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2022-11-04CMake: AMReX_INTALL Update (Shared) (#3503)Gravatar Axel Huebl 1-1/+5
Reflect new project precedence option `AMReX_BUILD_SHARED_LIBS` in superbuild install logic defaults for AMReX.
2022-11-03Docs: Dependencies w/ Ascent & SENSEI (#3502)Gravatar Axel Huebl 1-0/+2
Add Ascent and SENSEI minimal versions to our dependency doc page.
2022-11-02Summit (OLCF): Jupyter GPFS HDF5 Issues (#3498)Gravatar Axel Huebl 1-0/+6
Document how to work-around Jupyter HDF5 issues on OLCF until they fix it.
2022-11-02Perlmutter (NERSC): Finish Affinity Control (#3495)Gravatar Axel Huebl 2-17/+15
Slurm at Perlmutter is not yet configured to do proper affinity control itself. Thus, we do it ourselves. Co-authored-by: Kevin Gott <kngott@lbl.gov>
2022-11-02Allow arbitrary laser antenna normal in picmi (#3477)Gravatar Roelof Groenewald 1-3/+22
* 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
2022-11-02Release 22.11 (#3499)Gravatar Axel Huebl 11-13/+13
* AMReX: 22.11 * PICSAR: 22.11 * WarpX: 22.11
2022-11-02CUDA CI: Ubuntu 20.04+ (#3496)Gravatar Axel Huebl 3-9/+72
Migrate CUDA CI to use Ubuntu 18.04 -> 20.04
2022-10-31Perlmutter (NERSC): Update Modules & Jobscript (#3493)Gravatar Axel Huebl 3-18/+14
* 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 <kngott@lbl.gov> Co-authored-by: Kevin Gott <kngott@lbl.gov>
2022-10-31Implement D+D and D+He fusion (#3257)Gravatar Remi Lehe 12-137/+406
* 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 <59625522+EZoni@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2022-10-31AMReX: Weekly Update (#3492)Gravatar Axel Huebl 5-5/+5
2022-10-31Add BTD notes to FAQ section (#3473)Gravatar Ryan Sandberg 1-0/+17
* Begin writing BTD FAQ notes * FAQ notes on BTD * access figure from github online * update figure and improve faq answers
2022-10-31BTD fields with RZ + openPMD - single mode only (#3350)Gravatar Revathi Jambunathan 3-118/+317
* 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 <axel.huebl@plasma.ninja> * 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 <axel.huebl@plasma.ninja>
2022-10-29Modify naming of species in CI fusion test (#3490)Gravatar Remi Lehe 5-145/+145
* Generalize species names in fusion tests * Update benchmarks * Correct typo
2022-10-28For background stopping, added error checks of the user input (#3163)Gravatar David Grote 1-24/+39
* Added error checks of the user input * Fixed literals and const's
2022-10-28Fix Invalid Mem w/ Moving Window, LB & PMLs (#3450)Gravatar Luca Fedeli 2-28/+41
* 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
2022-10-28ABLASTR: Always Sync Option (#3467)Gravatar Axel Huebl 8-90/+110
* 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 <59625522+EZoni@users.noreply.github.com> * Use New Option in One CI Test * Fix Logic: Force only to be `true`, not `false` Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
2022-10-28add warning if PML and PSATD are used together (#3489)Gravatar Luca Fedeli 2-0/+21
2022-10-28Docs: LUMI (CSC) (#3488)Gravatar Axel Huebl 4-1/+134
* Docs: LUMI (CSC) Start documenting LUMI usage instructions for WarpX. * Add more system info
2022-10-28Add neumann BC in WarpX PICMI interface (#3487)Gravatar Remi Lehe 1-1/+2
2022-10-25Add warning to set zmin and zmax for ion-acc example (#3323)Gravatar Marco Garten 3-30/+43
* 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.
2022-10-25Replace "none" BC with Neumann for electrostatic (#3483)Gravatar David Grote 5-15/+25
* 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>
2022-10-25Diagnostics: print when writing openPMD/Ascent/Sensei and BTD ↵Gravatar Ryan Sandberg 23-64/+174
plotfile/openPMD (#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 <59625522+EZoni@users.noreply.github.com> * 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 <ezoni@lbl.gov> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-10-25CI: oneAPI with `-O1` (#3478)Gravatar Axel Huebl 1-0/+6
oneAPI 2022.2.0 hangs for `-O2` and higher: #3442
2022-10-24Add reduced diagnostics to `picmi.py` (#3475)Gravatar Roelof Groenewald 7-60/+295
* add reduced diagnostics to picmi * added test of picmi reduced diagnostics * changes requested during PR review
2022-10-24AMReX: Weekly Update (#3479)Gravatar Axel Huebl 5-5/+5
2022-10-24Fix stair-case solver in 2D Cartesian (#2942)Gravatar Remi Lehe 5-9/+26
* 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>
2022-10-24Do not query redundant `do_back_transformed_particles` (#3183)Gravatar Neïl Zaim 1-3/+1
* Do not query redundant do_back_transformed_particles * Only set m_do_back_transformed_particles to true if write_species is true
2022-10-21Fix unused import warnings in python analysis scripts (#3472)Gravatar Neïl Zaim 2-5/+2
* 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>
2022-10-21User-Specified Used Inputs File (#3462)Gravatar Axel Huebl 4-3/+15
Allow users to overwrite the default for the "used inputs" file that we write.
2022-10-19OLCF Jupyter: Mamba is Pre-Installed (#3471)Gravatar Axel Huebl 1-4/+1
Mamba is now pre-installed on OLCF Jupyter base images! :)
2022-10-18AMReX: Weekly Update (#3469)Gravatar Axel Huebl 10-32/+32
2022-10-17Update GCC Requirement (#3470)Gravatar Axel Huebl 1-1/+1
* 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
2022-10-13CI: Fix macOS OMP (#3465)Gravatar Axel Huebl 2-0/+16
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) ```
2022-10-12Correct particle positions outside refined injection (#3463)Gravatar Remi Lehe 3-33/+47
* Correct particle positions outside refined injection * Improve test * Update benchmark * Update Examples/Physics_applications/laser_acceleration/analysis_refined_injection.py
2022-10-11openPMD Engines: Allow Params w/o Type (#3460)Gravatar Axel Huebl 1-10/+20
The current implementation only accepted parameters for ADIOS2 engines if the engine type was also specified. That is not necessary, the default (bp4) will usually be taken and thus the documentation did not work. This fixes it, keeping the engine type optional in the inputs.
2022-10-11Docs: Expand Debugging Workflow (#3461)Gravatar Axel Huebl 1-0/+30
Add more instructions how to debug errors seen in *Release* mode.
2022-10-10AMReX: Weekly Update (#3459)Gravatar Axel Huebl 5-5/+5
2022-10-10Add functions for reading particle id and cpu numbers correctly (#3457)Gravatar Andrew Myers 5-9/+234
2022-10-10Partial refactoring of the utils directory (#3404)Gravatar Luca Fedeli 95-1599/+1997
* initial work to clean WarpX Utils * remove AMRCore from Ionization tables * progress * refactoring of a part of the utils directory * fix bug * fixed bug * fixed bug * remove debug line accidentally slipped into the code * remove debug line accidentally slipped into the code * remove debug line accidentally slipped into the code * cleaning * fixed bug
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>
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