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2023-05-22CUDA: Recommend 11.3+ (#3932)Gravatar Axel Huebl 1-1/+1
We already saw C++17 issues with the earlier CUDA releases in the 11.0 line and found on Summit (and with ImpactX) that CUDA 11.3+ is more reliable - and now widely available.
2023-05-22Doc: Summit ADIOS 2.8.1 (#3931)Gravatar Axel Huebl 1-1/+1
Update ADIOS2 on Summit to a more modern release.
2023-05-19Implement legacy mode for external laser file reading (#3923)Gravatar Ilian Kara-Mostefa 19-422/+1043
* Implement legacy mode * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix file_name initialization for RZ test * Clear commented-out code * Change permission * import sys in analysis_2d_binary.py & add checksum test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add explanations in class file and update the docs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ignore y_min and y_max allocation in 2D * fix syntax * Implement warnings, improving docs, fix indentation * [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> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2023-05-18Doc: ux,uy,uz momenta and improving docs (#3930)Gravatar Ilian Kara-Mostefa 1-8/+9
2023-05-17AMReX: Weekly Update (#3926)Gravatar Axel Huebl 5-5/+5
2023-05-16Fix calculation of `b0` in binary collisions (#3928)Gravatar Severin Diederichs 1-0/+1
2023-05-16Remove Harris laser (#3929)Gravatar Remi Lehe 5-154/+1
2023-05-16Bug fix - PEC - Remove duplicate boundary cell updates for rho and J (#3890)Gravatar Roelof Groenewald 12-653/+434
* break application of PEC to rho into separate loops over boxes * round #1: fix failing CI tests * also apply the fix to the `ApplyPECtoJfield` * round 2: fix failing CI tests * round 3: fix failing CI tests * refactor PEC handling for charge and current density * removed unused variable * round 4: fix failing CI tests * Fix `mirrorfac` calculation for `rho` * only apply rho and J PEC boundaries for Cartesian grid (for now) in `SyncCurrentAndRho()` * use the same kernel to apply PEC boundary to rho and J * perform J and rho PEC application for RZ but warn about incorrect results if r_max is PEC * do not apply PEC boundary for rho and J to r-max in RZ * set warning level to medium and increase abort_on_warning_threshold to high for failing CI tests
2023-05-16Doc: LASY 0.1.1 (#3920)Gravatar Axel Huebl 3-2/+3
* Doc: LASY 0.1.1 Document the LASY dependency for installs. * Keep Py versions simple
2023-05-15CMake: Simplify Lib Symlink (#3925)Gravatar Axel Huebl 1-6/+1
Use the same suffix logic as for the install to create the `libwarpx.ND.[so|dll]` in the build path.
2023-05-15Add a link to CMake documentation in the WarpX build section (#3924)Gravatar Ilian Kara-Mostefa 1-4/+4
* Add a links to CMake docs in cmake.rst Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-05-12Doc: ux,uy,uz Momenta (#3916)Gravatar Axel Huebl 1-3/+4
* Doc: ux,uy,uz Momenta The scales of these quantities in user-facing inputs are the scale of a momenta (gamma*beta or p/mc), not of a velocity. * Fix Math Formatting
2023-05-12Moving window: check pointers to F,G when applying shift (#3897)Gravatar Adam Bensoubaya 1-2/+2
* Moving window: check pointers to F,G when applying shift * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Apply suggestions from code review --------- Co-authored-by: Bensoubaya <adam@bc-d0-74-0-dd-e4.dhcp.lbnl.us> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2023-05-11Fix typo in Adastra cluster documentation (#3918)Gravatar Neïl Zaim 1-1/+1
2023-05-10Docs: Conda Dev w/ Boost (#3911)Gravatar Axel Huebl 1-2/+2
Add the `boost` package to the conda developer environment. Used for QED table generation.
2023-05-09Do not duplicate protected member of base class (#3915)Gravatar Edoardo Zoni 16-23/+0
2023-05-08Field Gather: Generalize FGcell (#3909)Gravatar Axel Huebl 1-3/+8
Replace explicit array with little formula for the range of the support function of shape factors.
2023-05-08AMReX: Weekly Update (#3907)Gravatar Axel Huebl 5-5/+5
2023-05-08Cleanup: rocFFT Includes (#3908)Gravatar Axel Huebl 2-6/+0
Newer versions fixed the include issue that required us to use `<cstddef>` includes before including rocFFT. Fixed with >4.3.
2023-05-08Enable field ionization from PICMI (#3298)Gravatar Neïl Zaim 6-15/+198
* Enable field ionization from PICMI * Implement Dave's suggestions and add automated test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update test benchmark * Add docstring for FieldIonization class --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-05-08ROCm 5.2+ (#3906)Gravatar Axel Huebl 6-12/+23
* rocFFT: 5.2+ Compatible More careful include for old versions of rocFFT/ROCm. * ROCm: 5.2+
2023-05-08remove unnecessary #include (#3891)Gravatar Luca Fedeli 1-1/+0
2023-05-08make Poisson Solver in ablastr depend only on ablastr (and AMReX) (#3892)Gravatar Luca Fedeli 1-2/+1
2023-05-08fix PoyntingVec calc (#3905)Gravatar Revathi Jambunathan 1-1/+1
2023-05-07Implement reading of laser files produced by lasy (#3871)Gravatar Ilian Kara-Mostefa 18-633/+1033
* Imported openPMD * Unable to add E * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Source/Laser/LaserProfilesImpl/LaserProfileFromTXYEFile.cpp * Updated read data t chunk * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Began modifying parse_tyxe_file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * set coordinates * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * corrected errors * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Clean up .H file * Extract grid coordinates * Corrected field name * Implement laser oscillations * More correct position * More correct position * Updated test script, corrected laser normalization * Cleaned up code * Began editing analysis.py (needs debugging) * Support reading complex data * Update AMReX depsndency to use Bcast with complexs * Update test * Update Source/Laser/LaserProfilesImpl/LaserProfileFromTXYEFile.cpp * Correct the implementation of the test with Gaussian profile, fix and clean up previous code * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add `lasy` in dependencies * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add checksum regression test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add enabling condition if WarpX is compiled with OpenPMD support * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update lasy download link * Updating analysis.py * Update LaserProfileFromTXYEFile.cpp * Fix compilation in 1D * Update LaserProfileFromTXYEFile.cpp for enabling condition if WarpX is compiled with OpenPMD support * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update LaserProfileFromTXYEFile.cpp * Change unused vectors to scalars and cleanup code * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update automated test * Implement reading chunks of openPMD file as an input parameter * Update checksum * Update warning message if WarpX is not compiled with openPMD support * Do not output By (too sensitive to noise) * Remove By from checksum * Update Source/Laser/LaserProfilesImpl/LaserProfileFromTXYEFile.cpp * Update Source/Laser/LaserProfilesImpl/LaserProfileFromTXYEFile.cpp * Update Source/Laser/LaserProfilesImpl/LaserProfileFromTXYEFile.cpp * Update inputs file for chunks reading * Correct dimensions assignment * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Code consistent with axilabels * Start support for 2D and 1D * Update LaserProfileFromTXYEFile.cpp for 2D reading * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Implementation of a 2D test * Implementation of 1D reading & 1D test * Fix call to trilinear_interp * Fix indentation * Implement RZ reading & test & fix 2D Checksum test * Update docs * Update WarpX-test.ini --------- Co-authored-by: Camille Woicekowski <camille.meala@berkeley.edu> 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>
2023-05-05More Managed Memory Fixes: Diagnostics (#3899)Gravatar Prabhat Kumar 2-3/+4
* Interpolate on GPU * another fix in Diagnostics
2023-05-05Prevent implicit capture on GPU for RZ sims (#3895)Gravatar Remi Lehe 1-1/+2
2023-05-05Change CartesianCKCAlgorithm.H (#3898)Gravatar Ilian Kara-Mostefa 1-1/+3
2023-05-05Fix: RTD (#3896)Gravatar Axel Huebl 1-1/+13
Use a newer Ubuntu that ships a recent OpenSSL when building Sphinx with RTD. This migrates a broken dependency for urllib3 in version 3+.
2023-05-04Fix: Laser-Ion Example Gather (#3894)Gravatar Axel Huebl 2-21/+26
Guarantee improved plasma stability for 2D with very low initial target temperature when using Esirkepov current deposition with energy-conserving field gather (default).
2023-05-04Replace 3 occurrencess of NULL with std::nullptr (#3893)Gravatar Luca Fedeli 2-3/+3
* replace NULL with std::nullptr everywhere * fix bug
2023-05-02Release 23.05 (#3887)Gravatar Axel Huebl 14-23/+25
* AMReX: 23.05 * PICSAR: 23.05 * WarpX: 23.05 * Update ES EB RZ Tests - slightly relaxed Phi - better selection of r outside cutcells
2023-05-02Fix: rocFFT 5.5 (#3888)Gravatar Axel Huebl 4-4/+8
``` /opt/rocm-5.5.0/include/rocfft.h:16:2: error: "This file is deprecated. Use the header file from /opt/rocm-5.5.0/include/rocfft/rocfft.h by using #include <rocfft/rocfft.h>" [-Werror,-W#warnings] warning "This file is deprecated. Use the header file from /opt/rocm-5.5.0/include/rocfft/rocfft.h by using #include <rocfft/rocfft.h>" ^ ```
2023-05-01Add documentation to compile and use WarpX on Adastra (CINES) supercomputer ↵Gravatar Luca Fedeli 4-0/+231
(#3852) * add documentation for Adastra supercomputer * add Adastra to toc * Update Docs/source/install/hpc/adastra.rst Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> --------- Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-05-01Use WARPX_ABORT_WITH_MESSAGE("msg") instead of ↵Gravatar Luca Fedeli 50-180/+207
amrex::Abort(Utils::TextMsg::Err("msg")) (#3879) * use WARPX_ABORT_WITH_MSG instead of amrex::Abort(Utils::TextMsg::Err(msg)) [WIP] * use WARPX_ABORT_WITH_MESSAGE * fix typo * fix missing parenthesis * remove spaces to prevent automatic text wrapping * remove wrong parenthesis
2023-05-01Doc: Latest HDF5 on Summit (#3838)Gravatar Axel Huebl 2-2/+2
* Doc: Latest HDF5 on Summit Update the Summit docs to use the latest available HDF5 module (v1.12.1). * Summit: hdf5/1.12.2
2023-05-01Docs: Boosted Frame Inputs (#3857)Gravatar Axel Huebl 1-8/+6
Outdated docs: No, all inputs are lab-frame, besides `stop_time`.
2023-04-29Fix typo in parameters doc (period -> intervals) (#3877)Gravatar Neïl Zaim 1-1/+1
2023-04-29CI: macOS Cache Less (#3878)Gravatar Axel Huebl 1-1/+3
Cache only selected brew paths in macOS, not all of `/usr/local`, which contains more runner specific software.
2023-04-29adding reconnection paper (#3886)Gravatar Revathi Jambunathan 1-0/+9
2023-04-28Add new paper using WarpX (#3882)Gravatar Remi Lehe 1-0/+5
* Add new paper using WarpX * [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>
2023-04-28correct a formatting error in the Fugaku documentation (#3885)Gravatar Luca Fedeli 1-0/+1
2023-04-28Build buffer masks on GPU (#3880)Gravatar Weiqun Zhang 2-47/+15
2023-04-28Moving window: fix logic to shift F,G fields w/ div(E),div(B) cleaning in ↵Gravatar Prabhat Kumar 1-4/+24
PML (#3884)
2023-04-27fix recently re-introduced bug (#3875)Gravatar Luca Fedeli 1-1/+2
2023-04-27Fix missing GPU synchronization when QED lookup tables are loaded or ↵Gravatar Luca Fedeli 5-1047/+1105
generated (#3873) Add thin wrapper aroung amrex::Gpu::DeviceVector in order to be able to use it in lookup tables also when managed memory is not used.
2023-04-26Shared memory charge and current deposition (#3368)Gravatar Andrew Myers 10-139/+1328
* Use GPU shared memory to accelerate charge deposition (#66) * WIP Apply charge deposition unconditionally in scratch memory * Ensure enough threads to touch every value in the array, even if there are no particles * Zero out the shared memory before accumulating into it * Replace box-aware accumulation of final results with simple pointers * Remove unused code * WIP * Account for shared memory being allocated per-block, not per grid/kernel * Wording * Fall back to non-shared memory for cases where the grid size is too big to fit, for now * Filter out additions of 0.0 from atomic accumulation * Restore non-GPU code path * Pick apart #if stuff to allow better formatting and comprehension * Fix egregious whitespace failure * Abort on insufficient shared memory, rather than falling back to global memory * Fix silly whitespace * Fix stray tab character * Sort and bin particles, pass bins to charge deposition * Contribute on a binned tile basis; memory errors now * Initialize array to the extent we actually allocated * Make sure we initialize the vector the tboxes with invalid Box objects * in 2D, we make sure we use the same particle position to tile box mapping as amrex * go ahead and skip empty bins in deposit charge * Quiet warning from HIP * Avoid signed/unsigned comparison * Code compiles for CPU ... * Rename intermediate buffer back to reduce extraneous diff bits * Remove another extraneous diff bit * Leave DPC++ out in the cold, since it expects different syntax for GPU-specific code * Reset failing value of rho that only slightly changes * Try tiling over ng_rho to capture particles moved into guard cells * Match box expansion in both call sites - maybe the third is also necessary * Grow last box by ng_rho as well. * Match macro syntax * Use WarpX dimensionality macros instead of AMREX_SPACEDIM * Add support for 1D case * Update benchmark checksums for ME tests * Fix macro used for 1D * Fix CUDA compilation * Rename variable to simplify diff * Clear up assertions now that stuff is working * Fix comment referring to current in ChargeDeposition.H * Fix warning about unused variable after assertion change * add runtime option * Convert flag variable from int to bool * Switch AMREX_SPACEDIM conditions to use WARPX_DIM_* macros * Once again, leave DPC++ out in the cold, as it doesn't support the same syntax as CUDA and HIP * Grow charge deposition boxes by the necessary amount * Mark a variable only used for assertions to suppress warnings * Fix compilation error for 1D * Re-add missing 1D support * Fix other bits of codfe specific to CUDA and HIP, and not DPC++ * restore missing accumulation of thread local charge into main fab. * reset benchmark for background_mcc because randomization makes it very sensitive * reset benchmark for Langmuir_multi_psatd_div_cleaning because diffing field is a numerical artifact * Calm nvcc about function missing a return * reset benchmark for background_mcc because it's randomized and numerically chaotic * reset benchmark for LaserAccelerationBoost because of numerical shift in momentum from charge deposition order * Remove extra nesting level * Skip sorting the particles and just access them according to the binned permutation * Load permutation pointer outside GPU kernel * Revert background_mcc benchmark values * Loosen overly-strict checksum tolerances in single-precision tests, rather than changing target values * Revert embedded_circle * Convert AMREX_ALWAYS_ASSERT to AMREX_ASSERT for particle bounds checking * Match assertion macro change from #2939 * Fix indentation * Disable shared memory charge deposition by default * Ignore variable only used in assertion * Add documentation of added input parameter warpx.do_shared_mem_charge_deposition * Add comments as suggested by Remi * Docs: Fix syntax issues in parameters.rst * Convert error check to unconditional assertion as requested * Make some arguments const to ease refactoring * Finished DepositCurrent function Ready to call the function from CurrentDeposition.H, but currently there is only a dummy function there * AMReX: Weekly Update * Reset: `reduced_diags_single_precision` * Reset: `background_mcc_dp_psp` * Merged with develop. runs on mpi no gpu * All funcs implemented. Compiles with bugs * Fixed typo in CurrentDeposition * Working on 2D version. there is bug jz doesn't line up correctly * Fixed 2d bug * Removed some debugging lines * Cleaning up comments * Added an input param for threads per block * Added a variable NS and START/STOP * Added a region for kernel * Not working on tilesize > 1 1 1 * Implemented Andrews new algo for max tilesize * Reduce the amount of shared memory needed by re-using the same buffer for all three components * Made default tilesize sort_bin_size LAST V1 COMMIT * bugfix - don't add 0.0 cells back to global memory. * Need to take abs before checking > 0.0 * Ran Whitespace Fixer As instructed * Updated Comments * change default tpb for current deposition to 128 * clean up comments * quiet compiler warning * remove unused variables * refactor shared current depo code * forgot to check in file * fix cpu compilation * fix uninitialized * fix typo * fix bad merge * Fixed default tilesize bug Previously had defualted shared_tilesize to sort_bin_size. This was overwritting the shared_tilesize. Some scanning shows that sort_bin_size isn't a very good default for tilesize anyways, so the new default is 1 1 1. * changed shared tilesize default to 6 6 8 Decision based on scan over tilesizes and ppc by @atmyers and @kaplannp * Put in switches for default tilesize 288 3d 144 2d Tested correctness in 2 and 3 d * Simplified parcticle contribution section In accordance to @AlexanderSinn feedback, and tested RZ, 2D, 3D * Cleanup tbox construction and depos->(depos+1)/2 in accordance to changes proposed by @AlexanderSinn. Tested on 3D 2D and RZ * Restored shared to previous version from 6acab48 Changes from before broke single precision * Found new spot to benefit from (depos_order+1)/2 * Cleaned up sloppy comments * Throw error on shared if no hip or cuda This commit makes the assumption that if you use shared, you must be using HIP or CUDA. This allows us to remove a bunch of macros that tried to quietly revert to non shared if you didn't use HIP/CUDA, and we now throw error if you try to run without HIP/CUDA * More cleanup to compile and test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add cost to GPU clock conditional Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Particles/Deposition/CurrentDeposition.H Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * add cost to GPU clock conditional Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * whitespace fix Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Updated tilesize docs, and change 1d/rz default * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Added docs for tpb * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Changed grow (depos_order+1)/2->depos_order Turns out, above fails for shape 2 * Change default to non share, and add error check throws errors if you try vay or esirkepov with shared, and defaults to not using shared for all algos. * update to use ablaster kernel timer Compiles and runs, but at step 80 diverges from dev --------- Co-authored-by: Phil Miller <unmobile+gh@gmail.com> Co-authored-by: Phil Miller <phil@intensecomputing.com> Co-authored-by: Tools <warpx@lbl.gov> Co-authored-by: kaplannp <kaplannp@gmail.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: kaplannp <56896283+kaplannp@users.noreply.github.com> Co-authored-by: kaplannp <kaplannp@whitman.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-04-26Don't rely on managed memory in SmartUtils (#3874)Gravatar Andrew Myers 1-5/+27
* Don't rely on managed memory in SmartUtils * use different copy * Policies Vector: Explicit Device Copy Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-04-24Docs: suppress Sphinx warning of duplicate bibliography labels (#3869)Gravatar Roelof Groenewald 1-0/+2
* suppress sphinx warning about duplicate bibliography labels * [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>
2023-04-24AMReX: Weekly Update (#3868)Gravatar Axel Huebl 5-5/+5
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