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2023-08-30Doc: PM new E4S (Boost, CCache) (#4252)Gravatar Axel Huebl 2-2/+2
With the old E4S packages gone, we need to update out `Boost` dependency.
2023-08-29Update .clang-tidy: remove bugprone-unchecked-optional-accessGravatar Axel Huebl 1-0/+1
also complains about .value(), which has an exception check
2023-08-29ChargeDeposition: Remove Global WarpX Variable (#4250)Gravatar Axel Huebl 3-36/+47
* ChargeDeposition: Remove Global WarpX Variable Remove Global WarpX variable use in `ChargeDeposition`. * CurrentDeposition: Add Missing Include
2023-08-30CMake: Verify WarpX_..._src paths exit (#4249)Gravatar Axel Huebl 5-0/+15
Give a clean error message if a `WarpX_thirdparty_src` directory does not exist.
2023-08-29Clang tidy CI test: add more readability checks to clang tidy CI test (#4146)Gravatar Luca Fedeli 101-717/+727
* add more readability checks to clang-tidy CI test * reformat check list * starting to address issues found with clang-tidy£ * addressing issues * remove check * address issues * address all issues * address issue found with github code scanning
2023-08-29Replace static function WarpX::CheckSignals() with direct call to ↵Gravatar Luca Fedeli 2-9/+2
SignalHandling::CheckSignals() (#4240)
2023-08-29Update Crusher Docs and Scripts (#4246)Gravatar Marco Garten 4-94/+256
* Update Crusher Docs and Scripts The updated Crusher scripts and documentation were kept very close to the ones for Frontier since they were found to work very well, currently. The original Frontier docs were authored by Axel Huebl <axelhuebl@lbl.gov>. * Directly ref to Frontier docs for system issues Due to the two systems having a lot of similarities now we just reference the section in the Frontier docs for the known system issues. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-08-29Fix: PICMI BTD Diags (#4248)Gravatar Axel Huebl 1-2/+2
Typos.
2023-08-29Add Python bindings to extract the timestep dt (#4244)Gravatar Remi Lehe 2-1/+5
* Add Python bindings to extract the timestep * More secure array access
2023-08-28Docs: Perlmutter (NERSC) Update (#4223)Gravatar Axel Huebl 1-4/+6
Update slurm changes and pinning.
2023-08-28Add LabFrameParticleDiagnostic to picmi (#4148)Gravatar David Grote 1-2/+66
2023-08-28Docs: WarpX HOFI Start-to-End Paper (#4221)Gravatar Axel Huebl 1-0/+5
Congratulations!! :)
2023-08-28AMReX: Weekly Update (#4243)Gravatar Axel Huebl 5-5/+5
2023-08-28Work-Around: Segfault in MPI_Init with HIP (#4237)Gravatar Axel Huebl 2-3/+22
* 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
2023-08-28Cleaning: Explicit Capture in Copy Lambda (#4238)Gravatar Axel Huebl 2-2/+6
In the spirit of a recent nvcc compiler bug, simplify the capture logic from implicit to explicit for the particle filter lambda.
2023-08-28Remove AddToMultiFabMap functions from WarpX class (#4242)Gravatar Luca Fedeli 2-23/+3
* Remove AddToMultiFabMap functions from WarpX class * fixed bug
2023-08-27remove unnecessary static variables from WarpX.H (#4239)Gravatar Luca Fedeli 3-22/+12
2023-08-26Frontier (OLCF): MPI_Waitall issues (#4235)Gravatar Axel Huebl 3-0/+31
* 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
2023-08-25Doc: HPC Python Separate (Static/Shared AMReX) (#4226)Gravatar Axel Huebl 18-77/+132
* 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>
2023-08-25Do not pre-processing routine in Python initialization (#4231)Gravatar Remi Lehe 2-10/+0
2023-08-25Fix: openPMD 1D/2D3V Constant Positions (#4227)Gravatar Axel Huebl 1-13/+33
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.
2023-08-24Fix: WarpX Version (#4218)Gravatar Axel Huebl 5-14/+27
* Fix: WarpX Version Fix the WarpX version info. * Fix Version: pyWarpX * Version: More Python __version__
2023-08-24CI: Shrink NVHPC Size (#4224)Gravatar Axel Huebl 2-10/+14
* 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)
2023-08-24Fix Python wrapper to extract `theta` (#4229)Gravatar Remi Lehe 1-3/+3
2023-08-24fix pc for BTD plotfile (#4228)Gravatar Revathi Jambunathan 1-8/+8
2023-08-24Fix Repeated Plasma Lens: Start (#4220)Gravatar Axel Huebl 2-23/+31
* 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
2023-08-24add error message if cuda 11.6 is used with the yee solver (#4222)Gravatar aveksler1 1-0/+10
2023-08-22Use only 8 cores to compile on Summit (#4195)Gravatar Remi Lehe 1-2/+2
2023-08-22BTD RZ test: add missing checksum analysis (#4202)Gravatar Edoardo Zoni 2-0/+25
* BTD RZ test: add missing checksum analysis * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-08-22 BoxArray in BTD has single box (#4208)Gravatar Revathi Jambunathan 5-20/+15
* 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
2023-08-22CMake: Fix `-fPIC` logic that triggers shared AMReX (#4211)Gravatar Axel Huebl 2-5/+9
Accidentially now always built AMReX was shared library, which is only needed if we build with Python.
2023-08-22fix undefined behavior in btd intervals (#4216)Gravatar Ryan Sandberg 1-14/+30
2023-08-22Remove unused/untested Python file (#4217)Gravatar Remi Lehe 2-145/+0
* Remove unused/untested Python file * Remove additional file
2023-08-22add flush (#4214)Gravatar Ilian Kara-Mostefa 1-4/+8
2023-08-22correct zinject_plane_boost (#4213)Gravatar Ilian Kara-Mostefa 1-1/+1
2023-08-22Hybrid grid type not implemented in RZ geometry (#4212)Gravatar Edoardo Zoni 2-0/+7
2023-08-21CI: Sphinx <7.2 for now (#4215)Gravatar Axel Huebl 1-1/+3
Because breathe is not yet ready.
2023-08-22pyWarpX.H: Add Include Guard (#4206)Gravatar Axel Huebl 1-0/+5
Add an include guard to this header file.
2023-08-21AMReX: Weekly Update (#4207)Gravatar Axel Huebl 5-5/+5
2023-08-21Add GPU-to-CPU mapping for Frontier (#4205)Gravatar Marco Garten 1-5/+6
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.
2023-08-21Affiliation update in Zenodo file (#4204)Gravatar Arianna Formenti 1-0/+5
2023-08-20Include `J` in diagnostic output when an electromagnetic solver is not used ↵Gravatar Roelof Groenewald 19-121/+239
(#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>
2023-08-19Fix: Remove Overly Exported Classes (#4200)Gravatar Axel Huebl 5-10/+5
* Fix: Remove Overly Exported Classes Luckily, many of them should not contain global state. * Add Missing WarpX.H Include
2023-08-17Add nodal electrostatic solver (#3982)Gravatar Arianna Formenti 6-113/+414
* added nodal electrostatic solver * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * sphere test for electrostatic nodal solver * add 3d single bunch test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * adds single bunch ci test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 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>
2023-08-17Electrostatic sphere tests: add missing checksum analysis (#4198)Gravatar Edoardo Zoni 4-20/+53
2023-08-17Automated test for externally loaded fields in the boosted frame (#4188)Gravatar Ilian Kara-Mostefa 5-1/+238
* Implement boosted frame automated test (1D) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Implement boosted frame automated test (1D) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 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>
2023-08-16Cleanup plasma injection (#4191)Gravatar David Grote 3-373/+426
* Extensive clean up of PlasmaInjection * Small cleanup of parseMomentum * Fix string argument reference * Remove unneeded surface_flux
2023-08-16fix time update (#4184)Gravatar Ilian Kara-Mostefa 1-1/+1
2023-08-15Update Python installation instructions on HPC (#4189)Gravatar Remi Lehe 10-21/+16
* Update Python installation instructions on HPC * Update Python installation instructions on HPC --------- Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-08-15affiliation update in Zenodo file (#4190)Gravatar Roelof Groenewald 1-1/+1
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