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* Work-Around: Segfault in MPI_Init with HIP
See:
https://docs.olcf.ornl.gov/systems/crusher_quick_start_guide.html#olcfdev-1655-occasional-seg-fault-during-mpi-init
* Move to ABLASTR
All that counts is that HIP is initialized before GPU-aware MPI.
* Add Exception
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In the spirit of a recent nvcc compiler bug, simplify the capture
logic from implicit to explicit for the particle filter lambda.
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* Remove AddToMultiFabMap functions from WarpX class
* fixed bug
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* Frontier (OLCF): MPI_Waitall issues
Document to use `export MPICH_SMP_SINGLE_COPY_MODE=NONE` in job scripts.
According to earlier attempts by Marco, this might not yet solve the issue,
but it is the documented workaround from the OLCF side so far, so we
should add it for now.
* Comments in LUMI Submission Template
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* Doc: HPC Python Separate
Currently, due to global variables used in AMReX to store implicit
state instead of using handlers, we cannot build shared libraries
for Python (pyAMReX + pyWarpX + pyImpactX) with a *static*
`libamrex_Nd.a`. Thus, we automatically build a shared AMReX
library in our superbuild the moment that we need Python bindings.
That can confuse people that just use the C++ application with
AMReX inputs files, which then also depends on this shared AMReX
library (which also needs to be copied around, for instance).
This update the HPC docs to just build App and bindings twice
(twice the time spent), to work around this current limitation
of AMReX.
* Apply suggestions from code review
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* Apply suggestions from code review
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* Docs: Update other cluster descriptions as well.
* Install Dependencies: `git fetch --prune`
Fix an issue first seen in blaspp/lapackpp where fetch
failed because an unused remote branch was gone.
---------
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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Add constant record components for position and positionOffset
in 1D3V and 2D3V simulations.
Follows our conventions in
https://warpx.readthedocs.io/en/latest/developers/dimensionality.html#conventions
and simplifies post-processing, e.g., emittance calculations.
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* Fix: WarpX Version
Fix the WarpX version info.
* Fix Version: pyWarpX
* Version: More Python __version__
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* CI: Shrink NVHPC Size
Try to shrink the size occupied in the NVHPC CI runs. Currently
running out-of-disk...
* NVHPC: Thin out Install
- remove profilers (big)
- remove static libs (big)
- remove examples (small)
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* Fix Repeated Plasma Lens: Start
The current implementation has problems finding the right
index of the current plasma lens if:
- the lens started before z=0
- the lens did not start between z=0...first-period
This should fix it.
* Document Start, Define an End
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* BTD RZ test: add missing checksum analysis
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* BoxArray in BTD has single box
* cleaning to remove all instances of max_box_size
* Assert BA size to be 1 for BTD and fix an inline comment
* fix typo
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Accidentially now always built AMReX was shared library,
which is only needed if we build with Python.
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* Remove unused/untested Python file
* Remove additional file
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Because breathe is not yet ready.
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Add an include guard to this header file.
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Frontier uses a Low-noise Mode Layout for its nodes which pins system
processes via the default core specification `-S 8` to the first core
every L3 region.
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(#4116)
* include current density in diagnostic output even if an electromagnetic solver is not used
* do not redeposit current for the magnetostatic solver
* update CI benchmarks for tests that previously did not register current density
* fix remaining failing CI test
* Apply suggestions from code review
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* do not output current density in collision tests
* update `JFunctor` constructor doc-string
* code cleanup - reduce code duplication
* specify `Ex Ey Ez Bx By Bz` fields to plot for collision CI tests
* specify `Er Et Ez Br Bt Bz` as output for rz collision test
* rename `InterpolateToDst` to `InterpolateMFForDiag`
* only deposit current density once per diagnostic output (if not already deposited)
* write deposited current for all directions into `current_fp` during diagnostic step deposition
* use `amrex::make_alias` to directly deposit current density into `warpx.current_fp` during diagnostic step deposition
* add class variable `solver_deposits_current` to `FullDiagnostics` so that there is only one place where the determination is made whether current should be deposited during diagnostic output
* correct logic to determine `m_solver_deposits_current`
---------
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* Fix: Remove Overly Exported Classes
Luckily, many of them should not contain global state.
* Add Missing WarpX.H Include
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* added nodal electrostatic solver
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* sphere test for electrostatic nodal solver
* add 3d single bunch test
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* adds single bunch ci test
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* updated tests
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* updated checksums nodal electrostatic
* Improve readability
* Change `assert` condition
* Clean up
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* Implement boosted frame automated test (1D)
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Implement boosted frame automated test (1D)
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* time_chunk_size=50
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* Extensive clean up of PlasmaInjection
* Small cleanup of parseMomentum
* Fix string argument reference
* Remove unneeded surface_flux
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* Update Python installation instructions on HPC
* Update Python installation instructions on HPC
---------
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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We use too many cores when we compile and thus get our compile
processes killed by the system. Let's use a bit less to stay
in the limits.
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updates:
- [github.com/Lucas-C/pre-commit-hooks: v1.5.3 → v1.5.4](https://github.com/Lucas-C/pre-commit-hooks/compare/v1.5.3...v1.5.4)
- [github.com/hadialqattan/pycln: v2.2.1 → v2.2.2](https://github.com/hadialqattan/pycln/compare/v2.2.1...v2.2.2)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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(#4153)
* added guidelines
* added impose t_lab from file as an option
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* removed unused comment
* fixed unconsistent variable type
* removed space
* rearranged code changes
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Python 3.7 went EOL last month. Time to bump up our supported
versions to 3.8+ as well.
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* Clang-tidy: add more misc-* checks to clang-tidy CI test
* address issues found with clang-tidy
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* pyAMReX: Build System
* CI Updates (Changed Options)
* Callback modernization (#4)
* refactor callbacks.py
* added binding code in `pyWarpX.cpp` to add or remove keys from the callback dictionary
* minor PR cleanups
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Added Python level reference to fetch the multifabs (#3)
* pyAMReX: Build System
* Added Python level reference to Ex_aux
* Now uses the multifab map
* Fix typo
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Add initialization and finalize routines (#5)
A basic PICMI input file will now run to completion.
* Regression Tests: WarpX_PYTHON=ON
* Update Imports to nD pyAMReX
* IPO/LTO Control
Although pybind11 relies heavily on IPO/LTO to create low-latency,
small-binary bindings, some compilers will have troubles with that.
Thus, we add a compile-time option to optionally disable it when
needed.
* Fix: Link Legacy WarpXWrappers.cpp
* Wrap WarpX instance and start multi particle container
* Fix test Python_pass_mpi_comm
* Start wrapper for multiparticle container
* Add return policy
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update fields to use MultiFabs directly
Remove EOL white space
Removed old routines accessing MultiFabs
Update to use "node_centered"
* Fix compilation with Python
* Update fields.py to use modified MultiFab tag names
* Remove incorrect, unused code
* Add function to extract the WarpX MultiParticleContainer
* Complete class WarpXParticleContainer
* Wrap functions getNprocs / getMyProc
* restore `install___` callback API - could remove later if we want but should maintain backward compatibility for now
* add `gett_new` and `getistep` functions wrappers; fix typos in `callbacks.py`; avoid error in getting `rho` from `fields.py`
* Update callback call and `getNproc`/`getMyProc` function
* Replace function add_n_particles
* Fix setitem in fields.py for 1d and 2d
* also update `gett_new()` in `_libwarpx.py` in case we want to keep that API
* added binding for `WarpXParIter` - needed to port `libwarpx.depositChargeDensity()` which is an ongoing effort
* Wrap function num_real_comp
* added binding for `TotalNumberOfParticles` and continue progress on enabling 1d MCC test to run
* add `SyncRho()` binding and create helper function in `libwarpx.depositChargeDensity` to manage scope of the particle iter
* Clean up issues in fields.py
* update bindings for `get_particle_structs`
* Fix setitem in fields.py
* switch order of initialization for particle container and particle iterator
* switch deposit_charge loop to C++ code; bind `ApplyInverseVolumeScalingToChargeDensity`
* move `WarpXParticleContainer.cpp` and `MultiParticleContainer.cpp` to new Particles folder
* added binding for `ParticleBoundaryBuffer`
* More fixes for fields.py
* Fix: Backtraces from Python
Add the Python executable name with an absolute path, so backtraces
in AMReX work. See linked AMReX issue for details.
* Cleaning
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Fix: Backtraces from Python Part II
Do not add Python script name - it confuses the AMReX ParmParser to
build its table.
* Fix: CMake Dependencies for Wheel
This fixes a racecondition during `pip_install`: it was possible
that not all dimensions where yet build from pybind before we
start packing them in the wheel for pip install.
* MCC Test: Install Callbacks before Run
Otherwise hangs in aquiring the gil during shutdown.
* addition of `Python/pywarpx/particle_containers.py` and various associated bindings
* Fix: CMake Superbuild w/ Shared AMReX
We MUST build AMReX as a shared (so/dll/dylib) library, otherwise
all the global state in it will cause split-brain situations, where
our Python modules operate on different stacks.
* add `clear_all()` to callbacks in order to remove all callbacks at finalize
* add `-DWarpX_PYTHON=ON` to CI tests that failed to build
* add `get_comp_index` and continue to port particle data bindings
* Add AMReX Module as `libwarpx_so.amr`
Attribute to pass through the already loaded AMReX module with the
matching dimensionality to the simulation.
* Fix for fields accounting for guard cells
* Fix handling of ghost cells in fields
* Update & Test: Particle Boundary Scraping
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* CI: Python Updates
- modernize Python setups
- drop CUDA 11.0 for good and go 11.3+ as documented already
```
Error #3246: Internal Compiler Error (codegen): "there was an error in verifying the lgenfe output!"
```
* CI: Python Updates (chmod)
* Add support for cupy in fields.py
* Add MultiFab reduction routines
* CI: CUDA 11.3 is <= Ubuntu 20.04
* changed `AddNParticles` to take `amrex::Vector` arguments
* setup.py: WarpX_PYTHON=ON
* update various 2d and rz tests with new APIs
* add `-DWarpX_PYTHON_IPO=OFF` to compile string for 2d and 3d Python CI tests to speed up linking
* CI: -DpyAMReX_IPO=OFF
* CI: -DpyAMReX_IPO=OFF
actually adding `=OFF`
* CI: Intel Python
* CI: macOS Python Executable
Ensure we always use the same `python3` executable, as specified
by the `PATH` priority.
* CMake: Python Multi-Config Build
Add support for multi-config generators, especially on Windows.
* __init__.py: Windows DLL Support
Python 3.8+ on Windows: DLL search paths for dependent
shared libraries
Refs.:
- https://github.com/python/cpython/issues/80266
- https://docs.python.org/3.8/library/os.html#os.add_dll_directory
* CI: pywarpx Update
our setup.py cannot install pyamrex yet as a dependency.
* ABLASTR: `ablastr/export.H`
Add a new header to export public globals that are not covered by
`WINDOWS_EXPORT_ALL_SYMBOLS`.
https://stackoverflow.com/questions/54560832/cmake-windows-export-all-symbols-does-not-cover-global-variables/54568678#54568678
* WarpX: EXPORT Globals in `.dll` files
WarpX still uses a lot of globals:
- `static` member variables
- `extern` global variables
These globals cannot be auto-exported with CMake's
`WINDOWS_EXPORT_ALL_SYMBOLS` helper and thus we need to mark them
manually for DLL export (and import) via the new ABLASTR
`ablastr/export.H` helper macros.
This starts to export symbols in the:
- WarpX and particle container classes
- callback hook database map
- ES solver
* CI: pywarpx Clang CXXFLAGS Down
Move CXXFLAGS (`-Werror ...`) down until deps are installed.
* GNUmake: Generate `ablastr/export.H`
* CMake: More Symbol Exports for Windows
* `WarpX-tests.ini`: Simplify Python no-IPO
Also avoids subtle differences in compilation that increase
compile time.
* Update PICMI_inputs_EB_API.py for embedded_boundary_python_API CI test
* Fix Python_magnetostatic_eb_3d
* Update: Python_restart_runtime_components
New Python APIs
* Windows: no dllimport for now
* CI: Skip `PYINSTALLOPTIONS` For Now
* CMake: Dependency Bump Min-Versions
for external packages picked up by `find_package`.
* Fix F and G_fp names in fields.py
* Tests: Disable `Python_pass_mpi_comm`
* Wrappers: Cleanup
* pyWarpX: Include Cleaning
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* fields.py: Fix F and G Wrappers
Correct MultiFab names (w/o components).
* Remove unused in fields.py
* Windows: New Export Headers
- ABLASTR: `ablastr/export.H`
- WarpX: `Utils/export.H`
* removed `WarpInterface.py` since that functionality is now in `particle_containers.py`; removed parts of `WarpXWrappers.cpp` that have been ported to pyamrex
* CMake: Link OBJECT Target PRIVATE
* CMake: Remove OBJECT Target
Simplify and make `app` link `lib` (default: static). Remove OBJECT
target.
* Fix in fields.py for the components index
* Update get_particle_id/cpu
As implemented in pyAMReX with
https://github.com/AMReX-Codes/pyamrex/pull/165
* WarpX: Update for Private Constructor
* Import AMReX Before pyd DLL Call
Importing AMReX will add the `add_dll_directory` to a potentially
shared amrex DLL on Windows.
* Windows CI: Set PATH to amrex_Nd.dll
* CMake: AMReX_INSTALL After Python
In superbuild, Python can modify `AMReX_BUILD_SHARED_LIBS`.
* Clang Win CI: Manually Install requirements
Sporadic error is:
```
...
Installing collected packages: pyparsing, numpy, scipy, periodictable, picmistandard
ERROR: Could not install packages due to an OSError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\hostedtoolcache\\windows\\Python\\3.11.4\\x64\\Lib\\site-packages\\numpy\\polynomial\\__init__.py'
Consider using the `--user` option or check the permissions.
```
* Hopefully final fixes to fields.py
* Update getProbLo/getProbHi
* Set plasma length strength
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* Fix fields method to remove CodeQL notice
* Update Comments & Some Finalize
* Move: set_plasma_lens_strength
to MPC
---------
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
Co-authored-by: David Grote <dpgrote@lbl.gov>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Dave Grote <grote1@llnl.gov>
Co-authored-by: Roelof Groenewald <regroenewald@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* Broadcast quantity & update tests
* Make only one rank create the lasy file
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---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* Update PICMI interface for Gaussian flux
* Update version of picmistandard
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* use same finite difference algo as for Yee with hybrid-PIC to calculate divE
* add `divE` and `divB` to field diagnostic in picmi.py
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Axel Huebl
Luca Fedeli
Remi Lehe
Revathi Jambunathan
aveksler1
Edoardo Zoni
Ryan Sandberg
Ilian Kara-Mostefa
Marco Garten
Arianna Formenti
Roelof Groenewald
David Grote
pre-commit-ci[bot]
