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Fix out-of-bound in the initialization of EB #2607

Merged
merged 4 commits into from
Dec 3, 2021
Merged

Fix out-of-bound in the initialization of EB #2607

merged 4 commits into from
Dec 3, 2021

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RemiLehe
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@RemiLehe RemiLehe commented Nov 30, 2021 •
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When compiling with EB in debug mode, I got an out-of-bound message at this line:
https://github.com/ECP-WarpX/WarpX/blob/development/Source/EmbeddedBoundary/WarpXInitEB.cpp#L140
It seems that some of the internal structures for EB in amrex (used e.g. in getType) have only 1 guard cells, whereas we pass a box that has more guard cells.

Instead, this PR does not add the guard cells in the box passed in getType, and instead the guard cells are filled by an additional FillBoundary.
Instead, this PR calls getType by passing a box that does not have guard cells (but adds the guard cells when actually touching the edge_length and face_area arrays.

@RemiLehe RemiLehe requested a review from lgiacome November 30, 2021 17:47
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lgiacome commented Nov 30, 2021 •
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I don't think I fully understand why this happens, but your solution looks great to me. We need the same changes in ScaleEdges , ScaleAreas and MarkCells, don't we?

@RemiLehe
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I don't think we need the same change for ScaleEdges, ScaleAreas and MarkCells, because these do not call the function getType.

The problem is really with getType, since it seems that, under the hood, getType looks up an internal EB structure which has only one guard cell, and does so for every single cell of the box that is passed to getType.

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Now I see, thanks a lot for the explanation.
Unfortunately, all the CI tests with EM and EB fail and it seems like the new changes don't work, but on my laptop they compile fine :/ is there a way to see a full traceback from the azure tests?

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EZoni commented Dec 1, 2021 •
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Unfortunately, all the CI tests with EM and EB fail and it seems like the new changes don't work, but on my laptop they compile fine :/ is there a way to see a full traceback from the azure tests?

@lgiacome Hi Lorenzo, in the table with all the checks on this page here you can click the link "Details" next to the red ones (the ones that failed), then click the link that will say "1 errors / 0 warnings" (or something similar), then click on the failing job (e.g. "embedded boundary" in this case), then click on "Build & test" and you'll see on your right the raw log with the backtraces printed out for the individual tests that failed (you can also view/download this raw log in a separate window, if needed). Keep in mind that those backtraces are not generated in DEBUG mode (we don't run in DEBUG mode on Azure), so the information might not be as clear and useful as the one you get in DEBUG mode. Anyways let me know if you find those backtraces by following these steps!

Update Note that I do see some tests crashing even locally. For instance, if I run locally ./run_test.sh embedded_boundary_cube on this branch fix_eb_out_of_bound, the test does crash, with backtraces. Hope this is useful info for debugging.

@ax3l ax3l added component: boundary PML, embedded boundaries, et al. bug Something isn't working bug: affects latest release Bug also exists in latest release version labels Dec 1, 2021
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lgiacome commented Dec 2, 2021

@EZoni thanks a lot for both the points! I'll look into running this locally then and see what's going on.

@RemiLehe RemiLehe changed the title When initializing EB quantities, do not explicitly touch guard cells, but call FillBoundary Fix out-of-bound in the initialization of EB Dec 2, 2021
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Looks great thanks Remi 👍

@ax3l ax3l self-assigned this Dec 2, 2021
@ax3l ax3l requested a review from WeiqunZhang December 2, 2021 18:28
@ax3l ax3l assigned WeiqunZhang and unassigned ax3l Dec 2, 2021
@ax3l ax3l merged commit 5a2d3e7 into ECP-WarpX:development Dec 3, 2021
roelof-groenewald added a commit to ModernElectron/WarpX that referenced this pull request Dec 3, 2021
@roelof-groenewald @ax3l
@EZoni @RemiLehe @lgiacome @KZhu-ME @peterscherpelz @dpgrote @PhilMiller @s9105947 @tropf @prkkumar
Update memaster (#110)
033b51e 
* Fix Init of Vector Members (ECP-WarpX#2595)

Fix default init of `Vector` member variables. The old construct
is not valid C++.

https://stackoverflow.com/a/11491003/2719194

* C++17: Work-Around NVCC gatherParticles (ECP-WarpX#2596)

The `noexcept` lambda does not compile in C++17 mode due to an NVCC compiler bug, at least in NVCC 11.3.109. Compiles in C++14 mode with the same compiler.

* requirements.txt - PICMI development version (ECP-WarpX#2588)

Document in `requirements.txt` on how to install a pre-release
version of PICMI.

* CONTRIBUTING: Update/Modernize (ECP-WarpX#2600)

* CONTRIBUTING: Update/Modernize

- Add GitHub account setup
- Add local git setup
- Modernize for CMake workflows

* Apply suggestions by Edoardo

Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>

* Replaced duplicated current deposition documentation (ECP-WarpX#2604)

* Throwing a warning if particle_shape>1 with EB (ECP-WarpX#2592)

* Aborting if particle_shape!=1 with EB

* Throw warning instead of aborting

* Checking at runtime if EB is initialized

* Added missing preprocessor directive

* Ignoring an unused variable

* Fix typo

* Improve style

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* Fix segfault when importing _libwarpx without initializing WarpX (ECP-WarpX#2580)

* Added check for if warpx was initialized when calling finalize

* Renamed to be warpx_initialized

* Fixed reference to global variable

Co-authored-by: Peter Scherpelz <31747262+peterscherpelz@users.noreply.github.com>

* Changed global variable to member of libwarpx

* Fixed syntax errors

* Remove custom arg from argv to avoid parmparse error

Co-authored-by: Peter Scherpelz <31747262+peterscherpelz@users.noreply.github.com>

* Added parallel pragma to ApplyBoundaryConditions (ECP-WarpX#2612)

* Note that CCache 4.2 introduced large CUDA improvements (ECP-WarpX#2606)

* Dimensionality Docs: Default (ECP-WarpX#2609)

Just adds the note that 3D is the default geometry.

* AMReX: Weekly Update (ECP-WarpX#2613)

* MergeBuffersForPlotfile: Barrier (ECP-WarpX#2608)

Make sure that all MPI ranks are in sync, i.e., have closed the
files that they wrote, before trying to merge them.

* Fix installation location for libraries (ECP-WarpX#2583)

During configuration the installation location for libraries is given by
dumping the cmake variable `CMAKE_INSTALL_LIBDIR`.
This commit adjusts the installation of WarpX libraries (WarpX_LIB=ON)
to respect this setting.

Co-authored-by: Rolf Pfeffertal <tropf@users.noreply.github.com>

* Release 21.12 (ECP-WarpX#2614)

* AMReX: 21.12

* PICSAR: 21.12

* WarpX: 21.12

* div(E,B) Cleaning Options for PSATD (ECP-WarpX#2403)

* Implement div(E)/div(B) Cleaning with Standard PSATD

* Cleaning

* Update Benchmark

* Add Nodal Synchronization of F,G

* OneStep_multiJ: Nodal Syncs, Damp PML

* OneStep_multiJ: Push PSATD Fields in PML

* div Cleaning Defaults (Domain v. PML)

* Include Fix of ECP-WarpX#2429 until Merged

* Reset Benchmark of Langmuir_multi_psatd_div_cleaning

* Multi-J: Remove PML Support

* Include Fix of ECP-WarpX#2474 Until Merged

* Exchange All Guard Cells for F,G

* Fix Defaults

* Update Test, Reset Benchmark

* Fix Defaults

* Cleaning

* Default update_with_rho=1 if do_dive_cleaning=1

* Update CI Test pml_psatd_dive_divb_cleaning

* Replace Warning with Abort

* Add 2D Langmuir Test w/ MR & PSATD (ECP-WarpX#2605)

* Add 2D Langmuir Test w/ MR & PSATD

* Add Missing Compile String

* Fix out-of-bound in Inverse FFT of F,G (ECP-WarpX#2619)

* Mention that the potentail should be constant inside EB (ECP-WarpX#2618)

* Mention that the potentail should be constant inside EB

* Update text

* Replace AMREX_SPACEDIM: Boundary & Parallelization (ECP-WarpX#2620)

* AMREX_SPACEDIM : Boundary Conditions
* AMREX_SPACEDIM : Parallelization
* Fix compilation
* Update Source/Parallelization/WarpXComm_K.H

* Fix out-of-bound in the initialization of EB (ECP-WarpX#2607)

* Call FillBoundary when initializing EB

* Avoid out-of-bound

* Bug fix

* Apply suggestions from code review

* update version number

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Lorenzo Giacomel <47607756+lgiacome@users.noreply.github.com>
Co-authored-by: Kevin Z. Zhu <86268612+KZhu-ME@users.noreply.github.com>
Co-authored-by: Peter Scherpelz <31747262+peterscherpelz@users.noreply.github.com>
Co-authored-by: David Grote <grote1@llnl.gov>
Co-authored-by: Phil Miller <phil@intensecomputing.com>
Co-authored-by: s9105947 <80697868+s9105947@users.noreply.github.com>
Co-authored-by: Rolf Pfeffertal <tropf@users.noreply.github.com>
Co-authored-by: Prabhat Kumar <89051199+prkkumar@users.noreply.github.com>
@KZhu-ME KZhu-ME mentioned this pull request Dec 7, 2021
Merged
@RemiLehe RemiLehe mentioned this pull request Dec 8, 2021
Merged
lgiacome added a commit to lgiacome/WarpX that referenced this pull request Dec 8, 2021
@lgiacome
Undoing ECP-WarpX#2607
00f6c04
RemiLehe pushed a commit that referenced this pull request Dec 13, 2021
@lgiacome
Fixing the initialization of the EB data in ghost cells (#2635)
9001fe9 
* Using ng_FieldSolver ghost cells in the EB data

* Removed an unused variable

* Fixed makeEBFabFactory also in in WarpXRgrid.cpp

* Fixed end of line whitespace

* Undoing #2607
roelof-groenewald added a commit to ModernElectron/WarpX that referenced this pull request Dec 14, 2021
@roelof-groenewald @ax3l
@prkkumar @lucafedeli88 @s9105947 @EZoni @PhilMiller @lgiacome @WeiqunZhang @NeilZaim @RemiLehe @KZhu-ME @atmyers
Memaster update to latest upstream development (#118)
cec979a 
* C++17, CMake 3.17+ (ECP-WarpX#2300)

* C++17, CMake 3.17+

Update C++ requirements to compile with C++17 or newer.

* Superbuild: C++17 in AMReX/PICSAR/openPMD-api

* Summit: `cuda/11.0.3` -> `cuda/11.3.1`

When compiling AMReX in C++17 on Summit, the `cuda/11.0.3` module
(`nvcc 11.0.2211`) dies with:
```
... Base/AMReX_TinyProfiler.cpp
nvcc error   : 'cicc' died due to signal 11 (Invalid memory reference)
nvcc error   : 'cicc' core dumped
```

Although this usually is a memory issue, it also appears in `-j1`
compiles.

* Replace AMREX_SPACEDIM: Evolve & FieldSolver (ECP-WarpX#2642)

* AMREX_SPACEDIM : Boundary Conditions

* AMREX_SPACEDIM : Parallelization

* Fix compilation

* AMREX_SPACEDIM : Initialization

* Fix Typo

* space

* AMREX_SPACEDIM : Particles

* AMREX_SPACEDIM : Evolve and FieldSolver

* C++17: structured bindings to replace "std::tie(x,y,z) = f()" (ECP-WarpX#2644)

* use structured bindings

* std::ignore equivalent in structured bindings

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* Perlmutter: December Update (ECP-WarpX#2645)

Update the Perlmutter instructions for the major update from
December 8th, 2021.

* 1D tests for plasma acceleration (ECP-WarpX#2593)

* modify requirements.txt and add input file for 1D Python pwfa

* add 1D Python plasma acceleration test to CI

* picmi version

* USE_PSATD=OFF for 1D

* Update Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration_1d.py

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* Update Regression/WarpX-tests.ini

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* Cartesian1D class in pywarpx/picmi.py

* requirements.txt: update picmistandard

* update picmi version

* requirements.txt: revert unintended changes

* 1D Laser Acceleration Test

* Update Examples/Physics_applications/laser_acceleration/inputs_1d

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* Update Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration_1d.py

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* add data_list to PICMI laser_acceleration test

* increase max steps and fix bug in pywarpx/picmi.py 1DCartesian moving window direction

* add data_lust to Python laser acceleration test

* picmistandard update

Co-authored-by: Prabhat Kumar <prabhatkumar@kraken.dhcp.lbl.gov>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* CMake 3.22+: Policy CMP0127 (ECP-WarpX#2648)

Fix a warning with CMake 3.22+.

We use simple syntax in cmake_dependent_option, so we are compatible with the extended syntax in CMake 3.22+:   https://cmake.org/cmake/help/v3.22/policy/CMP0127.html

* run_test.sh: Own virtual env (ECP-WarpX#2653)

Isolate builds locally, so we don't overwrite a developer's
setup anymore. This also avoids a couple of nifty problems that
can occur by mixing those envs.

Originally part of ECP-WarpX#2556

* GNUmake: Fix Python Install (force) (ECP-WarpX#2655)

Local developers and cached CI installs ddi never install `pywarpx`
if and old version existed. The `--force` must be with us.

* Add: Regression/requirements.txt

Forgotten in ECP-WarpX#2653

* Azure: `set -eu -o pipefail`

Lol, that's not the default.
We previously had `script` where it was the default.

Introduced in ECP-WarpX#2615

* GNUmake & `WarpX-test.ini`: `python` -> `python3`

Consistent with all other calls to Python in tests.

* Fix missing checksums1d (ECP-WarpX#2657)

* Docs: Fix missing Checksum Ref

* Checksum: LaserAcceleration_1d

* Checksum: Python_PlasmaAcceleration_1d

* Regression/requirements.txt: openpmd-api

Follow-up to 8f93e01

* Azure: pre-install `setuptools` upgrade

Might fix:
```
 - installing setuptools_scm using the system package manager to ensure consistency
 - migrating from the deprecated setup_requires mechanism to pep517/518
   and using a pyproject.toml to declare build dependencies
   which are reliably pre-installed before running the build tools

  warnings.warn(
TEST FAILED: /home/vsts/.local/lib/python3.8/site-packages/ does NOT support .pth files

You are attempting to install a package to a directory that is not
on PYTHONPATH and which Python does not read ".pth" files from.  The
installation directory you specified (via --install-dir, --prefix, or
the distutils default setting) was:

    /home/vsts/.local/lib/python3.8/site-packages/

and your PYTHONPATH environment variable currently contains:

    ''

Here are some of your options for correcting the problem:

* You can choose a different installation directory, i.e., one that is
  on PYTHONPATH or supports .pth files

* You can add the installation directory to the PYTHONPATH environment
  variable.  (It must then also be on PYTHONPATH whenever you run
  Python and want to use the package(s) you are installing.)

* You can set up the installation directory to support ".pth" files by
  using one of the approaches described here:

  https://setuptools.readthedocs.io/en/latest/easy_install.html#custom-installation-locations

Please make the appropriate changes for your system and try again.
```

* GNUmake `installwarpx`: `mv` -> `cp`

No reason to rebuild. Make will detect dependency when needed.

* Python GNUmake: Remove Prefix Hacks

FREEEEDOM. venv power.

* Azure: Ensure latest venv installed

* Python/setup.py: picmistandard==0.0.18

Forgotten in ECP-WarpX#2593

* Fix: analysis_default_regression.py

Mismatched checksum file due to crude hard-coding.

* PWFA 1D: Fix output name

Hard coded, undocumented convention: turns out this must be the name
of the test that we define in the ini file. Logical, isn't it. Not.

Follow-up to ECP-WarpX#2593

* Docs: `python3 -m pip` & Virtual Env (ECP-WarpX#2656)

* Docs: `python3 -m pip`

Use `python3 -m pip`:
- works independent of PATH
- always uses the right Python
- is the recommended way to use `pip`

* Dependencies: Python incl. venv

Backported from ECP-WarpX#2556.

Follow-up to ECP-WarpX#2653

* CMake: 3.18+ (ECP-WarpX#2651)

With the C++17 switch, we required CMake 3.17+ since that one introduced the `cuda_std_17` target compile feature.

It turns out that one of the many CUDA improvements in CMake 3.18+ is also to fix that feature for good, so we bump our requirement in CMake. Since CMake is easy to install, it's easier to require a clean newer version than working around a broken old one.

Spotted first by Phil on AWS instances, thx!

* fix check for absolute library install path (ECP-WarpX#2646)

Co-authored-by: Hannes T <s9105947@users.noreply.github.com>

* use if constexpr to replace template specialization (ECP-WarpX#2660)

* fix for setting the boundary condition potentials in 1D ES simulations (ECP-WarpX#2649)

* `use_default_v_<galilean,comoving>` Only w/ Boosted Frame (ECP-WarpX#2654)

* ICC CI: Unbound Vars (`setvars.sh`) (ECP-WarpX#2663)

Ignore:
```
/opt/intel/oneapi/compiler/latest/env/vars.sh: line 236: OCL_ICD_FILENAMES: unbound variable
```

* QED openPMD Tests: Specify H5 Backend (ECP-WarpX#2661)

We default to ADIOS `.bp` if available. Thus, specify HDF5 assumption

* C++17: if constexpr for templates in ShapeFactors (ECP-WarpX#2659)

* use if constexpr to replace template specialization

* Rmove Interface Annotations

* Replace static_assert with amrex::Abort

* Add includes & authors

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* ABLASTR Library (ECP-WarpX#2263)

* [Draft] ABLASTR Library

- CMake object library
- include FFTW wrappers to start with

* Add: MPIInitHelpers

* Enable ABLASTR-only builds

* Add alias WarpX::ablastr

* ABLASTR: openPMD forwarding

* make_third_party_includes_system: Avoid Collision

* WarpX: depend on `ablastr`

* Definitions: WarpX -> ablastr

* CMake: Reduce build objects for ABLASTR

Skip all object files that we do not use in builds.

* CMake: app/shared links all object targets

Our `PRIVATE` source/objects are not PUBLICly propagated themselves.

* Docs: Fix Warning Logger Typo (ECP-WarpX#2667)

* Python: Add 3.10, Relax upper bound (ECP-WarpX#2664)

There are no breaking changes in Python 3.10 that affect us.

Giving the version compatibility of Python and it's ABI stability,
there is no need at the moment to provide an upper limit. Thus,
relaxed now in general.

* Fixing the initialization of the EB data in ghost cells (ECP-WarpX#2635)

* Using ng_FieldSolver ghost cells in the EB data

* Removed an unused variable

* Fixed makeEBFabFactory also in in WarpXRgrid.cpp

* Fixed end of line whitespace

* Undoing ECP-WarpX#2607

* Add PML Support for multi-J Algorithm (ECP-WarpX#2603)

* Add PML Support for multi-J Algorithm

* Add CI Test

* Fix the scope of profiler for SYCL (ECP-WarpX#2668)

In main.cpp, the destructor of the profiler was called after
amrex::Finalize.  This caused an error in SYCL due to a device
synchronization call in the dtor, because the SYCL queues in amrex had been
deleted.  In this commit, we limit the scope of the profiler so that its
destructor is called before the queues are deleted.  Note that it was never
an issue for CUDA/HIP, because the device synchronization calls in those
backends do not need any amrex objects.

* Add high energy asymptotic fit for Proton-Boron total cross section (ECP-WarpX#2408)

* Add high energy asymptotic fit for Proton Boron total cross section

* Write keV and MeV instead of kev and mev

* Add @return doxystrings

* Add anisotropic mesh refinement example (ECP-WarpX#2650)

* Add anisotropic mesh refinement example

* Update benchmark

* AMReX/PICSAR: Weekly Update (ECP-WarpX#2666)

* AMReX: Weekly Update

* Reset: PEC_particle, RepellingParticles, subcyclingMR

New AMReX grid layout routines split grids until they truly reach
number of MPI ranks, if blocking factor allows. This changes some of
our particle orders slightly.

* Add load balancing test (ECP-WarpX#2561)

* Added embedded_circle test

* Add embedded_circle test files

* Removed diag files

* removed PICMI input file

* Update to use default regression analysis

* Added line breaks for spacing

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* Added description

* Fixed benchmark file

* Added load balancing to test

* Commented out load_balancing portion of test.
This will be added back in once load balancing is fixed.

* Add load balancing to embedded_boundary test

* Updated checksum

* Added embedded_circle test

* Add embedded_circle test files

* removed PICMI input file

* Update to use default regression analysis

* Added load balancing to test

* Commented out load_balancing portion of test.
This will be added back in once load balancing is fixed.

* Add load balancing to embedded_boundary test

* added analysis.py file in order to relax tolerance on test

* Ensure that timers are used to update load balancing algorithm

* Updated test name retrieval

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Roelof <roelof.groenewald@modernelectron.com>
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>

* Adding EB multifabs to the Python interface (ECP-WarpX#2647)

* Adding edge_lengths and face_areas to the Python interface

* Added wrappers for the two new arrays of data

* Adding a CI test

* Fixed test name

* Added customRunCmd

* Added mpi in test

* Refactor DepositCharge so it can be called from ImpactX. (ECP-WarpX#2652)

* Refactor DepositCharge so it can be called from ImpactX.

* change thread_num

* Fix namespace

* remove all static WarpX:: members and methods from DepositChargeDoIt.

* fix unused

* Don't access ref_ratio unless lev != depos_lev

* more unused

* remove function to its own file / namespace

* don't need a CMakeLists.txt for this

* lower case namespace, rename file

* Refactor: Profiler Wrapper

Explicit control for synchronization instead of global state.

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* ABLASTR: Fix Doxygen in `DepositCharge`

* update version number and changelog

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Prabhat Kumar <89051199+prkkumar@users.noreply.github.com>
Co-authored-by: Luca Fedeli <luca.fedeli@cea.fr>
Co-authored-by: Prabhat Kumar <prabhatkumar@kraken.dhcp.lbl.gov>
Co-authored-by: s9105947 <80697868+s9105947@users.noreply.github.com>
Co-authored-by: Hannes T <s9105947@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Phil Miller <phil.miller@intensecomputing.com>
Co-authored-by: Lorenzo Giacomel <47607756+lgiacome@users.noreply.github.com>
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Kevin Z. Zhu <86268612+KZhu-ME@users.noreply.github.com>
Co-authored-by: Andrew Myers <atmyers@lbl.gov>
lgiacome added a commit to lgiacome/WarpX that referenced this pull request Dec 16, 2021
@lgiacome
Fixing the initialization of the EB data in ghost cells (ECP-WarpX#2635)
5eabda7 
* Using ng_FieldSolver ghost cells in the EB data

* Removed an unused variable

* Fixed makeEBFabFactory also in in WarpXRgrid.cpp

* Fixed end of line whitespace

* Undoing ECP-WarpX#2607
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@WeiqunZhang WeiqunZhang Awaiting requested review from WeiqunZhang

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@RemiLehe @lgiacome @EZoni @ax3l @WeiqunZhang