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2021-09-21leveling_thinning: 2 MPI Ranks (#2321)Gravatar Axel Huebl 2-33/+33
Public CI only offers two virtual cores and thus only 2 MPI ranks. Oversubscription generally leads to unstable builds (sporadic suspension of processes by the host system) and newer MPI versions won't start at all without requesting oversubscription.
2021-09-21Python CI: Only 2 Ranks (#2320)Gravatar Axel Huebl 2-3/+3
Public CI only offers two virtual cores and thus only 2 MPI ranks. Oversubscription generally leads to unstable builds (sporadic suspension of processes by the host system) and newer MPI versions won't start at all without requesting oversubscription.
2021-09-21Rename eb_potential parameter (#2310)Gravatar Remi Lehe 4-5/+5
2021-09-21Fix Bug in PSATD Restart with Time Averaging (#2318)Gravatar Edoardo Zoni 6-1/+165
* Fix Bug in PSATD Restart with Time Averaging * PSATD Time Avg Restart: Add CI Test - restart test - use recommended boundary conditions for the spectral solver in z Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-09-20AMReX/PICSAR: Weekly Update (#2316)Gravatar Axel Huebl 5-8/+8
2021-09-20Rename WarpXWrappers.(h->H) (#2261)Gravatar Axel Huebl 5-4/+2
* Rename WarpXWrappers.(h->H) All our other header files use `.H`, so renaming this one for consistency. * Remove unused includes of WarpXWrappers.H
2021-09-20Docs: Link Older Developer Tutorial (#2311)Gravatar Axel Huebl 1-0/+7
Link slides from Maxence in 03/2020.
2021-09-20Fix: Status CUDA CIGravatar Axel Huebl 1-4/+1
Regression from #2312
2021-09-20Performance: ApplyStencil w/o Temporaries (#2314)Gravatar Axel Huebl 1-49/+23
* 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>
2021-09-17Evolve: Mark Step in Profile (#2308)Gravatar Axel Huebl 1-0/+2
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.
2021-09-17CI: Skip & Fail Draft PRs (#2312)Gravatar Axel Huebl 8-1/+17
Save resources on PRs marked as "Draft" by skipping & failing CI.
2021-09-17Set EB (electrostatic) potential with a function of space and time (#2297)Gravatar Roelof Groenewald 4-8/+73
* initial commit for adding a spatially varying potential for EBs * removed extra semi-colon * fixed issue causing oneAPI DPC++ build failure
2021-09-17Add picmi parameter (#2306)Gravatar Michael Kieburtz 1-1/+3
2021-09-17Move QEDEvents() before OneStep functions (#2289)Gravatar Neïl Zaim 14-211/+228
* Move QEDEvents() before OneStep functions * Update BW and QS automated tests * Fix a couple of bugs * Update benchmarks * Forgot to update one benchmark value
2021-09-14AMReX/PICSAR: Weekly Update (#2299)Gravatar Axel Huebl 5-8/+8
* PICSAR: Weekly Update * AMReX: Weekly Update
2021-09-13Docs: Spock CMake 3.20.2, ROCm 4.3.0 (#2288)Gravatar Axel Huebl 1-3/+3
* 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)
2021-09-13Store and read in (if present) dmaps in checkpoint files (#2248)Gravatar Andrew Myers 4-4/+71
* Store and read in (if present) dmaps in checkpoint files * also write number of procs to checkpoint
2021-09-13Enable particle creation from binary collisions (#2245)Gravatar Neïl Zaim 5-29/+312
* Enable particle creation from binary collisions * Do not directly use DeviceVector * Make defineAllParticleTiles () public
2021-09-13Remove unused variable from backtransformed diagnostics (#2296)Gravatar Neïl Zaim 2-5/+0
* Remove unused variable from backtransformed diagnostics * Also remove zmin_lab
2021-09-10Various updates related to defining embedded boundaries in Python (#2280)Gravatar David Grote 3-24/+48
* 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>
2021-09-10warpx_py_beforeEsolve & _afterEsolve with electrostatic solver (#2286)Gravatar Roelof Groenewald 1-0/+2
2021-09-10Initialize physical_species (#2273)Gravatar Neïl Zaim 1-1/+1
2021-09-10Include Diagnostics in Evolve Timer (#2278)Gravatar Tiberius Rheaume 1-11/+12
* 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>
2021-09-10Fix uninitialized particle data (#2282)Gravatar Neïl Zaim 1-6/+85
2021-09-09Fix floating point exception issue in single precision (#2284)Gravatar Luca Fedeli 1-1/+7
* fix fpe issue in single precision * fixed bug * fixed bug * make prettier * fixed bug * fixed bug * fixed bug * using constexpr as suggested by NZaim
2021-09-08Perlmutter: CMake 3.22 Preview (#2291)Gravatar Axel Huebl 1-13/+2
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).
2021-09-07Allow Restarts and Checkpoints in python picmi (#2274)Gravatar Nicholas Ruof 1-0/+30
* 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
2021-09-07CI: EB on Intel DPC++/SYCL (#2279)Gravatar Axel Huebl 1-1/+1
Compile with embedded boundaries with Intel's `dpcpp` compiler.
2021-09-07fix doc compilation on Spock (#2287)Gravatar MaxThevenet 1-1/+1
Co-authored-by: ax3l <axelhuebl@lbl.gov> Co-authored-by: ax3l <axelhuebl@lbl.gov>
2021-09-03Summit: Work-Around IBM MPI Collectives (#2283)Gravatar Axel Huebl 3-0/+12
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!
2021-09-03Summit: PICMI Update (#2275)Gravatar Axel Huebl 3-21/+48
* Summit: PICMI Update Update PICMI instructions post the RHEL8 upgrade of Summit (OLCF). * Summit: Batch-Node Compilation * Add optional ums modules
2021-09-02CI: Build EB (#2170)Gravatar Axel Huebl 7-1/+11
* 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.
2021-09-02AMReX Update: SENSEI (#2276)Gravatar Axel Huebl 4-4/+4
Update AMReX to include: - https://github.com/AMReX-Codes/amrex/pull/2283 - https://github.com/AMReX-Codes/amrex/pull/2285
2021-09-02Docs: Summit Ascent Update (#2241)Gravatar Axel Huebl 1-1/+1
* Docs: Summit Ascent Update Update the Summit Ascent install location. * new dir for gcc 9.3.0 * Update: HDF5 fix
2021-09-02Docs: Summit w/o Darshan (#2272)Gravatar Axel Huebl 3-5/+6
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.
2021-09-02Initializing the size BaseFab on Device (#2255)Gravatar Lorenzo Giacomel 1-3/+3
2021-09-02Release 21.09 (#2270)Gravatar Axel Huebl 10-12/+12
* Update: AMReX/PICSAR to 21.09 * WarpX: 21.09
2021-09-02Bug fix in call to RhoFunctor for RZ modes (#2271)Gravatar David Grote 3-3/+34
2021-09-01silence unused params errors in FlushFormatSensei (#2265)Gravatar Corey Wetterer-Nelson 1-20/+14
2021-09-01[mini-PR] Improved doc on fwd headers (#2267)Gravatar Luca Fedeli 1-3/+17
* improved doc on fwd headers * fix bug * fix bug
2021-08-31Docs: Perlmutter Aug 30th Update (#2262)Gravatar Axel Huebl 1-0/+1
Module changes from: https://docs.nersc.gov/systems/perlmutter/timeline/#august-30-2021
2021-08-31Docs: Summit umask (Permissions) (#2260)Gravatar Axel Huebl 4-0/+11
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.
2021-08-31Initializing geometric data also with the CKC solver (#2254)Gravatar Lorenzo Giacomel 1-0/+1
2021-08-31Add link to repo visual structure (#2256)Gravatar Andrei Berceanu 1-0/+2
* 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
2021-08-31Add profiling for charge deposition (#2253)Gravatar Phil Miller 2-0/+7
2021-08-30Added parsing in intervals (#2246)Gravatar David Grote 6-54/+83
* 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>
2021-08-30Glossary: OTP/2FA (#2251)Gravatar Axel Huebl 1-0/+2
Abbreviation used for NERSC/HPC users
2021-08-30Docs: ADIOS2 Fixed on Summit (#2239)Gravatar Axel Huebl 2-3/+2
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.
2021-08-30Docs: Perlmutter (#2229)Gravatar Axel Huebl 5-4/+191
* Docs: Perlmutter Start a documentation page for Perlmutter. * Cleaning - better links to docs - clean submission script * Perlmutter: Add I/O
2021-08-30Make buffer of scraped particles available to Python code (#2164)Gravatar Phil Miller 11-3/+435
* 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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