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2022-10-08Fix synchronization of nodal points in subcycling (#3455)Gravatar Remi Lehe 2-31/+35
* Fix synchronization of nodal points in subcycling * Update checksum
2022-10-08Updated 1D CI tests with particles because of update of yt (#3458)Gravatar David Grote 6-26/+27
* Updated 1D CI tests with particles * Updated required version of yt to 4.1.0 * Fixed CI analysis of collisionXYZ Fixed the fetching of the particle data
2022-10-06Spack Desktop: Simpler CUDA Visualization (#3337)Gravatar Axel Huebl 1-2/+8
* Spack Desktop: Simpler Visualization Reduce the dependencies for in situ vis, avoiding to build DevilRay in Ascent, which takes very long right now. We mostly use Ascent with VTK-m for now, so that works. * CUDA Ascent & VTK-M: static * ADIOS2: w/o CUDA See https://github.com/ornladios/ADIOS2/issues/3332
2022-10-05Doc: BLAS++/LAPACK++ on GitHub (#3449)Gravatar Axel Huebl 9-22/+22
* Doc: BLAS++/LAPACK++ on GitHub BLAS++ and LAPACK++ development has moved to GitHub :tada: Welcome! :) * Update bitbucket mention to GH * SLATE: Rename Missing Links Co-authored-by: Mark Gates <mgates3@icl.utk.edu>
2022-10-05openPMD: Shape of Constant Particle Records (#3451)Gravatar Axel Huebl 1-1/+4
We forgot to set the shape (particle number) of constant particle records. This violates the openPMD standard and complicates post-processing.
2022-10-03BTD: Improve Z-Slice Message (#3440)Gravatar Axel Huebl 1-1/+9
Add values that are checked to the msg, e.g., I see: ``` z-slice in lab-frame (0.049998) is outside the buffer domain physical extent (0.049998 to 0.050000). ```
2022-10-03Docs: Fix PICMI Builds (#3447)Gravatar Axel Huebl 3-5/+6
Unbreak the RTD build. We need to do this all relative to the root directory.
2022-10-03Doc: Dev FAQ Pinned Memory (#3437)Gravatar Axel Huebl 1-0/+17
* Doc: Dev FAQ Pinned Memory Since I spoke to two devs in 24hrs about the topic, let us document it. Co-authored-by: Ryan Sandberg <RSandberg@lbl.gov> Co-authored-by: David Grote <dpgrote@lbl.gov>
2022-10-03Release 22.10 (#3444)Gravatar Axel Huebl 11-13/+13
* AMReX: Weekly Update One commit after 22.10 release, to fix oneAPI DPC++ 2022.02: 22.10-1-g13aa4df0f5 * PICSAR: 22.10 * WarpX: 22.10
2022-10-02Use parser for input parameters of type long (#2506)Gravatar Neïl Zaim 5-24/+67
* Use parser for input parameters of type long * Revert "Use parser for input parameters of type long" This reverts commit 9573bb3f693f1247e77faa433fd96dc294e68361. * Use parser for inputs of type long * add safeCasttoLong function * Fix typo in comment
2022-10-02Major update of the Python/picmi documentation (#3329)Gravatar David Grote 15-145/+776
* Include WarpX specific documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Undo the precommit change of import in __init__.py * Docs: Install Pure Python WarpX PICMI Allows to use these classes in our Sphinx autodocs in the manual. * Sphinx: Add Napoleon Extension https://sphinxcontrib-napoleon.readthedocs.io * PICMI Doc Strings: Fix Some Warnings * Removed the DocumentedMetaClass since it was moved to picmistandard * Defined the languate in Docs/source/conf.py * Cleaned up minor issues in the rst files * Updated existing doc strings in picmi.py * Reformatted doc strings in Regression/Checksum/checksumAPI.py * Reformatted doc strings in Regression/Checksum * First set of WarpX specific documentation * Updated to picmistandard version 0.0.20 * Cleaned up the Python document page Fixed up the text to be more clear. Added section headers for each picmi class (for easy reference). * Further updates to picmi.py doc strings Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-10-02Sphinx Extension: Sphinx-Design (#3361)Gravatar Axel Huebl 3-0/+3
2022-10-02Lassen (LLNL): HDF5 1.12.2 (#3378)Gravatar Axel Huebl 1-1/+1
The HDF5 1.10.4 module on Lassen (LLNL) has severe performance issues. We saw that 1.10.5+ fixed those. We now have a new module, 1.12.2, that we can use.
2022-10-02Docs: BELLA MVA PoP & Ion PRAB Published (#3435)Gravatar Axel Huebl 1-5/+6
* Docs: BELLA MVA PoP Published Update the science hightlights with the final, published paper. * Levy et al. PRAB published, too
2022-09-30Implement tridiag solver for 1D (#3431)Gravatar David Grote 5-50/+280
* Added tridiag solve for 1D * Added tridiag solver to WarpX.H * Updated PICMI_inputs_1d.py to use float64 This was done so that it will compare to the tridiag to machine precision * Updated 1D capacitive_discharge test, adding pythonsolver flag * Update capacitive_discharge analysis_1d.py file with updated reference data * Add periodic boundary conditions, plus other fixes * Added CI test Python_background_mcc_1d_tridiag * Fix for parallel * Fixed CI test file prefix for PICMI_inputs_1d.py * Fixed comments
2022-09-29Add quiet option to Summit post-proc. docs (#3434)Gravatar Marco Garten 1-1/+5
The quiet option drastically reduces the in-cell output of package installation with mamba but does not completely silence.
2022-09-29Add 1d support to `_libwarpx.py` functions `get_particle_X` (#3421)Gravatar Roelof Groenewald 2-17/+24
* add 1d support to _libwarpx.py functions `get_particle_X` * add coverage of 1d `_libwarpx.get_particle_z` to test suite
2022-09-28AMReX/PICSAR: Weekly Update (#3412)Gravatar Axel Huebl 8-52/+52
* AMReX: Weekly Update * Roundoff Domain: Reset Checksums: - [x] 2D: `background_mcc_dp_psp` - [x] 3D: `pml_psatd_dive_divb_cleaning` - [x] SP: `reduced_diags_single_precision` * AMReX: Weekly Update Fix #3429
2022-09-26enforce 3 components for some laser parameters (#3423)Gravatar Luca Fedeli 1-0/+7
2022-09-24BTD diagnostics specified by intervals (#3367)Gravatar Ryan Sandberg 7-7/+185
* BTD diagnostics specified by intervals * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * address CI errors * refactor and test * no duplicate or out-of-order snapshots * update documentation and tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * clean for CI * still fighting CI * Update Source/Diagnostics/BTDiagnostics.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * refactor includes * add an explicit constexpr * Apply suggestions from code review Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * describe algorithm for BTD intervals list * revert to old description of num_snapshots_lab * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * preserve behavior of num_snapshots_lab Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2022-09-23fix labels in inputfiles (#3422)Gravatar Luca Fedeli 3-3/+3
2022-09-21CI: Test New v. Legacy BTD in `BTD_ReducedSliceDiag` (#3371)Gravatar Edoardo Zoni 3-37/+102
* CI: Test New BTD in `BTD_ReducedSliceDiag` * Compare Legacy BTD vs. New BTD * Fix Bug in Loading of openPMD Array Data * Fix CI Analysis
2022-09-21Fix update of particles flushed already in BTD (#3419)Gravatar Remi Lehe 1-1/+1
2022-09-21Fix compilation of RZ version on GPU (#3418)Gravatar Remi Lehe 1-3/+0
2022-09-20Add option to deposit laser on main grid (#3235)Gravatar Remi Lehe 4-6/+32
* Add option to deposit laser on main grid * Use `deposit_on_main_grid` * Update Source/Particles/LaserParticleContainer.cpp * Add documentation * Update documentation
2022-09-20PSATD: More Options for Time Dependency of J, Rho (#3242)Gravatar Edoardo Zoni 23-97/+198
* Rename PsatdAlgorithm as PsatdAlgorithmJConstantInTime * Add New Inputs: psatd.J_in_time, psatd.rho_in_time * Update PSATD Classes * Fix Bug for FDTD Build * Fix Warning for RZ PSATD Build * Fix Multi-J Loop w/ J Constant in Time * Clean up * Fix Error Message * Fix Time of Charge Deposition for Rho Linear * Add 3D Langmuir CI Tests w/ Multi-J Algo * Fix Checksums of New CI Tests * Remove Extra CI Tests (added in #3363) * Fix CI Tests w/ Multi-J PSATD * Add Docs for New Input Parameters * Galilean/Comoving PSATD Not Compatible w/ J Linear
2022-09-20Correct and test fusion module in RZ geometry (#3255)Gravatar Remi Lehe 6-16/+290
* Add particle rotation in NuclearFusionFunc.H * Minor * indent * initial work * fixed bugs and added species * update documentation * delete unused file * Add properties for neutron, hydrogen isotopes, helium isotopes * Update code to be more consistent * Correct typo * Parse deuterium-tritium fusion * Start putting in place the files for deuterium-tritium * Update documentation * Prepare structures for deuterium tritium * Fix typo * Fix compilation * Add neutron * Add correct formula for the cross-section * Correct compilation error * Fix nuclear fusion * Reset benchmarks * Prepare creation functor for 2-product fusion * First implementation of momentum initialization * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Use utility function for fusion * Minor modification of variable names * Fix GPU compilation * Fix single precision compilation * Update types * Use util function in P-B fusion * Correct compilation errors * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Correct errors * Update values of mass and charge * Correct compilation error * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Correct compilation error * Correct compilation error * Correct compilation error * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Reset benchmark * Use helium particle in proton-boron, to avoid resetting benchmark * Fixed proton-boron test * Revert "Fixed proton-boron test" This reverts commit 73c8d9d0be8417d5cd08a23daeebbc322c984808. * Incorporate Neil's recommendations * Reset benchmarks * Correct compilation errors * Add new deuterium tritium automated test * Correct formula of cross-section * Correct cross-section * Improve analysis script * Add test of energy conservation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add test of conservation of momentum * Progress in analysis script * Fix error in the initial energy of the deuterium particles * Add check of isotropy * Clean up the test script * Rewrite p_sq formula in a way to avoids machine-precision negative numbers * Add checksum * Clean up code * Add test for fusion in RZ geometry * Update code to take into account actual timestep * Update RZ test * Update RZ test * Increase number of particles * Impart radial memory on DT particles * Correct RZ momenta * Remove unused file * Update test * Fix definition of theta * Add new test * Add checksum * Update test * Update tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix Python analysis script * Remove CPU and ID from new benchmark Co-authored-by: Yinjian Zhao <yinjianzhao@lbl.gov> Co-authored-by: Luca Fedeli <luca.fedeli@cea.fr> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-09-20More fixes for capacitive_discharge PICMI tests (#3416)Gravatar David Grote 2-3/+3
2022-09-19Add beta function to BeamRelevant (#3372)Gravatar Marco Garten 2-23/+38
* Add beta function to BeamRelevant * Beta-function: add user docs
2022-09-19Fix value of particle container m_do_back_transformed_particles when there ↵Gravatar Neïl Zaim 1-2/+4
are multiple BT diagnostics (#3184)
2022-09-19Zenodo: Add Marco Garten (#3414)Gravatar Axel Huebl 1-0/+5
Add Marco to our Zenodo file.
2022-09-19Fixes to Physics_applications/capacitive_discharge/PICMI* (#3413)Gravatar David Grote 2-3/+3
2022-09-19Improve docstrings for some physical constants (#3410)Gravatar Luca Fedeli 1-5/+5
* improve documentation for numerical constants * add Antonin Sainte-Marie's suggestion for a docstring * Update tau (from PR review)
2022-09-19Display an ASCII art logo on standard output (#3382)Gravatar Luca Fedeli 7-1/+50
* display WarpX ascii art * fix bug * function is now noexcept * fix bug * fixed bug
2022-09-19ABLASTR: Fix Stray Include in ChargeDeposition (#3406)Gravatar Axel Huebl 1-0/+1
This include into WarpX should not be here and is unused. Same as #3393.
2022-09-19ABLASTR: Constants (#3405)Gravatar Axel Huebl 2-31/+92
* ABLASTR: Constants Add a new header for constants to ABLASTR. Move over constants from WarpX as its content. * Cleanup: Use amrex::Real Literals * Add Conversion: ElectronVolts Conversions for energy, momentum and mass
2022-09-18Update highlights with new PRX paper (#3408)Gravatar Remi Lehe 1-2/+2
* Update highlights with new PRX paper * Update Docs/source/highlights.rst
2022-09-15add species name to a couple of error messages (#3381)Gravatar Luca Fedeli 1-2/+4
2022-09-15Use blaspp::gemm on GPU for Hankel transform (#3383)Gravatar Remi Lehe 6-55/+77
* Use gemm on GPU for Hankel transform * Add stream synchronization * Add `amrex` * blas::gemm call: add `queue` with device id * CMake: BLAS++ Missing Deps * Update installation instructions for Summit * CMake: BLAS++ should not need curand * Add paths to blaspp/lapackpp * Move Queue Constructor to Constructor * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Correct name of profiled area * Use gemm for inverse Hankel transform * Add missing comma * Clean up the code so that it compiles for CPU * Clean up code ; update documentation * Update Comment Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Tools/machines/summit-olcf/summit_warpx.profile.example Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Add stream synchronization * Switch to streamsynchronize * Update comments Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-09-14Frontier/Crusher: Less Invasive libFabric Work-Around (#3396)Gravatar Axel Huebl 4-4/+12
From Steve Abbott (HPE): > There's a known problem with the default libfabrics memory > registration cache monitor that impacts codes that allocate and > free MPI buffers frequently. What you're doing now, > FI_MR_CACHE_MAX_COUNT=0 is a big hammer that disables the memory > registration cache all together. That can have a negative > performance impact, because memory registration is a heavy > operation, but it doesn't seem to be hitting WarpX very hard. If > you're mostly following an allocate-communicate-free pattern, the > memory registration cache won't help you anyway. > > An alternative is to set FI_MR_CACHE_MONITOR=memhooks , which uses > an alternative cache monitor that doesn't have the same problem. I > tested on an 8 node WarpX case we have in a bug and only saw a 2% > speedup over FI_MR_CACHE_MAX_COUNT=0, and that speedup was in > FillBoundary which I'm guessing is the only place you might have > some MPI buffer reuse. If you start to scale out you may want to > try it. > > We're working on a new default cache monitor that won't have this > problem but I'm not sure the timeline for it. We'll make sure that > when it gets pushed out we'll let you know, but for now you have to > keep using either of these two environment variables.
2022-09-13ABLASTR: Fix Stray Include in DepositCharge (#3393)Gravatar Axel Huebl 1-1/+0
This include into WarpX should not be here and is unused.
2022-09-13use getWithParser (#3394)Gravatar Revathi Jambunathan 1-2/+2
2022-09-12ABLASTR: Move Used Inputs Helper (#3376)Gravatar Axel Huebl 5-12/+64
Move the helper to write a file for used inputs to ABLASTR.
2022-09-12AMReX: Weekly Update (#3387)Gravatar Axel Huebl 5-5/+5
2022-09-12Docs: Crusher (OLCF) for PSATD+RZ (#3386)Gravatar Axel Huebl 3-2/+26
Document BLAS++/LAPACK++ usage with HIP on OLCF Crusher.
2022-09-12Docs: Update Crusher (OLCF) (#3380)Gravatar Axel Huebl 1-7/+7
Use the newest available ROCm and CCE modules.
2022-09-09`SyncCurrent`: Split Filter and Sum over Guard Cells (#3222)Gravatar Edoardo Zoni 12-164/+212
* Split ApplyFilterandSumBoundaryJ * Fix Bug * Fix Bug * Fix CI * Pass Correct Periodicity to SumBoundaryJ * Use ApplyFilterJ and SumBoundaryJ w/ MR * Fix Bug (duplicate loops over dimensions) * Use ApplyFilterJ and SumBoundaryJ w/ MR * Clean up Variable Names in ApplyFilterJ * Increase Guard Cells of All MultiFabs, Not Only J * Reset CI Checksums
2022-09-09Frontier/Crusher: rocFFT Cache Control (#3366)Gravatar Axel Huebl 4-1/+31
rocFFT in ROCm 5.1+ tries to [write to a cache](https://rocfft.readthedocs.io/en/latest/library.html#runtime-compilation) in the home area by default. This does not scale.
2022-09-09Updated name for Elisa Rheaume in zenodo & Field Probe files (#3379)Gravatar Elisa Rheaume 7-7/+7
2022-09-09Fix: ABLASTR nvcc Phi Fine/Coarse (#3374)Gravatar Axel Huebl 1-12/+44
Poisson solver: work around an NVCC compile error downstream in ImpactX. This is likely due to nesting of lambdas.
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