - Default: VFSWITCH + PME (backward compatible)
Includes reduction.h and scan.h with hierarchical Blelloch and Hillis-Steele algorithms. Uses preprocessor guards for CHARMM API compatibility (BLADE_STANDALONE for standalone builds).
Refactoring for code clarity: - Add msldEwaldType parameter to pair kernel - Explicit mode-specific lambda force calculation - Mode 0 (PMEL not specified) now works like Mode ON - Matches DOMDEC behavior in ebonded_domdec.F90
- Single Ctrl+C: sets interrupt flag for graceful stop - 3x rapid Ctrl+C: force immediate exit - API: blade_install/restore_signal_handler, blade_check_interrupt
- GPU-side detection with atomic flag - Reports first atom with invalid velocity - Helps identify simulation instabilities
- verbose=0: minimal output (default) - verbose=1: progress output (MINI> lines, setup messages) - verbose=2: debug output (detailed energy, gradient info) - blade_set_verbose() API for external control
- Remove deprecated eecats energy term - Add descriptive comments to energy enum - Add PNOE reference position fields (c0x, c0y, c0z) - Add is_pnoe flag for NOE restraint type
BLaDE declares blade_log() without implementing it. Consumers (standalone build, CHARMM) provide implementations.
Routes logging to stdout. Only compiled for standalone builds.
Use blade_log.h declaration instead. Core is now clean of platform-specific code.
When ON (default), includes blade_log.cpp for standalone builds. When OFF (submodule), consumer provides blade_log implementation.
Makes standalone build intent explicit in the cmake configuration.
Routes all output through blade_log API for CHARMM compatibility.
Memory allocation info is debug-level output.
Heuristic parameters are debug-level output, not normal progress.
PSF progress is normal-level output, shown with verbose >= 1.
- potential.cxx: Add back if (boRestCount>0), if (anRestCount>0), if (diRestCount>0) guards to prevent zero-size allocations - minimize.cu: Add stalled minimization detection with extra damping when energy is unchanged between steps - minimize.cu (SDFD): Add initial damping and dxRMS cap These fixes restore physics-correct behavior that was present in CHARMM's working version.
- Fix memory leak: add cudaFree(nanFlag_d) to State destructor - Fix NaN detection: change fprintf to fatal() to terminate on NaN/Inf - Set vdwMethod/elecMethod enums from API parameters - Add vdwmethod/elecmethod keywords for standalone input parsing - Update RUN PRINT output to show method names - Fix CMakeLists.txt comment: blade_log.cpp -> blade_log.cxx
Add per-block lambda control to the standalone BLaDE input script parser: - Allocate thetaFriction and blockFixed arrays in nblocks section - Propagate 'msld gamma' to per-block thetaFriction array - New 'msld friction <block> <value>' keyword for per-block friction - Extended 'msld fix' to accept block indices (e.g. 'msld fix 2 5') - Zero mass/velocity for fixed blocks in Msld::initialize() so the integrator skips those DOFs (isfinite(1/sqrt(0)) == false) - Add test_ffix.inp test case for RNaseH_peptide system
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Pull request overview
This PR syncs standalone BLaDE forward with reliability improvements, expanded parser/runtime controls, and multiple physics/kernel enhancements (PMEL/FSHIFT/VSHIFT, per-block friction, partial FFIX, NaN/Inf detection), along with a modernized standalone build flow.
Changes:
- Add platform-independent logging (
blade_log) and adjust verbosity behavior across setup/parser/runtime paths. - Extend dynamics/minimization/runtime robustness (Ctrl+C handling, NaN/Inf detection, minimization step-size behavior).
- Expand nonbonded / MSLD / domdec capabilities (VDW/ELEC method enums, PMEL handling, per-block friction & partial FFIX, scan helpers, dynamic partner-array growth).
Reviewed changes
Copilot reviewed 39 out of 39 changed files in this pull request and generated 8 comments.
Show a summary per file
| File | Description |
|---|---|
| test/ec2acc/input_test | Fix EC2ACC test input to explicitly specify PDB coordinate type. |
| test/RNaseH_peptide/blade/test_ffix.inp | Add standalone parser test for per-block friction + partial FFIX. |
| src/update/update.cu | Add NaN flagging in update kernels; per-lambda friction/noise usage. |
| src/update/rex.cxx | Route replica-exchange logs via blade_log. |
| src/update/pressure.cu | Reduce default verbosity and route pressure-coupling logs via blade_log. |
| src/update/minimize.cu | Refine minimization output/verbosity; NaN/Inf energy checks; adaptive step behavior. |
| src/system/system.cxx | Route system/help output via blade_log; update verbose help text. |
| src/system/structure.h | Extend structure APIs (PSF reader signature; NOE/DiRest signatures). |
| src/system/structure.cxx | Route structure parsing logs via blade_log; add NOE validation + PNOE params. |
| src/system/state.h | Add NaN-flag plumbing and per-lambda friction/noise pointers in LeapState. |
| src/system/state.cxx | Allocate/free NaN flag; build per-block friction/noise arrays; check NaN flag in recv_energy. |
| src/system/selections.cxx | Route selection logs via blade_log. |
| src/system/potential.h | Clarify energy term enum; extend NOE/DiRest structs (PNOE + flat-bottom width). |
| src/system/potential.cxx | Gate some logs by verbosity; guard allocations when restraint counts are zero; copy DiRest width. |
| src/system/parameters.cxx | Route parameter parsing/dump logs via blade_log; remove noisy debug print. |
| src/system/coordinates.cxx | Route coordinates help/NYI output via blade_log. |
| src/run/run.h | Add interrupt/scanalgorithm APIs; add EVdw/EElec enums; add minimization print frequency. |
| src/run/run.cu | Implement Ctrl+C flagging + public API; add scanalgorithm plumbing; route run output via blade_log. |
| src/restrain/restrain.cu | Add PNOE handling and r=0 guard in NOE; implement flat-bottom torsion width for DiRest. |
| src/nbdirect/nbdirect.cu | Replace boolean switching with VDW/ELEC method dispatch (3×3 combinations); add FSHIFT + VSHIFT support. |
| src/msld/msld.h | Add per-block theta friction and per-block fixed flags; add C API for both. |
| src/msld/msld.cu | Implement per-block friction/fixed blocks; partial FFIX parsing; update PMEL pair filtering; bias term mapping. |
| src/main/scan.h | Add multi-block scan utilities with selectable algorithm and workspace management. |
| src/main/reduction.h | Add multi-block reduction utilities for real/real3/real33 with workspace support. |
| src/main/defines.h | Add make_real3 helper macro for float/double builds. |
| src/main/blade_log.h | Introduce platform-independent logging API declaration (blade_log). |
| src/main/blade_log.cxx | Provide standalone blade_log implementation (stdout/fflush). |
| src/io/variables.cxx | Route variables output/debug through blade_log. |
| src/io/io.cxx | Route interpreter/energy display/fatal/file-open logging through blade_log. |
| src/io/control.cxx | Route if/while control-flow logs through blade_log. |
| src/domdec/domdec.h | Add overflow flag and partner-array reallocation hook for domdec culling. |
| src/domdec/domdec.cu | Allocate/free overflow flag; gate domdec diagnostic logs by verbosity. |
| src/domdec/cull.cu | Add overflow detection + retry growth for partner arrays; add reallocation helper. |
| src/domdec/assign_excl.cu | Route exclusion reallocation note via blade_log. |
| src/domdec/assign_blocks.cu | Add large-ndiv multi-block scan-based block-bound assignment path + scan benchmarking. |
| src/bonded/pair.cu | Extend pair kernels to method enums; add FSHIFT support; PMEL mode-specific nbex scaling/forces. |
| src/CMakeLists.txt | Modernize CMake/CUDA toolchain discovery; add BLADE_STANDALONE option; set CUDA arch list; link NVTX if available. |
| doc/MAIN.txt | Document partial FFIX form and run setvariable scanalgorithm. |
| Compile.sh | Replace environment-module build flow with portable CMake build script + options. |
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Summary
This draft PR collects the standalone BLaDE updates from
stanislc/BLaDEthat are ahead ofRyanLeeHayes/BLaDE:master.Main changes include:
BLADE_STANDALONEandCompile.shoptions for precision, units, install, clean, and reconfigureblade_logand verbosity controls, then route setup/runtime output through the logging APIMINI>progress outputvdwmethod/elecmethodcontrolsValidation
rtk ./Compile.sh -j 8rtk git diff --check upstream/master..HEAD6727200ongpu2080/gollum154: completed with exit0:06727201ongpu2080/gollum154: completed with exit0:0Notes
This PR intentionally targets only the standalone BLaDE repository. CHARMM integration-specific differences are not included here.