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* Streamline profiling documentation
* Add Updates: Full Profile, OLCF Links, Commas
* Spelling of Section Titles
* nsys: Add Environment Options
Especially for unwritable /tmp, which happens often in HPC.
* nsys: add mkdir for TMPDIR
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* Update documentation
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Doc: Major Cori Update
Update Cori instructions after the major upgrade yesterday.
Before using the new modules, remove the old, pre-build software:
```bash
rm -rf $HOME/sw/knl $HOME/sw/haswell $HOME/sw/gpu $HOME/sw/cori_gpu
```
* Cori: Work-Around ADIOS 2.7.1 ZeroMQ
Disable due to https://github.com/ornladios/ADIOS2/issues/2709
* Fix haswell/knl mismatch
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* minimum digits for plotfile cell and particle data is 5
* Apply suggestions from code review
* Update Source/Diagnostics/BTDiagnostics.cpp
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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- improve the `--force-reinstall` logic to not trigger a forced re-install
of WarpX Python dependencies
- install WarpX Python dependencies upfront
- add a first "testing" section to show how to run `./run_tests.sh` on Cori
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Now that we support "dynamic" levels, we need to differentiate
between the maximum allowed refinement level (maxLevel) and the
currently maximum used level (finestLevel) of a simulation.
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do_particles_in_pml (#2974)
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* RZ: Use WarpX::ncomps more consistently
We used `2*modes - 1` in many places, which is harder to follow then
the variable we have.
* Update Comments
* Replace leftover `ncomp` -> `m_ncomps`
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* CMake: ABLASTR as library
previously only an object collection.
* CMake: Fix `set_warpx_binary_name`
Should only change WarpX library and app build, not the library name
of ABLASTR.
* Use ABLASTR_ALWAYS_ASSERT_WITH_MESSAGE
Over AMReX and WarpX equivalent macros.
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updates:
- [github.com/hadialqattan/pycln: v1.2.4 → v1.2.5](https://github.com/hadialqattan/pycln/compare/v1.2.4...v1.2.5)
- [github.com/mgedmin/check-manifest: 0.47 → 0.48](https://github.com/mgedmin/check-manifest/compare/0.47...0.48)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* FAQ: Forward Declarations
* Fwd Declarations: Extend Example
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* Langmuir 2D Tests: Better Analysis Plots
* Remove Unused Import
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Just a missing space we saw in the warning message between the
sentences.
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* Add ParticleReductionFunctor
* Adds a by-cell particle average diagnostic
* Averaged quantity is given by an input parser in (x,y,z,ux,uy,uz)
* Coordinates in these parsers are in the WarpX convention
* Users specify which species the averages are calculated for. The
averages are calculated for each given species individually.
* If there are no particles in a cell, the average will be zero.
* add documentation for ParticleReductionFunctor
* add test for cell-averaged particle diagnostics
* set benchmarks for praticle_fields_diags and particle_fields_diags_single_precision
* small changes to parameter docs and test script (addressing David's comments)
* Apply suggestions from code review
* remove unnecessary comments in python test script
* remove unused variable
* fixed inaccurate comments
* use static_cast<int> pattern
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* add comment in ParticleReductionFunctor.H
* warpx.serialize_ics -> warpx.serialize_initial_conditions
* AMREX_SPACEDIM to WARPX_DIM_3D and WARPX_DIM_XZ
* fix compile errors from dimensionality conditionals
* fix compile errors
* Apply suggestions from code review
* clarify docs
* add include headers
* update docs
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* WarpX/PICSAR Version Define: File
Move the `-D` defines that contain the latest WarpX commit to a
config file. Using always the latest commit counteracts `ccache`
since the signature of the compilation call changes every commit.
* Avoid Rebuilding WarpX.cpp
* Support WarpXVersion.H in GNU Make
* AMReX: Update to latest commit
Co-authored-by: Weiqun Zhang <weiqunzhang@lbl.gov>
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* ABLASTR: Move TextMsg
Since this is used in a ABLASTR header, we need to compile this
in ABLASTR, so ImpactX can use it as well. Otherwise we have missing
symbols for that utility.
* Fix typo in GNUmake
* Apply Wording Update for Doxygen
Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it>
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* default CFL to 0.999 instead of 0.7, and update doc
* Apply suggestions from code review
* set CFL explicitly in tests to avoid failing tests
* set cfl to 0.7 in CI test ion_stopping
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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We automatically trigger a dependency to `mpi4py` when MPI is used.
This makes sure this requirement stays consistent.
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* Clean Pip Staging Directory
The distutils staging (`build` -> `_tmppythonbuild`) directory that
pip uses to collect build artifacts is not by default cleaned between
multiple `pip` runs.
This can be confusing when we recompile, because old `libwarpx*` files
can be still in it that are not present in our own `build/lib/`.
This cleans that staging directory before builds now.
It also sets the whole `build_base` so that no artifact lands in the
default, which was `build/`. So far, `bdist.linux-x86_64/` still was
out-of-tree.
* Python_background_mcc_1d: Add CMake Options
Add missing CMake options in `WarpX-tests.ini`.
This must have been merged in parallel to when we modernized our
regression tests end of last year. #2556
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* Clean up the use of ndt for collisions
* Update BackgroundStopping to match changes
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* Added BackgroundStopping
* Added BackgroundStopping CI test
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* For background stopping, allowed parsed background density and temperature
* Updated background stopping CI test
* For background stopping, temperature is specified in Kelvin
* Added documentation for background stopping
* Added ion stopping plus other fixes
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Made dt level dependent
* Revert "Made dt level dependent"
This reverts commit 1aed9654d24ff1411a7b5fd8558891e0688f0032.
The collisions should be done using the time step of the lowest level.
* Add a comment about dt
* Add const declaration
* Added comment regarding stopped particle
* Several fixes and clean up of the documentation
* Update CI benchmark
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* initial work to add msg formatter
* wip
* replace AMREX_ALWAYS_ASSERT_WITH_MESSAGE with WarpX equivalent
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Will work for old (upper) and new (lower) versions of ccache, so we
don't have to be on the look out when we update.
```
path: |
~/.ccache
~/.cache/ccache
```
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`~/.ccache` -> `~/.cache/ccache`
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* CI: Newer CCache for HIP
* CI: CCache for GNUmake CUDA
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* WarpX Static Attributes: Clean Up Types
* Use true/false For Booleans
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* CI: Newer CCache for CUDA
ccache on Ubuntu 18 and 20 is << v4.2
* pip: also use ccache
Modern `pip` does not build in a random temporary dir anymore but
in `$PWD/build`. With absolute paths established, we can use `ccache`
to speed up this big build as well.
* macOS: Fix `cache_dir`
Not in $HOME.
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* Added PrintMainPICparameters() function to print out fundamental PIC parameters in the command line.
* Cleaning.
* More cleaning.
* Fixed and moved `PrintMainPICparameters()` call after `CheckGuardCells()` call.
* Fixed style.
* Fixed style: added 'D' (shortcut for 'dimension')
* Clean up.
* Some more clean up.
* Cnanges in `WarpX::PrintMainPICparameters ()`:
* Added message that in order to use Yee/CKC/ECT solver, WarpX needs to be built with FDTD solver.
* Some more clean up.
* Remove verbose else branch
... if PSATD is compiled but not used
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* Rename `serialize_ics` as `serialize_initial_conditions`
* Add Backward Compatibility Check
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* Refactor Vay Deposition Functions
* Use rho Index Type for FFT of D
* Improve Doxygen Strings
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approximation) (#2899)
* Macroscopic Maxwell solver: do not update fields in EB
* Correct unused variable
* Add test with macroscopic solver
* Add automated test
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* AMReX: 22.03
* PICSAR: 22.03
* WarpX: 22.03
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* file_min_digits: 5->6
100k+ step runs are quite common in WarpX. To simplify
post-processing scripts, increase the default to pad to 6 digits.
This might break some hand-written scripts that use `?????`
wild-cards over `*` wildcards in regex and thus need to be updated.
But it at the same time simplifies regexes for analysis of data
series and listing of such file series.
* Update Scripts to Handle New File Names
* Fix CI Test pml_x_psatd
* Fix CI Test divb_cleaning_3d
* Fix CI Tests with EB Support
* Fix CI Tests with RZ Support
* Fix CI Tests with PICMI Support
* Use glob in Analysis of Collision Tests
* Use rstrip in Analysis of Collision Tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Fix CI Tests for Langmuir_multi_1d/psatd
* Fix CI Tests for LaserInjection_1d
* Checkpoint-Restart Tests: 5 Digits
`regtest.py` in `regression_testing` hard-codes 5 digits:
```diff
--- a/regtest.py
+++ b/regtest.py
@@ -734,7 +734,7 @@ def test_suite(argv):
shutil.move(test.diffDir, orig_diff_dir)
# get the file number to restart from
- restart_file = "%s_chk%5.5d" % (test.name, test.restartFileNum)
+ restart_file = "%s_chk%6.6d" % (test.name, test.restartFileNum)
```
* PICMI Restart Tests: `warpx_file_min_digits = 5`
Same as other CI restart tests: hard-coded value in regression
suite makes this necessary.
X-ref: https://github.com/AMReX-Codes/regression_testing/issues/119
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* Fix bug in setting weight with refine_plasma option.
* update benchmark for RefinedInjection test.
* run with the right number of OMP and MPI
* also use refine_plasma=1
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* Add More Doxygen Strings
* Add two additions
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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Add missing CMake options in `WarpX-tests.ini` for the
`Python_restart_eb` test. This must have been merged in parallel to
when we modernized our regression tests end of last year.
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Add for all diagnostics the equivalent of `<diag>.file_min_digits`.
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* CI: Cache for GitHub Actions
Use caches for `ccache` on GitHub actions.
* CI: Clean Up Windows
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Remi Lehe
Phil Miller
Axel Huebl
Revathi Jambunathan
David Grote
pre-commit-ci[bot]
Edoardo Zoni
Hannah Klion
Maxence Thévenet
Ryan Sandberg
Roelof Groenewald
Luca Fedeli
Prabhat Kumar
Olga Shapoval
Andrew Myers
