Proceedings 2023 ESPResSo meetings

Proceedings of the 2023 ESPResSo meetings

2023-12-05

Coding day progress report

• LB particle coupling bugfix ready for merge
• electrode tutorial bugfix was merged
• cluster analysis work is still in progress
• center-of-mass virtual site feature works on 1 core, MPI parallelization is still needed
• removal of the Particle struct from P3M to make P3M a self-contained library: progress blocked by undefined symbols
• thermostat global variables refactoring is blocked by integrators refactoring

2023-11-14

Machine learning tutorial

• atomistic simulation are not the main target of ESPResSo
• fit a potential to a coarse-grained polyelectrolyte to model solvent interactions and polymer dynamics
• consider coupling to IPSuite
• system of interest: polymer melts, such as alkane chains, possibly polyacrylic acid or polystyrene sulfonate chains

Dropping support for Jupyter Classic

• migrate ESPResSo tutorials to JupyterLab

2023-10-24

Global variables progress report

• next refactoring milestone in #4816
• prototype supports multiple ESPResSo systems in the same simulation scripts
  • prototype available in jngrad/multiverse
  • long-range algorithms are not yet ready for multi-system simulations

Summer school wrap-up

• For next time:
  • organize community meeting fully remote and outside the summer school
  • defer BBQ for 30 min to improve poster session experience
  • switch from hybrid back to onsite due to low online participation
    • some lectures might still be recorded for the YouTube channel

Next coding day

• circa November

2023-09-12

HPC benchmark results

• ESPResSo 4.2.1 was benchmarked on HPC Vega up to 1024 cores
• benchmark report due end of September
• the FFT algorithms on CPU and GPU lose a lot of performance when the simulation box is not cubic
  • relevant to ELC simulations, where a gap space is needed in the z-direction
  • relevant to P3M simulations that use more than 1 MPI rank

Global variables progress report

• the box geometry and cell structure are now part of the System class in the core
• most MPI callbacks were removed from the core
• script interface of non-bonded interactions needs a rewrite

Summer school preparations

• we have a CIP pool test account and a Zoom workstation
  • ESPResSo is in ~/Documents/espresso/build
  • can run pypresso or ipypresso from any location
  • tutorial alias: moves to the tutorial folder and starts Jupyter
  • soltut alias: moves to the solutions and starts Jupyter

2023-08-22

ELC tutorial

• simulation is still too slow
• ELC part is complete
• ELCIC is still a work in progress

Ekin tutorial

• 50% complete

Coding sprint results

• LB/EK refactor: lb and ekcontainer are now members of the System class, the system.actors list was removed
• the LB collide-then-stream ("push scheme") was switched to stream-then-collide ("pull scheme"), which can be coalesced into a single kernel, but then boundary conditions must be completely rewritten
• ghost force reduction: remove synchronization barrier by computing the forces twice, instead of accumulating the forces on ghost particles and communicating them at every time step; add a particle flag to switch this behavior, since not all algorithms can avoid a ghost force reduction
• GCMC tutorial: pretty much done
• split non-bonded interactions in 3 kernels for central forces, non-symmetric forces and Coulomb-based forces: the goal is to speed-up short-range force calculations using a new memory layout
• P3M and other long-range interactions are being rewritten to take particle property arrays instead of an array of particles
• investigate zero-centered LB (PDFs with subtracted background rho_0) for faster kernels
• fine-grained events for reaction methods: reduce amount of calls to on_particle_change in the reaction methods, and split on_particle_change into more specialized event to avoid reconstructing the cell system upon trivial particle changes
• center of mass virtual sites: issues with implementation in the core

2023-07-11

Removing global variables

• approx. 90 global variables remain, which are an issue for machine learning and parallel tempering
• electrostatics and magnetostatics actors will soon be members of the System class instead of going to the actors list (#4749)
• lb will follow next (depends on another PR)
• in total, 8 global variables will be removed

Here is the proposed new syntax:

system.magnetostatics.solver = espressomd.magnetostatics.DipolarDirectSumCpu(...)
system.electrostatics.solver = espressomd.electrostatics.P3M(...)
system.electrostatics.extension = espressomd.electrostatic_extensions.ICC(...)
system.ekcontainer.solver = espressomd.electrokinetics.EKFFT(...)
system.ekcontainer.add(espressomd.electrokinetics.EKSpecies(...))
system.lb.set(espressomd.lb.LBFluidWalberla(...))

system.electrostatics.clear()
system.magnetostatics.clear()
system.ekcontainer.clear()
system.ekcontainer.solver = None
system.lb.clear()

Status of parallel observables

• instead of communicating all particles to MPI rank 0 and then extract the quantity of interest, extract the quantity on each rank and communicate the buffer
• for reductions like weighted sums, do a partial reduction on each rank and a final reduction across all ranks

Status of the new tutorials

• advection-diffusion-reaction tutorial: started
• capacitor plate tutorial: ELCICC setup is in progress
  • the goal is calculate the force on an ion between two charged plates with ICC, and then measure the capacitance

2023-06-13

Removing global variables

• tracking ticket: #2628
• the ESPResSo global variables are causing a lot of issue with integration of new features
  • GPU LB for example is blocked because the GPU primary context expires before the device memory is deallocated, causing a runtime crash at the end of a simulation
  • machine-learning projects are stalled because the state of an ESPResSo system cannot be reset, and restarting a Python kernel is not feasible on clusters where kernels are tied to allocated slurm jobs
• a C++ System class will be introduced to collect some of the global state of ESPRessSo into the espressomd.system.System class (#4741)

Coding day progress report

• swimmers
  • per-particle gamma for Langevin/Brownian/lattice-Boltmann was added (#4743)
    • per-particle anisotropic gamma with rotation is unclear in LB: how to do point-coupling of torques in LB?
  • swimmers will be re-implemented as virtual sites (RudolfWeeber/espresso#61)
    • pre-requisite for GPU LB
• observables
  • currently, with particle-based observables, we need to communicate the entire particle information to MPI rank 0, and then the relevant property is extracted, which leads to a communication bottleneck
  • the relevant property could be evaluated on the local MPI ranks, and the result could be sent in a much more compact buffer to MPI rank 0
• center of mass virtual site
  • virtual site that tracks the center of a collection of particles, to help redistribute forces e.g. from umbrella sampling
• new feature: particle dipole field calculation (#4626)
• consider running coding days over 3 days to maximize productivity outside the lecture period
• everyone: cleanup ICP wiki pages, especially about ESPResSo to better find the resources we provide to get started developing

2023-05-23

waLBerla progress report

• the waLBerla implementations of EK/LB are now part of the development branch of ESPResSo
• still missing: forces on boundaries, EK thermalization, GPU LB
• GPU LB:
  • currently each MPI rank manages its pdfs field on device memory
  • one could instantiate a single entire field on the device and only communicate particle data with MPI rank 0
  • particle coupling needs to be rewritten as GPU kernels

Coding day progress report

• LB pressure tensor: awaiting review
• LB shear profile regression is no longer affecting the current waLBerla LB implementation
• EK thermalization: RNG and kernels mostly ready, new RNG class was needed in the codegen script
• removing particle ranges from P3M: goal is to rewrite kernels to take position and charge iterators, and return forces
• parallel observables: currently the observables are only calculated on MPI rank 0 and require a full copy of all particles; the parallel version should run the kernel in parallel on the local particles and reduce the results to MPI rank 0
• remove code duplication in the Langevin and LB friction coupling, such that anisotropic particles can be coupled in LB
• implement virtual particle type that tracks the center of mass of a collection of particles to help distribute a force on all particles from that collection, e.g. for umbrella sampling
• Lees-Edwards particle coupling: the position and velocity offsets need to be interpolated in the shear boundary

multiXscale project

• main objectives for ESPResSo:
  • use high-performance code
  • write GPU-enabled lattice-based algorithms
  • write demonstrator using batteries physics

2023-03-21

4.2.1 bugfix release

• release notes and PR
• tasks:
  • checkpointing (Mariano, Ingo, David)
  • Brownian and Langevin dynamics (Christoph, Chinmay)
  • reaction method bugfixes (Pablo, Keerthi, David)
  • active matter tutorial (Somesh)
  • visualizer: arrow materials, collision detection (Ingo)
  • LB GPU (Alex)
• investigate Lees-Edwards effects on cluster analysis, fractal dimension, polymer observables (JN)

waLBerla GPU progress report

• branch: jngrad/espresso@walberla_cuda
• LBWalberlaImpl class rewritten to instantiate CUDA fields instead of CPU fields
• all LB setters and getters pass the tests, macroscopic accessors are 100% CUDA code
• particle coupling and LB boundaries are implemented
• VTK writers not yet implemented
• needs performance improvements

2023-02-06

waLBerla integration progress report

• checkpointing now works in parallel
• thermalized electrokinetics is not ready yet
• GPU LB is not ready yet (custom interface needs to be written)

Monte Carlo Python re-implementation

• MC methods were rewritten as Python code by Pablo
• overhead from MPI callbacks in the hot loop (make_reaction_attempt)
• priority is to be able to write the acceptance probability in Python

2023-01-17

Build system changes

• the custom GPU detection code was replaced with native CUDA support from CMake 3.22 (#4642)
• specify the CUDA compiler and toolkit with CUDACXX=/path/to/nvcc cmake .. -D CUDAToolkit_ROOT=/path/to/toolkit

Upcoming 4.2.1 bugfix release

• bugs with high severity:
  • broken checkpointing: LB boundaries, particle director and dipole moment
  • broken reactions when using concurrent reactions that delete particles
  • broken configurational moves in reactions
  • broken Brownian integration of fixed particles
• draft release notes: 4.2.1

Multiscale proposal

• contributions to community codes: LAMMPS, ESPResSo, waLBerla, kinetic lattice models
• deliverables:
  • filesystem-based environments containing dependencies tailored for HPC (EESSI)
  • waLBerla-ESPResSo integration including CUDA kernels
  • refactoring electrostatics algorithms (e.g. replacing MPI FFT by shared memory FFT)

waLBerla integration

• ESPResSo is still missing the CUDA setters and getters (populations, density, etc.)
• ekin checkpointing is a work in progress

Coding day

• planned for mid-February