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Link slides from Maxence in 03/2020.
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Regression from #2312
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* Performance: ApplyStencil w/o Temporaries
Most of the time in this code is spend in allocating/freeing the
temporary. Wrap invalid values to zero on the fly instead.
* Filter: Fix scomp forwarding
Update Source/Filter/Filter.cpp
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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Mark individual steps in the profiler.
This makes it easier to see the individual step timing in our
tiny profiler and it also helps to see with NVTX (and equivalent)
annotations to find the exact start/end of a time step in traces.
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Save resources on PRs marked as "Draft" by skipping & failing CI.
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* initial commit for adding a spatially varying potential for EBs
* removed extra semi-colon
* fixed issue causing oneAPI DPC++ build failure
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* Move QEDEvents() before OneStep functions
* Update BW and QS automated tests
* Fix a couple of bugs
* Update benchmarks
* Forgot to update one benchmark value
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* PICSAR: Weekly Update
* AMReX: Weekly Update
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* Docs: Spock CMake 3.20.2
Slightly update CMake to avoid that we run into
https://gitlab.kitware.com/cmake/cmake/-/issues/21887
at some point. (Proactively guarding this.)
* Spock: ROCm 4.3.0
Update ROCm (tested)
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* Store and read in (if present) dmaps in checkpoint files
* also write number of procs to checkpoint
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* Enable particle creation from binary collisions
* Do not directly use DeviceVector
* Make defineAllParticleTiles () public
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* Remove unused variable from backtransformed diagnostics
* Also remove zmin_lab
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* Various updated related to defining embedded boundaries in Python
* Fix typo in comment
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
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* Include Diagnostics in Evolve Timer
* Update WarpXEvolve.cpp
* Update WarpXEvolve.cpp
* Update WarpXEvolve.cpp
Removed White Spaces
* return warpx_py_afterstep and adds comments
* Update Source/Evolve/WarpXEvolve.cpp
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
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* fix fpe issue in single precision
* fixed bug
* fixed bug
* make prettier
* fixed bug
* fixed bug
* fixed bug
* using constexpr as suggested by NZaim
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Use the new Perlmutter CMake module with the improved `FindMPI.cmake`
logic for HPE/Cray that we contributed upstream.
This will be part of CMake 3.22 (the Perlmutter module is built from
the CMake development branch and contains the patch already).
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* Add a class to output checkpoint diagnostics in picmi
* Add argument to picmi Simulation for restarting from a checkpoint
* Changes to make the checkpoint work
* Change inheritance for Checkpoint and rename variables in Simulation
* Remove file exists check
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Compile with embedded boundaries with Intel's `dpcpp` compiler.
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Co-authored-by: ax3l <axelhuebl@lbl.gov>
Co-authored-by: ax3l <axelhuebl@lbl.gov>
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Fix crashes on Summit at scale (>~224 nodes) due to failing Barriers
in IBM's MPI stack.
Seen mostly with I/O routines and only since the RHEL8 upgrade.
We see no signfiicant performance impact from this work-around until
OLCF & IBM fix the problem (OLCFHELP-3545).
An alternative work-around via
```
export OMPI_MCA_coll_ibm_collselect_mode_barrier=failsafe
```
was tested and is a tiny bit slower than just falling back to HCOLL
or OMPI's barrier implementations via
```
export OMPI_MCA_coll_ibm_skip_barrier=true
```
Thanks to Brian Smith at OLCF for the support!
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* Summit: PICMI Update
Update PICMI instructions post the RHEL8 upgrade of Summit (OLCF).
* Summit: Batch-Node Compilation
* Add optional ums modules
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* CI: Build EB
Perform compile tests with EB on.
This should help to ensure CUDA, DPC++, HIP and Windows builds work
with EB on the long-term.
* CI Wheels: EB + RZ not yet supported
* DPC++: Compiler ICE with EB
Disable for now and report upstream in a follow-up.
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Update AMReX to include:
- https://github.com/AMReX-Codes/amrex/pull/2283
- https://github.com/AMReX-Codes/amrex/pull/2285
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* Docs: Summit Ascent Update
Update the Summit Ascent install location.
* new dir for gcc 9.3.0
* Update: HDF5 fix
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We see problems again at runtime with missing libs. We don't need Darshan by
default, so let's unload it to make our stack more stable.
We also avoid sourcing the profile again in the batch script: we inherit the
environment and modules loaded at submission.
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* Update: AMReX/PICSAR to 21.09
* WarpX: 21.09
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* improved doc on fwd headers
* fix bug
* fix bug
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Module changes from:
https://docs.nersc.gov/systems/perlmutter/timeline/#august-30-2021
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After the update to RHEL8, Summit changed the default
permissions of newly created files and directories (for the
worse).
This has been reported as OLCFHELP-3442 but we face some
resistance from support to triage this properly at the moment.
Since we need to continue to keep working, we change the `umask`
(aka defaults for new files & dirs) manually so that group
members of the same project can read files and access dirs.
For files and dirs created since this update and not yet using
this `umask`, please use the following fix.
```
find . -type -d -exec chmod a+rx {} \;
find . -type -f -exec chmod a+r {} \;
```
Replace `.` (current directory) with another path if needed.
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* Add link to repo visual structure
Add a link to the GitHub visualization of the repository structure. Full description at https://next.github.com/projects/repo-visualization
* Link: md->rst syntax
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* Added parsing in intervals, minor clean up of querywithparser routines
* Split up documentation
* Added documentation
* Added tests to inputs_2d_multi_rz_rt
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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Abbreviation used for NERSC/HPC users
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The adios2 system module is now fixed on Summit.
We don't need to load the openpmd-api module for CMake, as we
build it on-the-fly at the moment against the ADIOS2 and HDF5
modules.
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* Docs: Perlmutter
Start a documentation page for Perlmutter.
* Cleaning
- better links to docs
- clean submission script
* Perlmutter: Add I/O
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* Added wrapper to get number of particle species tracked by the scraper
Not sure if this is going to be useful, but it demonstrates a method to get information
from the ParticleBoundaryBuffer into Python.
* Stubbed out the main wrapper functions
* Added parameters to wrapper
* Added wrapper for getting the number of particles scraped of a species on a boundary
* added picmi arguments to scrape particles at the domain boundary
* Added wrapper to get the full particle buffer into python
* rearanged the getBuffer properties code a little
* Added docstrings +other suggested changes
* Added num_particles_impacted_boundary docstring
* fixed mistake in docstring
* Changed boundary parameter to be a string for clarity
* Fixed issue with the boundary parameter for scraping
* Fixed issue with the boundary input for scraping stats wrapper
* Added demonstration of particle scraping wrapper
* Added analysis.py file
* Fix typo in one of the dimension maps
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
* Added before esolve to warpx evolve
* added test for the scraped particle buffer wrappers
* Moved python PICMI particle boundary scrape test
* Renamed test file to the correct name
* Removed old test
* added special functionality to get the timestep at which particles were scraped
* removed debug print
* added python wrapper for the clearParticles() function of the scraper buffer
* added special wrapper function to get the timesteps at which the particles in the boundary buffer were scraped
* updated test to match the non-PICMI test for the particle scraper buffer
* Fix uncaught rebase mistake
* re-activated picmi test of accessing the scraped particle buffers via python
* added documentation for the new parameters involved in the scraped particle buffer and fixed remaining issue with picmi test
* changes requested during code review
Co-authored-by: mkieburtz <michaelkieburtz@gmail.com>
Co-authored-by: Roelof <roelof.groenewald@modernelectron.com>
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
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Weekly update to latest AMReX.
No changes in PICSAR.
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Rename scripts and docs since our CI uses several providers now
(currently: GitHub actions, Azure pipelines and other providers).
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* adding base implementation of the conformal solver
* adding some preprocessor directives
* qualifying the isnan's correctly
* getting rid of some unused fields
* computing S_stab on the fly
* using empty in length check
* Source/FieldSolver/FiniteDifferenceSolver/EvolveB.cpp
* replaced a looponcpu with a parallelfor
* trying to not pass lending/borrowing info by reference in evolveB
* passing data using dataPtr
* converting inds into a device vector
* simplifying some +=
* extracting the inds BaseFabs as DataPtr
* Revert "extracting the inds BaseFabs as DataPtr"
This reverts commit bc709d2fcaa347c119514de79a3f57169a05af65.
* implementing new way ogf handling cell extensions (gpu compatible)
* fixing some white spaces
* removed a typo
* made a function static
* tidying up
* tidying up
* getting rid of the rho vector
* moving the rho update to evolveE
* refectoring the cell extension
* small chenge in input parameters
* updating WarpX.H
* bug fix
* fixing another bug
* rotating the cube
* updated gitignore
* using the conformal soler in the cube test
* fixing the signature of a function
* trying to fix the setVal problem
* Revert "trying to fix the setVal problem"
This reverts commit c7d0e5e3709b730ff570183b2a6df5f587ca4640.
* trying to fix the setVal problem
* cleaning some comments
* removing an abort in device code
* Including geometric information in the external field initializer
* cleaned up the test
* moving the geometric data initialization before the external fields initialization
* changing way of saving info about intruded cells
* fixed some white spaces
* Using S_mod instead of S_red and S_enl
* substituting a std::vector with amrex::Array1D
* bug fix in the uint8_t -> coords maps
* Condensed ect cell info into one single MultiFab
* fixing some includes
* fixing some more includes
* fixed a typo
* making some functions available in gpu code
* using tilebox instead of validbox for the geometry initialization
* communicating the geometric info in the guard cells
* fixing the guard cells initialization for ect
* fixing an unused parameter
* fixing an unused parameter
* ignored some unused variables when EB is not supported
* cleaning up
* cleaning up
* ignored some unused variables when EB is not supported
* evolving rho just for ect
* handling some more unused variables
* removing some white spaces
* adding the rotated cube test
* removed some white spaces
* change cells into faces
* small fix in unused parameters
* fixed a comment
* for safety for now just initialize the geometric data when lev==maxLevel
* adding some preprocessor directives to isolate EB code
* updating Makefile stuff
* Improving the rotated cube test
* bug fix in mesh refinement
* fixing boundary conditions in rotated cube test
* deactivating MPI in rotated cube test
* activating mpi in test
* improving outputs of cells extension
* improved the documentation
* Update Source/EmbeddedBoundary/WarpXInitEB.cpp
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
* Update Source/EmbeddedBoundary/WarpXInitEB.cpp
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
* Removed some obsolete isnan's
* undone change to gitignore
* adding some missing AMREX_GPU_DEVICEs
* Changing some amrex::Real(0) into 0.
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Making some variables const
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Adding amrex:: to some ignore_unused
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Enhancing readability of some parallelfor's
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Removed some unecessary includes
* Fixing some tags
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Fixing the function CountExtFaces
* added a comment for Rhofield
* Fixed a typo in CountExtCells
* trying to remove accesses to private members in ComputeEdgeLengths
* making some functions public
* undoing some useless changes
* undoing some useless changes
* adding some AMREX_GPU_DEVICEs
* adding some unused variables
* adding some AMREX_GPU_DEVICEs to fix warnings
* fixing relative error
* Making several variables const
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Fixed a comment
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* changing some double to amrex::Real
* removing commented lines
* changing some double to amrex::Real
* removing commented lines
* inizialing nelems_x,y,z to avoid a warning
* Fixing number of cells
* Adding missing analysis routine in rotated cube test
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Making some variables constexpr
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
* Improving some reduce operations
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
* reading time directly from the output
* fixed a few data types
* fixing another int
* Replacing or->||, and->&&, not->!
* Adding license info
* Adding a white space
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* removed some unused imports
* Moving the doxygen documentation
* Including AMReX_LayoutData.H
* removing some useless parameters
* adding ect solver to the doc
* Removing some useless reductions
* Small change for consistency
* Handling the resizing of arrays
* Handling correctly the resing of arrays
* Fixing some whitespaces
* Fixing an indentation
* Improving a comment
* Removed a useless initialization
* Renamed Rhofield to ECTRhofield
* Renamed Rhofield to ECTRhofield
* Added some if conditions to isolate some EB related code
* Improved some comments
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* Made some functions not member of WarpX anymore
* Isolated some EB-only code
* Isolated some EB-only code
* Using the square brackets to access vectors
* Ignoring some unused variables
* Bug fix in initialization
* Removed a redundant if
* Using enumeration for connectivity and improved names
* Added a comment
* added a few comments
* Removed some useless template parameters
* Printing some info only in verbose mode
* Revert "Removed some useless template parameters"
This reverts commit 2c527980e6872c0212767c27f00e2b53ecbcfd0a.
* Fixed a bug with the neighbours enumeration
* Initializing geom data alsoo in the ghost cells
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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```
error #3196-D: The enclosing parent function ("ComputeEdgeLengths") for an extended __device__ lambda cannot have private or protected access within its class
```
For:
- `ComputeEdgeLengths`
- `ComputeFaceAreas`
- `ScaleEdges`
- `ScaleAreas`
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Forgot an include.
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Axel Huebl
Roelof Groenewald
Michael Kieburtz
Neïl Zaim
Andrew Myers
David Grote
Tiberius Rheaume
Luca Fedeli
Nicholas Ruof
MaxThevenet
Lorenzo Giacomel
Corey Wetterer-Nelson
Andrei Berceanu
Phil Miller
Edoardo Zoni
