HarrisSheet development merge 240124 #138
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Update the Lassen (LLNL) documentation for their RHEL8 transition and Python support.
On workspace
Module update on Quartz requires changes. Switching to Clang 14 as the compiler.
Failed on freetype (no module).
Avoid an implicit upgrade of matplotlib.
Work-around for pytorch/pytorch#108934
Switch from Clang 12 to GCC 11 on Lassen (LLNL), due to issues seen in PyTorch and a risk of general vectorization issues in Clang/LLVM for PPC64le in LLVM at this point.
Document Python (PICMI) and ML support for Quartz (LLNL).
* added collider reduced diags * added test * fixed xy_ave and xy_std * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed usage of IntVect and removed print * Set up automated CI test To-do: - Fix bug (erroneous arithmetic operation) - Remove unused parameters from input file * Fix warning: set mass only if WARPX_QED * Use amrex::ParticleReal for mass * Update Make.package to fix GNU Make build * reduced_data.value() only once * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Merge `development` into `coll_rel_red_diags` * updated 3d beam test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated 3d test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * `m_write_header` instead of `m_IsNotRestart` * added angles * updated 3d beam test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added 3 particle test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added warning * updated diags names * updated analysis multiple particles * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added positrons to test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update CI test * Reuse input file parser from Tools * Apply suggestions from code review * Apply suggestions from code review * changed order of diags and added docs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Apply WarpX style conventions * Fix CodeQL alerts * assert in RZ and removed fine ref levs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix compilation in 2D * Fix compilation in RZ * Update Docs/source/usage/parameters.rst Co-authored-by: Axel Huebl <[email protected]> * Update Source/Diagnostics/ReducedDiags/ColliderRelevant.cpp Co-authored-by: Axel Huebl <[email protected]> * Update Source/Diagnostics/ReducedDiags/ColliderRelevant.cpp Co-authored-by: Luca Fedeli <[email protected]> * Update Source/Diagnostics/ReducedDiags/ColliderRelevant.cpp Co-authored-by: Luca Fedeli <[email protected]> * Update Source/Diagnostics/ReducedDiags/ColliderRelevant.H Co-authored-by: Axel Huebl <[email protected]> * Update Source/Diagnostics/ReducedDiags/ColliderRelevant.H Co-authored-by: Axel Huebl <[email protected]> * minimized number of kernel launches and parallel ops * updated constructor of ReduceDiags * fixed based on comments * updated docs: if QED not enable * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed ReducedDiags constructor * two passes instead of one for robusteness * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed bugs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix 1D build (typo `wtot` instead of `w_tot`) * refixed compile in RZ * check io process in chi_ave computation * updated test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Temporary fix: remove IOProcessor * Update Source/Diagnostics/ReducedDiags/ColliderRelevant.cpp Co-authored-by: Axel Huebl <[email protected]> * Apply suggestions from code review * Remove `Debug` compilation mode from CI test * CI test analysis: check all particles have same charge * Use `m_beam_name` instead of `species_names` --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Edoardo Zoni <[email protected]> Co-authored-by: Edoardo Zoni <[email protected]> Co-authored-by: Axel Huebl <[email protected]> Co-authored-by: Luca Fedeli <[email protected]>
* Add warpx_intervals option to BTD * Add warpx_intervals to LabFrameParticleDiagnostics
* AMReX: Weekly Update * PICSAR: Use Tag
Document & automate how to install `cupy` on Perlmutter.
The lower and upper bounds are already present within PICMI.
…4253) * Clang-tidy: add misc-definitions-in-headers check * address issues found with clang-tidy * remove std::cout added for debug purposes * add back newline
Useful on very fresh Ubuntu/WSL/Docker environments where not even `built-essential` was installed. Also available on all operating systems now, so no downside to list: https://anaconda.org/conda-forge/make/
Document how to install the CUDA Toolkit with Conda for development.
* Prevent NaNs in collisions between particles * Avoid another division by 0 t# Please enter the commit message for your changes. Lines starting
* fix check of PML + Silver Mueller compatibility * complete check * refactoring * fix logic bug
Moving the source directories and build instructions for WarpX
itself from `$HOME` to the per-user NFS directory
`/usr/workspace/${USER}/lassen/src`, which has a larger default
quota.
* Implement Galilean PML * Activate the PML * Add automated test * Fix compilation error * Fix more compilation errors * Fix more compilation error * Fix more compilation bugs * Fix more compilation bugs * Clean up code, debug CI * Fix CI * Use both collocated and staggered k vectors * Reset CI benchmark * Update test * Add Doxygen, clean up methods signature * Improve abort messages * Implement correct analytical equations * Remove class PsatdAlgorithmGalileanPml * Add Doxygen strings for class `PsatdAlgorithmPml` * Update clang tidy --------- Co-authored-by: Edoardo Zoni <[email protected]>
…X#4203) * Use cupy when available * cupy helper & copy-to-host helper * cupy helper & copy-to-host helper * Fix get_species_charge_sum (revert) * Import Updates * Pass copy_to_host through the particle gather routines * Add documentation for the Python particle gather routines * Fix fetch of particle theta, passing copy_to_host, and use numpy when copy to host * Avoid cupy for copy_to_host - explicit copy in AMReX possible - this way, we can support AoS data copies * Add cupy struct reference --------- Co-authored-by: Axel Huebl <[email protected]>
Update the Boost and CCache modules to use the latest E4S (23.05) GCC/11.2.0 stack on Perlmutter.
…X#4300) * added `get_charge_density` to pybind `WarpXParticleContainer` and exposed useful fields.py functionality directly for a mf * reduce code duplication in `_WarpXMultiFABWrapper`; changed arguments to strings from f-strings * add `mf_name` argument option to `_MultiFABWrapper` instead of creating a child class * add back deleted docstring
* AMReX: 23.11 * pyAMReX: 23.11 * WarpX: 23.11
* AMReX: Weekly Update * pyAMReX: Weekly Update * PICSAR: Weekly Update
Python: Use a fresh Virtualenv Brew Python is too broken/inconsistent in packages like `six`, `matplotlib`, `pandas` et al.
* 2 modifs * 1 modif
* Doc: Laser Pulse Manip. for LPI Add commonly used acronyms for laser pulse manipulation and instability mitigation in laser-plasma interaction physics. * Update glossary.rst
updates: - [github.com/hadialqattan/pycln: v2.3.0 → v2.4.0](hadialqattan/pycln@v2.3.0...v2.4.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* parser to define ref patches * fix def for 1D and add RZ * fix 1D Z def * remove function def for fine_taglo/hi * fix warning and error strig * fix warning message
…r of the WarpX class (ECP-WarpX#4404) * make authors a private variable of the WarpX class instead of a public static variable * update docstring
* Add gaussian_parse_momentum_function * Update initial_distribution benchmarks * Remove blank line at end of initial_distribution.json * Update doc * Minor clean up in the CI test * Further clean up of the doc * Add new option to PICMI * Add documentation for option in PICMI
* Make sure code is aligned properly * Minor adjustments, mainly to method arguments * More corrections * More corrections * More corrections 2
…-WarpX#4339) * Set the particle fields directly to the constant external fields * Change "get" to "query" for the external fields * Fix PairGenerationTransformFunc * More fixes * Yet more fixes for QED * Make temporary a const * Broke vector into separate reals * Fix ColliderRelevant.cpp * Fix ParticleExtrema * Updated comment regarding static * Clean up for clang-tidy
* Clang-tidy CI test: add almost all modernize-* checks * address issues found with clang-tidy * address issues found with clang-tidy * fix bug * fixed bug * fix bugs * address issue found with clang-tidy * fix residual issues found with clang-tidy * fix issue related to modernize-use-default-member-init check * address issues found with clang-tidy * fix issues found with clang-tidy
* move AnyFFT.H into ablastr * place anyfft under ablastr/math/fft * add logic to enable fft in ablastr via flag ABLASTR_USE_FFT * ABLASTR FFT: Build System Update Co-authored-by: Axel Huebl <[email protected]>
* AMReX: Weekly Update * pyAMReX: Weekly Update
We must not oversubscribe the two (2) CI cores with the number of processes times threads we use in tests.
Typo, this should not be `==`.
* add new option to initialize external fields on grid upto a max user-defined level * ensure to init level > max level to 0 * fix logic for init * Edoardo's fixes for typo Co-authored-by: Edoardo Zoni <[email protected]> * Update Source/WarpX.H Co-authored-by: Edoardo Zoni <[email protected]> * fix bug * adding picmi interface with doc for Analytical initial field * allocinit fields to simplify default behavior in initialization with constant and parser up to max levels * default not needed anymore * no need for a default * fix incomplete paranthesis * fix doc to remove default and include Dave's suggestion * Update doc string * fix incorrect rebase --------- Co-authored-by: Edoardo Zoni <[email protected]> Co-authored-by: Axel Huebl <[email protected]>
Always add - `warpx.do_dynamic_scheduling=0` - `warpx.serialize_initial_conditions=1` to CPU CI jobs, so we cannot forget it when it matters (e.g., random numbers in distributions).
* Add class definition convention and reword function definition convention * Use code-block and modify documentation.rst to conform to conventions * Small fix to code-block * Fix typo and add new lines * Revert new lines * Indents code-blocks and words in between * Use less code blocks * Use "amrex::Print" instead of "Print"
RevathiJambunathan
merged commit 4ce48bc
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RevathiJambunathan:HarrisSheetinX
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