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Docs: Cori PICMI Instructions #2219

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merged 2 commits into from
Aug 23, 2021
Merged

Docs: Cori PICMI Instructions #2219

merged 2 commits into from
Aug 23, 2021

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ax3l
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@ax3l ax3l commented Aug 20, 2021 •
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Too tricky to get right to just cross-link - add documentation how to build & run PICMI interfaces on Cori.

Thanks to @tsung1029 for testing those with me 👍

I found an unrelated problem with FFTW from the cray-fftw module along these lines, which is fixed now as well for PSATD builds.

@ax3l ax3l added component: documentation Docs, readme and manual machine / system Machine or system-specific issue component: Python Python layer labels Aug 20, 2021
@ax3l ax3l requested a review from dpgrote August 20, 2021 21:37
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Docs: Cori PICMI Instructions
ff07677 
Too tricky to get right to just cross-link - add documentation how to
build & run PICMI interfaces on Cori.
dpgrote
dpgrote approved these changes Aug 23, 2021
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This looks good, but I have one comment about a possible confusion.

Docs/source/install/hpc/cori.rst

if [ -d "$HOME/sw/venvs/knl_warpx" ]
then
source $HOME/sw/venvs/knl_warpx/bin/activate
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This command might be confusing since the commands to setup the virtual environment are described after this line. Maybe add a comment like "This assumes that the knl_warpx virtual environment has been setup (see below).".

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It's intentionally guarded: nothing will happen if the directory (-d) does not yet exist.
That way, one can follow the instructions top-to-bottom in the page :)

@ax3l ax3l merged commit 88fd029 into ECP-WarpX:development Aug 23, 2021
@ax3l ax3l deleted the doc-coriPICMI branch August 23, 2021 17:33
roelof-groenewald added a commit to ModernElectron/WarpX that referenced this pull request Aug 25, 2021
@roelof-groenewald @ax3l
@RevathiJambunathan @EZoni @NeilZaim @RemiLehe @c-wetterer-nelson @oshapoval @dpgrote @lucafedeli88 @EtherealMC-Bit @atmyers @peterscherpelz @Yin-YinjianZhao
Merge upstream development (#58)
fb6cf79 
* AMReX/PICSAR: Weekly Update (ECP-WarpX#2199)

Weekly update to latest AMReX.
No changes in PICSAR.

* do_pml should not be parsed anymore. (ECP-WarpX#2183)

* do_pml not parsed. remove code that was added to support both types of boundary interface

* add paranthesis

* fix eol and move to BackwardCompatibility

* missing semicolon

* Update Source/WarpX.cpp

* clean input files in examples

* delete do_pml in performance test input

* fixing an example input file in docs

* Update Source/WarpX.cpp

Co-authored-by: Axel Huebl <[email protected]>

* cleaning up docs

* Update Docs/source/usage/parameters.rst

* fix eol

Co-authored-by: Axel Huebl <[email protected]>

* Multi-J (Hybrid): Fix Bug with Current Centering (ECP-WarpX#2181)

* Use less guard cells in ParallelCopy of refined level's UpdateAuxilaryData (ECP-WarpX#2144)

* Use less guard cells in ParallelCopy of refined level's UpdateAuxilaryData
* Update Source/Parallelization/WarpXComm.cpp
* Add inline comments and use explicit type for ng_src

Co-authored-by: Edoardo Zoni <[email protected]>

* Update Scripts: .ini file (ECP-WarpX#2191)

Update regression tester .ini files as well in weekly/release
updates of AMReX and PICSAR.

* Minor fix to the documentation of the plasma lens (ECP-WarpX#2200)

* CI: Cancel Prev. GH Action on Push (ECP-WarpX#2202)

Save CI resources by canceling already running or waiting builds
if a PR is updated.

This was previously only done for Azure and now also for GH actions.

* openPMD-api: 0.14.2 (ECP-WarpX#2150)

This updates our requirements to openPMD-api 0.14.2+

Among others, this release introduced resizable data sets, which we
will soon use for particle backtransformed diagnostics.

* update use-sensei flag (ECP-WarpX#2192)

* update use-sensei flag
also add FlushFormatSensei.cpp to CMakeLists

* CMake: WarpX SENSEI Option

Co-authored-by: Axel Huebl <[email protected]>

* Rho Diags: Do Not Allocate `rho_fp/cp`, Remove `plot_rho`, `setplot_rho` (ECP-WarpX#2203)

* Bug fixed: looping over all species now within `OneStep_multiJ` (ECP-WarpX#2207)

* Bug fixed: looping over all species now within 'OneStep_multij'

* Bug fixed: looping over all laser particles within DepositCharge in multi-J

* Implemented the parsing of integer input parameters (ECP-WarpX#2138)

* Implemented the integer parser

* Updated comment

* Updated documentation

* Fixed unused parameters

* Added some additional documentation

* Reworked the implementation so that expressions are evaluated as real and rounded to the nearest integer

* Fixed loop type

* Copied over initial value of variable to the real instance

* Update Source/Utils/WarpXUtil.cpp

make result const

* Update Source/Utils/WarpXUtil.cpp

make result const

* Update Source/Utils/WarpXUtil.cpp

Fix comment

* Added safeCastToInt

* Fixed adding of safeCastToInt

* Cleaned up safe casting routine

* Added parsing of more integer inputs

* Cleaned up the integer parser, removing unneeded cast from int to real

* Made x a const in safeCastToInt

Co-authored-by: Neïl Zaim <[email protected]>
Co-authored-by: Axel Huebl <[email protected]>

* Ionization.H: Fix Bug (Division by Zero) (ECP-WarpX#2214)

* Add plot_raw_rho in parameters doc (ECP-WarpX#2212)

* add plot_raw_rho in parameters doc

* Update Docs/source/usage/parameters.rst

Co-authored-by: Luca Fedeli <[email protected]>

Co-authored-by: Luca Fedeli <[email protected]>

* Docs: Summit with RHEL8 (ECP-WarpX#2216)

Summit has undergone a major software update to RHEL8.
The default compilers and CUDA version have been modernized, among
others providing C++17 support by default.

Also, our scientific I/O stack is now system-provided, thanks to our
Spack and E4S efforts 🎉

Please update your `warpx.profile` on Summit, re-build your Python
virtual environment and re-compile your executables.

* Improved error handling when the libwarpx shared object library can't be loaded (ECP-WarpX#2215)

* Improved error handling when the libwarpx shared library can't be loaded

* Removed extra newline

* Improved check and ended program on error

* Particle boundary scrape (ECP-WarpX#2124)

* Some prelimary refactoring.

* missing header

* implement scraping particles that leave the domain boundaries into buffers

* fix tabs

* missing return

* merging

* remove redefinition

* functor to work around cuda bug.

* handle 2D

* Add support for EB buffer

* protect for AMREX_USE_EB, static_assert that EB and RZ aren't both on.

* fix unused

* add inputs file

* add test

* fix bugs, remove print

* fix test

* fix test path.

* remove no-op code

* adding clear particles method

* attempt at adding time stamp

* Use integer step number instead of physical time to timestamp particles; also put shared code into named functor.

* move call to before apply boundary conditions

* use more descriptive inputs parameter

* Update Source/Particles/ParticleBoundaryBuffer.cpp

* fix comp bug

* move CopyAndTimestamp to cpp file

* also move IsOutsideProblemDomain functor

* Rename to m_particle_boundary_buffer

- Name: currently only used for boundary scraping
- Singular: only one instance

* Fix missing EOF newline

* Typo: author

* Param Read / Init: Cleanup For

Simplify

Co-authored-by: Roelof Groenewald <[email protected]>
Co-authored-by: Axel Huebl <[email protected]>

* Updated the installation instructions (ECP-WarpX#2218)

* Docs: OLCF ADIOS2 Currently Broken

Tickets open:
- OLCFHELP-3319
- ornladios/ADIOS2#2836

* Allow Silver-Mueller boundary conditions to only be applied in certain directions (ECP-WarpX#2220)

* Apply Silver-Mueller boundary only in requested direction

* Include a test with independent Silver-Mueller boundary conditions

* Correct typo in implementation

* Added transform of fields from lab to boosted frame (ECP-WarpX#2201)

* Evolve: Reorder py_afterstep and cur_time break (ECP-WarpX#2213)

* Docs: Cori PICMI Instructions (ECP-WarpX#2219)

* Docs: Cori PICMI Instructions

Too tricky to get right to just cross-link - add documentation how to
build & run PICMI interfaces on Cori.

* Link: Jupyter Instructions

* No particle resorting when no species (ECP-WarpX#2136)

* default sort interval for particles if there are not species

* declare parmparse

Co-authored-by: Edoardo Zoni <[email protected]>

* fix eol

* define and set sort_interval default to -1 and then reset them to 4 for GPU, -1 for CPU if there are species/lasers in the input

Co-authored-by: Edoardo Zoni <[email protected]>

* AMReX/PICSAR: Weekly Update (ECP-WarpX#2222)

Weekly update to latest AMReX.
No changes in PICSAR.

* Scalar field interpolator from grid to particle position (ECP-WarpX#2221)

* refactored distance to EB calculation to have a more general function to interpolate from a scalar field on the grid to a given position

* changed RZ error message to general interpolation function

* changed function names to specify that scalar field interpolation is for a nodal field only

* Check for unused WarpX environment variables when compiling (ECP-WarpX#2208)

* Added check for unused 'WarpX' environment variables

* Changed the approach of this

- Go through environment variables as they are used to set cmake flags, and then
  check any remaining if they start with warpx.

* Improved the warning message

Co-authored-by: Axel Huebl <[email protected]>

* Ascent/SENSEI: Add Profiler (ECP-WarpX#2204)

* Ascent/SENSEI: Add Profiler

Add overall write profilers to Ascent & SENSEI.
Add detailed profile for sub-operaions (blueprint, publish, execute)
to Ascent as well.

* Simplify One-Time Profiler Vars

* Enable restart with PSATD (ECP-WarpX#1367)

* Enable restart with PSATD

* Add new restart test

* Add new input file

* New CI Test: Fix Inputs, Fix Analysis Script

* Reuse input for Restart with FDTD

* Read time_of_last_gal_shift from Checkpoint

* Upload Benchmark for restart_psatd

* Update Benchmark for restart_psatd

Co-authored-by: Edoardo Zoni <[email protected]>

* Use the function `SyncRho` and the array `rho_fp` in the Electrostatic solver (ECP-WarpX#1811)

* Use `SyncRho` in Electrostatic solver

* Reuse rho_fp arrays

* Allocate arrays for rho

* Fix unused variable

* Fix bug in rho deposition

* Only use rho_fp in lab-frame Poisson solver

* Update test cases

* Incorporate PR comments

* Avoid an NaN in collision module (ECP-WarpX#2225)

* Update inputs_3d

* Update inputs_2d

* Update inputs_2d

* Update inputs_3d

* fix nan

* removed check for final timestep diagnostics in CI tests, should revert once installafterdiagnostics is implemented

Co-authored-by: Axel Huebl <[email protected]>
Co-authored-by: Revathi  Jambunathan <[email protected]>
Co-authored-by: Edoardo Zoni <[email protected]>
Co-authored-by: Neïl Zaim <[email protected]>
Co-authored-by: Remi Lehe <[email protected]>
Co-authored-by: Corey Wetterer-Nelson <[email protected]>
Co-authored-by: Olga Shapoval <[email protected]>
Co-authored-by: David Grote <[email protected]>
Co-authored-by: Luca Fedeli <[email protected]>
Co-authored-by: Michael Kieburtz <[email protected]>
Co-authored-by: Andrew Myers <[email protected]>
Co-authored-by: Peter Scherpelz <[email protected]>
Co-authored-by: Edoardo Zoni <[email protected]>
Co-authored-by: Yinjian Zhao <[email protected]>
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