Update upstream development #202
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* Correct particle positions outside refined injection * Improve test * Update benchmark * Update Examples/Physics_applications/laser_acceleration/analysis_refined_injection.py
Fix: ``` $ cmake -S . -B build_dp ... -- The C compiler identification is AppleClang 13.0.0.13000029 -- The CXX compiler identification is AppleClang 13.0.0.13000029 ... CMake Error at /usr/local/Cellar/cmake/3.24.2/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:230 (message): -- Configuring incomplete, errors occurred! Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) ``` ``` libomp 14.0.6 is already installed but outdated (so it will be upgraded). ==> Downloading https://ghcr.io/v2/homebrew/core/libomp/manifests/15.0.2 ==> Downloading https://ghcr.io/v2/homebrew/core/libomp/blobs/sha256:a4e0796616d09221e2a486c95f9aa7c12d3c617e594b1d463a8f479bd4fa45c2 ==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sha256:a4e0796616d09221e2a486c95f9aa7c12d3c617e594b1d463a8f479bd4fa45c2?se=2022-10-13T20%3A50%3A00Z&sig=a68J671xfsvWip4TqYo5%2B2E0U5AswwCQDocHLNc6XXE%3D&sp=r&spr=https&sr=b&sv=2019-12-12 ==> Upgrading libomp 14.0.6 -> 15.0.2 ==> Pouring libomp--15.0.2.big_sur.bottle.tar.gz ==> Caveats libomp is keg-only, which means it was not symlinked into /usr/local, because it can override GCC headers and result in broken builds. For compilers to find libomp you may need to set: export LDFLAGS="-L/usr/local/opt/libomp/lib" export CPPFLAGS="-I/usr/local/opt/libomp/include" ==> Summary 🍺 /usr/local/Cellar/libomp/15.0.2: 7 files, 1.7MB ==> Running `brew cleanup libomp`... Disable this behaviour by setting HOMEBREW_NO_INSTALL_CLEANUP. Hide these hints with HOMEBREW_NO_ENV_HINTS (see `man brew`). Removing: /usr/local/Cellar/libomp/14.0.6... (7 files, 1.6MB) Removing: /Users/runner/Library/Caches/Homebrew/libomp--14.0.6... (548.8KB) ```
* NVCC generates code that tends to trigger ICEs in GCC 7.x * CTAD erratum in GCC 8: https://gcc.gnu.org/projects/cxx-status.html#cxx17
Mamba is now pre-installed on OLCF Jupyter base images! :)
Allow users to overwrite the default for the "used inputs" file that we write.
* Fix unused import warnings in python analysis scripts * [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>
* Do not query redundant do_back_transformed_particles * Only set m_do_back_transformed_particles to true if write_species is true
* Fix stair-case solver in 2D Cartesian * Generalization for the macroscropic solver * Update automated test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update benchmark Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* add reduced diagnostics to picmi * added test of picmi reduced diagnostics * changes requested during PR review
oneAPI 2022.2.0 hangs for `-O2` and higher: ECP-WarpX#3442
…e/openPMD (ECP-WarpX#3424) * print when writing openPMD, Ascent, Sensei * remove unnecesssary variables, include min_digits * print snapshot id when writing btd * fix ascent print * compile without warnings * still working on Ascent * still working Ascent * Print when BTD buffer is flushed * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * print when writing openPMD, Ascent, Sensei * remove unnecesssary variables, include min_digits * print snapshot id when writing btd * fix ascent print * compile without warnings * still working on Ascent * still working Ascent * Print when BTD buffer is flushed * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add warning message if BTD not full * adjust for CI, no in-situ vis BTD * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * revert to correct plotfile naming * change warning topic to BTD * nicer format for print statements * extend examples to fill BTD * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Reset Checksums of BTD_ReducedSliceDiag * Upgrade CI Test LaserAccelerationBoost * Apply suggestions from code review Co-authored-by: Edoardo Zoni <[email protected]> * improve BTD warning notes * edit final step notes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix formatting 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]>
* Replace "none" BC with Neumann for electrostatic * Added checking for Neumann boundaries * Updated documentation regarding Neumann BCs * [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>
* Add warning to set zmin and zmax for ions and also change the ion acceleration example to set these parameters so that users are aware that memory overflow could happen for production-size examples furthermore, correct units in comment after definition of r0 and Lcut Replace zmin and zmax with variables for electrons * Reset checksum for regression test Reset benchmark for LaserIonAcc2d test because the particle initialization in the input changed.
* Docs: LUMI (CSC) Start documenting LUMI usage instructions for WarpX. * Add more system info
* ABLASTR: Always Sync Option Add an option to ABLASTR/WarpX to always sync nodal cells that are owned by multiple blocks. This can be used for debugging. * Fix typo Co-authored-by: Edoardo Zoni <[email protected]> * Use New Option in One CI Test * Fix Logic: Force only to be `true`, not `false` Co-authored-by: Edoardo Zoni <[email protected]> Co-authored-by: Edoardo Zoni <[email protected]>
* workaround to fix invalid memory access while using PML + Moving Window + Load Balancing + Timers * fixed bug * add argument to shiftMF to avoid updating cost for PML
…rpX#3163) * Added error checks of the user input * Fixed literals and const's
* Generalize species names in fusion tests * Update benchmarks * Correct typo
* cell center BTD functors for RZ with openpmd * add RZ modes to output varnames too * update varnames once and set map for RZ fields in BTfunctor * fix access to varname field instead of unallocated m_varnames, and update hi ki-index after flush * set back trasnformed fields to false if fields_to_plot is none. Separate PArticle and Field io further. Also, clean up Particle Buffer initialize so its consistent with Field box, boxarray, dmap, and geom * clean commented line * assert for single rz mode * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove unused var * Apply suggestions from code review From Axels' review Co-authored-by: Axel Huebl <[email protected]> * adding comments, doxygen, and clean-up Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Axel Huebl <[email protected]>
* Begin writing BTD FAQ notes * FAQ notes on BTD * access figure from github online * update figure and improve faq answers
* Implement D+D -> n+He3 fusion * Fix logic for fusion reaction * Check products in a different place * Correct compilation error * Implement D+D -> T+p cross-section * Update example * Use clearer naming convention for fusion types * Revert changes to example input script * Add analysis script * Progress on tests * Use 2 species in test * Correct momentum of colliding species * Update test * Update test * Generalize species names in fusion tests * Update benchmarks * Correct typo * Updated scripts * Update script so that it works for D+T and D+D * Update CI * Add benchmark file * Correct typo * Fix compilation on GPU * Update RZ CI test * Implement Deuterium-Helium reaction * Apply suggestions from code review Co-authored-by: Edoardo Zoni <[email protected]> Co-authored-by: Edoardo Zoni <[email protected]>
* Perlmutter (NERSC): Update Modules Update after major system upgrade. * Perlmutter (NERSC): Update Jobscript * Perlmutter (NERSC): Remove Early Access Warning * Perlmutter (NERSC): Process Affinity Co-authored-by: Kevin Gott <[email protected]> Co-authored-by: Kevin Gott <[email protected]>
Migrate CUDA CI to use Ubuntu 18.04 -> 20.04
* AMReX: 22.11 * PICSAR: 22.11 * WarpX: 22.11
* allow arbitrary laser antenna normal - picmi * always check that laser propagation direction is along the normal direction of the antenna if the antenna normal is given
Slurm at Perlmutter is not yet configured to do proper affinity control itself. Thus, we do it ourselves. Co-authored-by: Kevin Gott <[email protected]>
Document how to work-around Jupyter HDF5 issues on OLCF until they fix it.
Add Ascent and SENSEI minimal versions to our dependency doc page.
Reflect new project precedence option `AMReX_BUILD_SHARED_LIBS` in superbuild install logic defaults for AMReX.
* Add SymPy Notebook to Derive PSATD Equations * Add Comments * Remove Redundant Simplification, Reduce Cost * Clear Cell Output * Don't Need IPython.display.Math * Remove Unused Function * Improve Inline Comments * Improve Markdown Cells * Add Automated Verification of ODEs Solution * Fix Bug in Automated Verification * Diagonalize only M for W1,W2,W3
…centering, time averaging (ECP-WarpX#3508) Additional MultiFabs for Vay deposition, current centering, and time averaging need to be allocated after load-balancing, otherwise the simulation crashes.
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A comment as I may not get to this for a while: I believe some failures are that in Electrostatic you need to use 'neumann' rather than 'none' for that boundary condition now. The other is that AMReX-Codes/amrex#2981 has modified the potential inside EBs, which I believe is causing some of our tests to fail now. Note the comments here ECP-WarpX#3469 that caused WarpX checksums to change for similar reasons. |
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