Nathan Mannall
fe0bc9bdf4
Restructure random number generation in MPIFractalVolume
...
- Better variable names to hopefully make it clearer how the algorithm
works
- Reduce the number of calls to `rng.standard_normal()` by combining
calls that were at the start and ends of the for loops
- Remove unnecessary calls to `rng.standard_normal()` at the end of the
final iteration of the for loops
2025-07-04 14:31:06 +01:00
Nathan Mannall
435f9afa35
Improve MPI fractal surface generation performance
2025-07-04 14:30:25 +01:00
Nathan Mannall
bc6513c81c
Improve MPI fractal volume generation performance
2025-07-02 14:47:27 +01:00
Nathan Mannall
0724590925
Add mpi4py-fft to conda environment
2025-06-30 17:25:14 +01:00
Nathan Mannall
39040adde5
Remove sphinx :ref: command from README
2025-06-30 17:21:01 +01:00
Nathan Mannall
154370b8a0
Exclude generated docs from pre-commit hooks
2025-06-30 17:01:49 +01:00
Nathan Mannall
5122fe02d4
Add domain decomposition diagram to accerlator docs
2025-06-30 16:57:59 +01:00
Nathan Mannall
8bfbe63cb0
Clarify why FFTs cause fractal box decomposition limitations
2025-06-30 16:38:26 +01:00
Nathan Mannall
70497fe2a3
Add documentation about the reframe test suite
2025-06-30 16:30:48 +01:00
Nathan Mannall
2eac3b41dd
Add contributing guide to docs
2025-06-30 16:21:45 +01:00
Nathan Mannall
591dba9db8
Update HPC docs
2025-06-27 17:59:45 +01:00
Nathan Mannall
e9a247e4dc
Add -mpi deprecation warning and use console code blocks
2025-06-27 16:20:22 +01:00
Nathan Mannall
e040ef7bd4
Add FFTW and MPI to build requirements
2025-06-27 16:06:31 +01:00
Nathan Mannall
a020d9df35
Fix bug from assuming no MPI neighbour would always be -1
2025-06-27 12:39:30 +01:00
Nathan Mannall
3c8d9e126a
Remove unused dependency from conda_env.yaml
2025-06-25 13:51:52 +01:00
Nathan Mannall
125492624d
Add note about VTKHDF change to docs
2025-06-25 13:47:26 +01:00
Nathan Mannall
8c72d033fc
Correct commandline help messages
2025-06-25 13:45:55 +01:00
Nathan Mannall
2ac675d589
Add instructions to build h5py with MPI support
2025-06-25 13:44:01 +01:00
Nathan Mannall
2706517b89
Update command line arguments table
2025-06-25 13:43:07 +01:00
Nathan Mannall
53f07ed821
Update package overview and wrap text
2025-06-25 13:34:01 +01:00
Nathan Mannall
5fe678fba3
Add guidance for using MPI domain decomposition
2025-06-25 13:27:46 +01:00
Nathan Mannall
b101bfe835
Remove unused dependencies from requirements.txt
...
- pytest is not used
- Dependency on PyEVTK has been removed by adopting VTKHDF
- reframe-hpc should be optional (only required to run the test suite)
2025-06-20 12:24:57 +01:00
Nathan Mannall
652da89ad4
Add support for VTKHDF snapshots
2025-06-20 12:17:07 +01:00
Nathan Mannall
3443071097
Log MPI + OpenMP configuration
2025-06-19 16:09:40 +01:00
Nathan Mannall
c98915d3fe
Fix overflow bug for cell count with large models
2025-06-19 15:54:58 +01:00
Nathan Mannall
7bbe924283
Add PML objects and fix import locations in API docs
...
- Correct import location for 'output' user objects
- Add documentation for PMLFormulation and PMLThickness userobjects
2025-06-19 15:21:20 +01:00
Nathan Mannall
df8a6bd956
Merge branch 'devel' into mpi
2025-06-19 15:21:19 +01:00
Nathan Mannall
2295b71e78
Remove need for git lfs to store large files
...
- Reduce the size of the regression files for testing geometry objects
- Don't save geometry objects when testing geometry commands. This means
the regression check is done using the receiver output rather than
reading the geometry directly. Some tests still output the geometry
for reference (useful if tests fail to check the geometry that was
built).
2025-06-19 15:18:31 +01:00
Nathan Mannall
35ba0e2f6d
Use smaller regression files to test geometry views
...
- This removes the need to use git lfs to store the large files
2025-06-19 15:17:35 +01:00
Nathan Mannall
1759073c28
Use MPI to communicate partition sizes
...
- This was being read from the VTKHDF file, however, this causes a race
condition if not all ranks have written their partition sizes to the
file yet.
2025-06-19 15:17:35 +01:00
Nathan Mannall
447c484e53
Log closing VTKHDF file
2025-06-19 15:17:35 +01:00
Nathan Mannall
e842fcd949
Fix deadlock bug when some ranks finish early
...
- When some ranks finish quicker than others, if the ranks one of the
ranks still running encounters an error it will attempt to call
MPI.Abort. As some ranks will have already exited, this was causing
deadlock without the error actually appearing.
2025-06-19 15:17:35 +01:00
Nathan Mannall
5e8277ceff
Use Dim and Dir enums from utilities.mpi
2025-06-19 15:17:35 +01:00
Nathan Mannall
b71d1fb078
Remove unused geometry_objects.py
...
- Rename the output_controllers directory to geometry_outputs
2025-06-19 15:17:35 +01:00
Nathan Mannall
024cf46adb
Fix broken reference links
2025-06-19 15:17:35 +01:00
Nathan Mannall
b390a83266
Fix logo not displaying on getting started page
2025-06-19 15:17:35 +01:00
Nathan Mannall
0d4397f8b8
Fix input API documentation
...
- Minor corrections to some code documentation
2025-06-19 15:17:35 +01:00
Nathan Mannall
8adb2781bf
Allow docs to be built without pip install of gprmax
2025-06-19 15:17:35 +01:00
Nathan Mannall
ff1929754a
By default build docs in a build directory
2025-06-19 15:17:35 +01:00
Nathan Mannall
386d7517db
Merge branch '53-create-mpi-fractal-objects' into mpi
2025-06-19 15:17:34 +01:00
Nathan Mannall
e4766e22e2
Remove logger.exception from outside try except block
2025-06-19 15:17:34 +01:00
Nathan Mannall
ededfd6855
Update grass for parallel build
2025-06-19 15:17:34 +01:00
Nathan Mannall
bb8f998b38
Fix bug when restoring tests using ReceiverMixin
...
- 'output_file' is not stored in the run report by reframe. Therefore,
trying to access 'test_dependency.output_file' where 'test_dependency'
is a restored test case was returning None and causing an error.
- Instead, created a new function to build an output file path that
can be reused by the ReceiverMixin class.
2025-06-19 15:17:34 +01:00
Nathan Mannall
45222e62f4
Merge branch '27-mpi-geometry-views' into mpi
2025-06-19 15:17:33 +01:00
Nathan Mannall
183588a930
Update geometry view regression checks to vLEN strings
2025-06-19 15:17:32 +01:00
Nathan Mannall
ad34534291
Update old or missing copyright messages
2025-06-19 15:16:57 +01:00
Nathan Mannall
573c205cf3
Make add data functions private in VtkHdfFile class
...
- Adding cell and point data is very dependent on the type of the VTKHDF
file. Therefore these should be private in the base class so an
instance of the VtkHdfFile class can only add field data.
2025-06-19 15:16:57 +01:00
Nathan Mannall
1af5d69161
Update GeometryViewLines for parallel build
2025-06-19 15:16:57 +01:00
Nathan Mannall
84d88fcb7b
Merge branch 'devel' into mpi
2025-06-19 15:16:56 +01:00
Nathan Mannall
d9120db856
Prevent int overflow at large model sizes
2025-06-19 15:16:40 +01:00
