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View Code? Open in Web Editor NEWA fast finite volume code designed to run on many architectures, such as GPU, CPU and manycores, using Kokkos.
Home Page: https://idefix.readthedocs.io/
License: Other
A fast finite volume code designed to run on many architectures, such as GPU, CPU and manycores, using Kokkos.
Home Page: https://idefix.readthedocs.io/
License: Other
Merges viscosity -> master
Viscosity implementation
In GitLab by @neutrinoceros on Jan 26, 2021, 23:40
Currently, a single TimeIntegrator
log entry is printed in the following format
TimeIntegrator: t=999.851 Cycle 644000 dt=0.00159374
3.41014e+06 cell updates/second
It would be cleaner to log in fixed-width columns such as
Timeintegrator: t | Cycle | dt | cell updates/s
Timeintegrator: 999.851 | 644000 | 0.00159374 | 3.41014e+06
such that the final log file could easily be reduced to a csv-compatible form, for instance
./idefix > run.log
cat run.log | grep Timeintegrator | awk -F ":" '{print $2}'
Merges doc_updates -> master
In GitLab by @neutrinoceros on Dec 5, 2020, 18:27
Merges ci_collision_warning -> master
HAVE_ENERGY is set in definitions.hpp by user, but there is nothing checking that it is actually 1. Worse: if HAVE_ENERGY is defined to 0, then the code is inconsistent since there are #ifdef HAVE_ENERGY in the Hydro class (which assumes energy is defined), but at the same time, PRS is absent from Vc since HAVE_ENERGY=0.
In GitLab by @neutrinoceros on Jan 25, 2021, 11:56
Merges doc_freq_output -> master
A nitpicky change in ini files' documentation
In GitLab by @soufsouf on Dec 4, 2020, 16:38
Merges rewrite_reimann -> master
In GitLab by @neutrinoceros on Jan 7, 2021, 19:11
Merges ci-conf -> master
Add the following rules to avoid unnecessary CI queuing
Note: maybe it's preferable to run integration test no matter what on master... I will think about this.
Merges VsiEquilibrium -> master
In GitLab by @neutrinoceros on Jan 12, 2021, 22:04
Merges pin_kokkos -> master
This is intended to solve the issue of not having a properly pinned version for Kokkos as submodule.
Judging by how the diff looks, it seems to me that we already have a pinned version. Note that this change is technically a backpedalling move to Kokkos 3.1.01, which is exactly one commit earlier than the previously pinned version. My bet is that it won't break anything on Idedfix's side, and the benefit is that this version has a well identified release number attached, which is always preferable to a somewhat unstable and impossible-to-recall git sha (IMHO).
Merges fixViscosity -> master
-fix a remaining bug in viscous implementation
-add a regression viscous disc test (test both isothermal with
non-constant cs and non-constant viscosity)
-check that dt is not too small
Merges doc_updates -> master
In GitLab by @neutrinoceros on Jan 26, 2021, 23:20
Currently idefix prints the total runtime in seconds, like for instance
Completed in 8064.1 seconds and 644094 cycles
it'd be nicer to get it in a %d%h%m%s
format
Merges soufiane -> master
Include Soufiane's fixes to main trunk
In GitLab by @neutrinoceros on Dec 9, 2020, 10:04
Merges 3-pipeline-broken-due-to-bash-errors-in-checks-sh -> master
Closes #3
In GitLab by @neutrinoceros on Jan 7, 2021, 19:22
Merges more_hooks -> master
Add:
markdown-toc
: auto-gen a Table of Content in README.md (after I placed a <!-- toc -->
token manually)no-commit-to-branch
: forbid direct (accidental) commits to mastercheck-merge-conflict
: prevent accidental committing of git-conflict markerscheck-yaml
: check that yaml files (.gitlab-ci.yml
) are parseable. This is not a proper validation against gitlab's expectations but it's a first level defense against mistakes.In GitLab by @neutrinoceros on Jan 14, 2021, 15:07
Merges rwi-test -> master
Add a small test setup based on my 2020 paper
Produce vortices at the inner rim of a disk-cavity via Rossby Wave Instability.
Merges Nonideal -> master
Implement nonideal MHD effetcs
In GitLab by @neutrinoceros on Jan 6, 2021, 20:14
Merges pre-commit-hook_linter -> master
Adopt pre-commit hooks to lint and auto-fix some nitpicky style mistakes instead of a custom bash script + a vendored clone of cpplint.py
.
pre-commit simplifies the linting process by
Some of the hooks used here will also auto-fix mistakes instead of just reporting them (like trailing whitespaces and space-tabs mixing).
Note that pre-commit hooks are installed in isolated environments so they do not interact with the external one.
Note that the following rules originally enforced by test/style/check_idefix_style.sh
are currently not reproduced
}}
#pragma
sstd::
before sqrt
or cbrt
However, I the first 2 of those could be auto-fixed with a clang-format hook (which would de facto make cpplint useless).
In the process I did some house keeping to separate linting for actual tests in gitlab's CI config file.
In GitLab by @neutrinoceros on Dec 9, 2020, 12:58
Merges yt_support2 -> master
In GitLab by @neutrinoceros on Jan 5, 2021, 10:53
Merges doc -> master
minor improvements to README.md
Most notably, add the url for compiled docs.
In GitLab by @neutrinoceros on Jan 12, 2021, 13:14
Merges auto-license-header -> master
meaningful changes:
the rest are semi-automated changes
When the grid size is large, the total number of grid points computed by TimeIntegrator to display the performance during the last integration gets an overflow, leading to negative perfs. The bug is here:
double rawperf = (timer.seconds()-lastLog) / (data.mygrid->np_int[IDIR]*data.mygrid->np_int[JDIR]*data.mygrid->np_int[KDIR]*cyclePeriod);
Merges variableIsothermal -> master
Merges FixUCTContact -> master
modified the OrszagTang test so that it now use Pluto results as a
reference
Added reference Pluto OrszagTang test in test/Pluto/MHD
Merges docSetup -> master
some additional information regarding the code. Still a lot to write, but the programming guide might be helpful
In GitLab by @neutrinoceros on Dec 4, 2020, 15:48
Merges ignore_gen_files -> master
Ignore a bunch of generated files
In GitLab by @neutrinoceros on Dec 8, 2020, 14:32
Merges yt_support -> master
This doesn't work yet. The resulting dump-files have a "geometry"
int field but the value is not initialised.
In GitLab by @neutrinoceros on Jan 25, 2021, 14:23
Compiling idefix generates a lot of occurrences of this warning on my machine
warning: argument unused during compilation: '--gcc-toolchain=/usr' [-Wunused-command-line-argument]
I think this comes from Kokkos. I think it'd be worth disabling it if there's nothing else we can do about it because it tends to shadow more important warnings and errors.
I'm noting this down for later reference, when/if I find a solution to this.
Merges refurbOutputs -> master
This push introduces a new global Output class, which manage Vtk, dumps, user analysis and user-defined fields in vtk files.
Most notably, it changes the Setup class: Output is given as an argument of the constructor, and there is no MakeAnalysis method anymore. Analysis should now be enrolled by the Output object.
Analysis is now performed, and is used in the HallWhistler test as an example.
This push also cleans up dependencies and moves signal handling to the Input class, which is more logical (a signal is just another type of input).
Should also be coming later in this push the handling of user-def fields in vtk outputs.
In GitLab by @neutrinoceros on Jan 17, 2021, 12:04
Merges no_executable_bits -> master
Add a pre-commit hook to forbid executable bits are accidentally added to text files without shebang and correct the 22 ones files in question found in the repo.
Because most of them are inifiles, here's how I corrected them in just two lines.
git ls-files **/*.ini | xargs chmod -x
chmod -x idefix_pytools/sod.py
In GitLab by @neutrinoceros on Jan 7, 2021, 11:46
Job #188859 failed for 48431a7e0347b9e7caacbf1828e4e38ae6262965:
In GitLab by @neutrinoceros on Jan 26, 2021, 11:20
-restart
is especially useful when a walltime was set on the job scheduler. Currently, this option takes an int
argument to represent the output number to restart from. However, when chaining jobs, it is not necessarily trivial to predict which output number is going to be last outputted. Detecting it at runtime is a simple enough task, but copy-pasting the required code in jobs submission scripts seems like a poor choice (in particular if it's buggy). I suggest we implement such a feature in idefix itself so that -restart
implicitly targets the latest existing output when the number is unspecified.
Merges docSetup -> master
In GitLab by @neutrinoceros on Jan 7, 2021, 14:37
Merges pre-commit.clang-format -> master
Pipeline won’t run on several machines because of checks.sh which have been modified to automatically detect idefix path. (See error last night in the pipeline)
This should be fixed so that it is more robust, or reverted to previous checks.sh.
In GitLab by @neutrinoceros on Jan 7, 2021, 11:48
Merges hotfix_deploy_ci -> master
fix #4
solution was documented on stack-overflow
while I'm at it I added a pre-commit hook to validate .gitlab-ci.yml locally
edit: taking this back. The hook in question is broken because it doesn't automatically install one of its deps.
In GitLab by @neutrinoceros on Jan 14, 2021, 17:39
Merges python_testing_framework -> master
Currently the repo shows up as 25% Python while it's really just a handful of lines duplicated over and over
I propose a to unify the python testing framework into a single reusable module.
In GitLab by @neutrinoceros on Jan 27, 2021, 10:09
Merges hotfix_khi_test -> master
In GitLab by @neutrinoceros on Jan 7, 2021, 22:17
Merges contrib-docs -> master
Merges fixRoeWarning -> master
The examples have both gamma set explicitely in setup.cpp calling Hydro::SetGamma()
, and examples using gamma in input.ini which is initialized by Hydro
constructor.
We should have only one method to initialise gamma.
In GitLab by @neutrinoceros on Dec 4, 2020, 12:15
Merges update_readme -> master
Let's get started: two minor improvements in the readme.
In GitLab by @neutrinoceros on Dec 8, 2020, 20:57
Merges hotfix_python_version_ci -> master
In GitLab by @neutrinoceros on Dec 6, 2020, 19:02
Merges update_doc -> master
Not aimed at fixing each and every typo, just the ones I found already
In GitLab by @neutrinoceros on Jan 25, 2021, 12:12
Merges vtk_output_cleanup -> master
fix copy-pasted parameters from Pluto that were unused in Idefix
Merges fixHall -> master
the DataBlockHost constructor does not sync the hydro data!
This needs to be done manually
In GitLab by @neutrinoceros on Dec 18, 2020, 14:58
Merges update_gitignore -> master
In GitLab by @neutrinoceros on Dec 4, 2020, 12:20
Merges test_from_anywhere -> master
WIP (don't merge this yet)
Changes to test/checks.sh
so that it's not required to run cd $IDEFiX_DIR/test
to run the script.
I also want to add a warning there in case the env var ($IDEFiX_DIR
) has an external and different def.
Merges docSetup -> master
Completed documentation for the setup class
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