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wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach - #3951

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wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach#3951
yrrepy wants to merge 44 commits into
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@yrrepyyrrepy commented May 30, 2026•
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Closed#3942
in favor of the alternative approach, (this PR).

Switching to the per-mesh Mesh.to_hdf5 design, each mesh subclass serializes itself, mirroring the existing to_xml_element super-call pattern) instead of a central dispatch helper.

This PR:

  1. Fixes: openmc.WeightWindowsList.from_wwinp('wwinp') fails when processing wwinp files that are larger than ~2GB
  2. Speeds-up WeightWindowsList processing (which gets to be slow with multi-GB wwinp).

This enables support for many-GB wwinp files and faster processing of them.

Checklist

  • I have performed a self-review of my own code
  • I have run clang-format (version 18) on any C++ source files (if applicable)
  • I have followed the style guidelines for Python source files (if applicable)
  • I have made corresponding changes to the documentation (if applicable)
  • I have added tests that prove my fix is effective or that my feature works (if applicable)

yrrepy added 5 commits May 22, 2026 14:02
@yrrepy
Speed up check_iterable_type for numpy float/complex arrays
aa90915
Float/complex ndarrays are dtype-validated, so the per-element
isinstance() scan is redundant. Also construct upper_ww_bounds in
WeightWindows.__init__ as an ndarray multiplication (not a list
comprehension) so the upper-bounds setter benefits too. ~11x speedup
on 172M-element wwinp inputs (397 s -> 35 s).
@yrrepy
Bypass XML round-trip in WeightWindowsList.export_to_hdf5
6c4ad09
The XML serialization raised MemoryError on bound arrays >~200M
elements -- lxml's intermediate ASCII allocation fails before the
text node can be built. Write HDF5 directly via h5py, mirroring
the C++ WeightWindows::to_hdf5 writer.
Critical details for C++ compatibility:
- Bounds are 2D (ne, n_voxels) on disk (4D would segfault the
C++ tensor::Tensor<double> reader).
- max_lower_bound_ratio is written unconditionally (default 1.0).
- Root attrs filetype and version are required by
openmc_weight_windows_import.
Adds Mesh.to_hdf5 on each structured mesh subclass, mirroring the
existing Mesh.to_xml_element pattern. UnstructuredMesh raises
NotImplementedError (wwinp cannot produce one).
@yrrepy
Tighten check_iterable_type fast path: validate expected_type
9817c8e
The dtype-trust fast path returned for any float/complex ndarray of
matching depth, even when expected_type was int or another class --
the docstring promised element-type validation but the fast path
skipped it. Gate the fast path on expected_type in (Real, float,
complex) so it only fires when dtype.kind in 'fc' actually satisfies
the contract.
@yrrepy
Restore UnstructuredMesh support via TemporarySession fallback
cf1c44f
The direct-h5py writer cannot serialize an UnstructuredMesh from pure
Python: vertex and connectivity data live in the external .exo/.h5m
file and only exist in memory after LibMesh/MOAB loads them via
openmc.lib.init. Dispatch on mesh type up front: structured meshes
take the new fast path; UnstructuredMesh falls back to the previous
TemporarySession + openmc.lib.export_weight_windows route, which also
restores honoring of init_kwargs on that path.
Removes the dead NotImplementedError branch from _write_mesh_group.
@yrrepy
Comment cleanup
40539f1
@yrrepy
yrrepy requested a review from pshriwise as a code ownerMay 30, 2026 15:10
@yrrepyyrrepy mentioned this pull request May 30, 2026
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GuySten
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Comment threadopenmc/mesh.py
Comment threadopenmc/mesh.py Outdated
Comment threadopenmc/weight_windows.py Outdated
@GuySten
GuySten requested a review from paulromano as a code ownerJune 1, 2026 22:06
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Looks good to me.
@yrrepy, if you agree with my changes and no one else objects, I will merge tomorrow.

@GuyStenGuySten added the Merging Soon PR will be merged in < 24 hrs if no further comments are made. label Jun 2, 2026
@yrrepy

yrrepy commented Jun 3, 2026

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I'm swamped with other work right now, so I can't follow up on this right now. Can only pivot back in a week or 10 days unfortunately.
Can you TLDR what the current problems are that you trying to overcome?

@GuySten

GuySten commented Jun 4, 2026•
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The very specific combination of using libmesh and not using mpi makes openmc crash when trying to write to hdf5 from c-api.
I cannot reproduce this behavior locally because when I install libmesh from the moose channel it comes compiled with mpi and I still did not manage to compile libmesh myself.

paulromano
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Thanks @yrrepy for the PR here and @GuySten for reviewing. I'd like to take a look at this one before merging so putting a placeholder review for now. Will provide actual comments shortly.

@paulromanopaulromano mentioned this pull request Aug 7, 2026
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wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach by yrrepy · Pull Request #3951 · openmc-dev/openmc · GitHub
Skip to content
wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach - #3951
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Open
wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach#3951
yrrepy wants to merge 44 commits into
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@yrrepy
@yrrepyyrrepy
commented
May 30, 2026•

edited

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Closed#3942

in favor of the alternative approach, (this PR).
Switching to the per-mesh Mesh.to_hdf5 design, each mesh subclass serializes itself, mirroring the existing to_xml_element super-call pattern) instead of a central dispatch helper.
This PR:
  1. Fixes: openmc.WeightWindowsList.from_wwinp('wwinp') fails when processing wwinp files that are larger than ~2GB
  2. Speeds-up WeightWindowsList processing (which gets to be slow with multi-GB wwinp).
This enables support for many-GB wwinp files and faster processing of them.
Checklist
  •  I have performed a self-review of my own code
  •  I have run clang-format (version 18) on any C++ source files (if applicable)
  •  I have followed the style guidelines for Python source files (if applicable)
  •  I have made corresponding changes to the documentation (if applicable)
  •  I have added tests that prove my fix is effective or that my feature works (if applicable)
yrrepy
added 5 commits
May 22, 2026 14:02
@yrrepy
Speed up check_iterable_type for numpy float/complex arrays
aa90915
Float/complex ndarrays are dtype-validated, so the per-element
isinstance() scan is redundant. Also construct upper_ww_bounds in
WeightWindows.__init__ as an ndarray multiplication (not a list
comprehension) so the upper-bounds setter benefits too. ~11x speedup
on 172M-element wwinp inputs (397 s -> 35 s).
@yrrepy
Bypass XML round-trip in WeightWindowsList.export_to_hdf5
6c4ad09
The XML serialization raised MemoryError on bound arrays >~200M
elements -- lxml's intermediate ASCII allocation fails before the
text node can be built. Write HDF5 directly via h5py, mirroring
the C++ WeightWindows::to_hdf5 writer.
Critical details for C++ compatibility:
- Bounds are 2D (ne, n_voxels) on disk (4D would segfault the
C++ tensor::Tensor<double> reader).
- max_lower_bound_ratio is written unconditionally (default 1.0).
- Root attrs filetype and version are required by
openmc_weight_windows_import.
Adds Mesh.to_hdf5 on each structured mesh subclass, mirroring the
existing Mesh.to_xml_element pattern. UnstructuredMesh raises
NotImplementedError (wwinp cannot produce one).
@yrrepy
Tighten check_iterable_type fast path: validate expected_type
9817c8e
The dtype-trust fast path returned for any float/complex ndarray of
matching depth, even when expected_type was int or another class --
the docstring promised element-type validation but the fast path
skipped it. Gate the fast path on expected_type in (Real, float,
complex) so it only fires when dtype.kind in 'fc' actually satisfies
the contract.
@yrrepy
Restore UnstructuredMesh support via TemporarySession fallback
cf1c44f
The direct-h5py writer cannot serialize an UnstructuredMesh from pure
Python: vertex and connectivity data live in the external .exo/.h5m
file and only exist in memory after LibMesh/MOAB loads them via
openmc.lib.init. Dispatch on mesh type up front: structured meshes
take the new fast path; UnstructuredMesh falls back to the previous
TemporarySession + openmc.lib.export_weight_windows route, which also
restores honoring of init_kwargs on that path.
Removes the dead NotImplementedError branch from _write_mesh_group.
@yrrepy
Comment cleanup
40539f1
@yrrepy
yrrepy
requested a review
from pshriwise
as a code ownerMay 30, 2026 15:10
@yrrepyyrrepy
mentioned this pull request
May 30, 2026
 Closed

5 tasks
GuySten
GuySten
reviewed
May 30, 2026
View reviewed changes
Comment threadopenmc/checkvalue.py
Outdated

Comment threadopenmc/mesh.py
Comment threadopenmc/mesh.py
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Comment threadopenmc/weight_windows.py
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@GuySten
GuySten
requested a review
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Looks good to me.
@yrrepy, if you agree with my changes and no one else objects, I will merge tomorrow.
@GuyStenGuySten
added
the 
Merging Soon
PR will be merged in < 24 hrs if no further comments are made.
label
Jun 2, 2026
@yrrepy
yrrepy
commented
Jun 3, 2026

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I'm swamped with other work right now, so I can't follow up on this right now. Can only pivot back in a week or 10 days unfortunately.

Can you TLDR what the current problems are that you trying to overcome?
@GuySten
GuySten
commented
Jun 4, 2026•

edited

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The very specific combination of using libmesh and not using mpi makes openmc crash when trying to write to hdf5 from c-api.

I cannot reproduce this behavior locally because when I install libmesh from the moose channel it comes compiled with mpi and I still did not manage to compile libmesh myself.
paulromano
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Thanks @yrrepy for the PR here and @GuySten for reviewing. I'd like to take a look at this one before merging so putting a placeholder review for now. Will provide actual comments shortly.
@paulromanopaulromano
mentioned this pull request
Aug 7, 2026
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wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach by yrrepy · Pull Request #3951 · openmc-dev/openmc · GitHub
Skip to content
wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach - #3951
Open
yrrepy wants to merge 44 commits into
openmc-dev:developfrom 
yrrepy:wwinp_2GB_faster
Open
wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach#3951
yrrepy wants to merge 44 commits into
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@yrrepy
@yrrepyyrrepy
commented
May 30, 2026•

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Closed#3942

in favor of the alternative approach, (this PR).
Switching to the per-mesh Mesh.to_hdf5 design, each mesh subclass serializes itself, mirroring the existing to_xml_element super-call pattern) instead of a central dispatch helper.
This PR:
  1. Fixes: openmc.WeightWindowsList.from_wwinp('wwinp') fails when processing wwinp files that are larger than ~2GB
  2. Speeds-up WeightWindowsList processing (which gets to be slow with multi-GB wwinp).
This enables support for many-GB wwinp files and faster processing of them.
Checklist
  •  I have performed a self-review of my own code
  •  I have run clang-format (version 18) on any C++ source files (if applicable)
  •  I have followed the style guidelines for Python source files (if applicable)
  •  I have made corresponding changes to the documentation (if applicable)
  •  I have added tests that prove my fix is effective or that my feature works (if applicable)
yrrepy
added 5 commits
May 22, 2026 14:02
@yrrepy
Speed up check_iterable_type for numpy float/complex arrays
aa90915
Float/complex ndarrays are dtype-validated, so the per-element
isinstance() scan is redundant. Also construct upper_ww_bounds in
WeightWindows.__init__ as an ndarray multiplication (not a list
comprehension) so the upper-bounds setter benefits too. ~11x speedup
on 172M-element wwinp inputs (397 s -> 35 s).
@yrrepy
Bypass XML round-trip in WeightWindowsList.export_to_hdf5
6c4ad09
The XML serialization raised MemoryError on bound arrays >~200M
elements -- lxml's intermediate ASCII allocation fails before the
text node can be built. Write HDF5 directly via h5py, mirroring
the C++ WeightWindows::to_hdf5 writer.
Critical details for C++ compatibility:
- Bounds are 2D (ne, n_voxels) on disk (4D would segfault the
C++ tensor::Tensor<double> reader).
- max_lower_bound_ratio is written unconditionally (default 1.0).
- Root attrs filetype and version are required by
openmc_weight_windows_import.
Adds Mesh.to_hdf5 on each structured mesh subclass, mirroring the
existing Mesh.to_xml_element pattern. UnstructuredMesh raises
NotImplementedError (wwinp cannot produce one).
@yrrepy
Tighten check_iterable_type fast path: validate expected_type
9817c8e
The dtype-trust fast path returned for any float/complex ndarray of
matching depth, even when expected_type was int or another class --
the docstring promised element-type validation but the fast path
skipped it. Gate the fast path on expected_type in (Real, float,
complex) so it only fires when dtype.kind in 'fc' actually satisfies
the contract.
@yrrepy
Restore UnstructuredMesh support via TemporarySession fallback
cf1c44f
The direct-h5py writer cannot serialize an UnstructuredMesh from pure
Python: vertex and connectivity data live in the external .exo/.h5m
file and only exist in memory after LibMesh/MOAB loads them via
openmc.lib.init. Dispatch on mesh type up front: structured meshes
take the new fast path; UnstructuredMesh falls back to the previous
TemporarySession + openmc.lib.export_weight_windows route, which also
restores honoring of init_kwargs on that path.
Removes the dead NotImplementedError branch from _write_mesh_group.
@yrrepy
Comment cleanup
40539f1
@yrrepy
yrrepy
requested a review
from pshriwise
as a code ownerMay 30, 2026 15:10
@yrrepyyrrepy
mentioned this pull request
May 30, 2026
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GuySten
GuySten
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Comment threadopenmc/checkvalue.py
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Comment threadopenmc/mesh.py
Comment threadopenmc/mesh.py
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Comment threadopenmc/weight_windows.py
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@GuySten
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Looks good to me.
@yrrepy, if you agree with my changes and no one else objects, I will merge tomorrow.
@GuyStenGuySten
added
the 
Merging Soon
PR will be merged in < 24 hrs if no further comments are made.
label
Jun 2, 2026
@yrrepy
yrrepy
commented
Jun 3, 2026

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I'm swamped with other work right now, so I can't follow up on this right now. Can only pivot back in a week or 10 days unfortunately.

Can you TLDR what the current problems are that you trying to overcome?
@GuySten
GuySten
commented
Jun 4, 2026•

edited

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The very specific combination of using libmesh and not using mpi makes openmc crash when trying to write to hdf5 from c-api.

I cannot reproduce this behavior locally because when I install libmesh from the moose channel it comes compiled with mpi and I still did not manage to compile libmesh myself.
paulromano
paulromano
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Jun 5, 2026
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Thanks @yrrepy for the PR here and @GuySten for reviewing. I'd like to take a look at this one before merging so putting a placeholder review for now. Will provide actual comments shortly.
@paulromanopaulromano
mentioned this pull request
Aug 7, 2026
 Open

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wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach by yrrepy · Pull Request #3951 · openmc-dev/openmc · GitHub
Skip to content
wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach - #3951
Open
yrrepy wants to merge 44 commits into
openmc-dev:developfrom 
yrrepy:wwinp_2GB_faster
Open
wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach#3951
yrrepy wants to merge 44 commits into
openmc-dev:developfrom 
yrrepy:wwinp_2GB_faster
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@yrrepy
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commented
May 30, 2026•

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Closed#3942

in favor of the alternative approach, (this PR).
Switching to the per-mesh Mesh.to_hdf5 design, each mesh subclass serializes itself, mirroring the existing to_xml_element super-call pattern) instead of a central dispatch helper.
This PR:
  1. Fixes: openmc.WeightWindowsList.from_wwinp('wwinp') fails when processing wwinp files that are larger than ~2GB
  2. Speeds-up WeightWindowsList processing (which gets to be slow with multi-GB wwinp).
This enables support for many-GB wwinp files and faster processing of them.
Checklist
  •  I have performed a self-review of my own code
  •  I have run clang-format (version 18) on any C++ source files (if applicable)
  •  I have followed the style guidelines for Python source files (if applicable)
  •  I have made corresponding changes to the documentation (if applicable)
  •  I have added tests that prove my fix is effective or that my feature works (if applicable)
yrrepy
added 5 commits
May 22, 2026 14:02
@yrrepy
Speed up check_iterable_type for numpy float/complex arrays
aa90915
Float/complex ndarrays are dtype-validated, so the per-element
isinstance() scan is redundant. Also construct upper_ww_bounds in
WeightWindows.__init__ as an ndarray multiplication (not a list
comprehension) so the upper-bounds setter benefits too. ~11x speedup
on 172M-element wwinp inputs (397 s -> 35 s).
@yrrepy
Bypass XML round-trip in WeightWindowsList.export_to_hdf5
6c4ad09
The XML serialization raised MemoryError on bound arrays >~200M
elements -- lxml's intermediate ASCII allocation fails before the
text node can be built. Write HDF5 directly via h5py, mirroring
the C++ WeightWindows::to_hdf5 writer.
Critical details for C++ compatibility:
- Bounds are 2D (ne, n_voxels) on disk (4D would segfault the
C++ tensor::Tensor<double> reader).
- max_lower_bound_ratio is written unconditionally (default 1.0).
- Root attrs filetype and version are required by
openmc_weight_windows_import.
Adds Mesh.to_hdf5 on each structured mesh subclass, mirroring the
existing Mesh.to_xml_element pattern. UnstructuredMesh raises
NotImplementedError (wwinp cannot produce one).
@yrrepy
Tighten check_iterable_type fast path: validate expected_type
9817c8e
The dtype-trust fast path returned for any float/complex ndarray of
matching depth, even when expected_type was int or another class --
the docstring promised element-type validation but the fast path
skipped it. Gate the fast path on expected_type in (Real, float,
complex) so it only fires when dtype.kind in 'fc' actually satisfies
the contract.
@yrrepy
Restore UnstructuredMesh support via TemporarySession fallback
cf1c44f
The direct-h5py writer cannot serialize an UnstructuredMesh from pure
Python: vertex and connectivity data live in the external .exo/.h5m
file and only exist in memory after LibMesh/MOAB loads them via
openmc.lib.init. Dispatch on mesh type up front: structured meshes
take the new fast path; UnstructuredMesh falls back to the previous
TemporarySession + openmc.lib.export_weight_windows route, which also
restores honoring of init_kwargs on that path.
Removes the dead NotImplementedError branch from _write_mesh_group.
@yrrepy
Comment cleanup
40539f1
@yrrepy
yrrepy
requested a review
from pshriwise
as a code ownerMay 30, 2026 15:10
@yrrepyyrrepy
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Looks good to me.
@yrrepy, if you agree with my changes and no one else objects, I will merge tomorrow.
@GuyStenGuySten
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PR will be merged in < 24 hrs if no further comments are made.
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@yrrepy
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I'm swamped with other work right now, so I can't follow up on this right now. Can only pivot back in a week or 10 days unfortunately.

Can you TLDR what the current problems are that you trying to overcome?
@GuySten
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Jun 4, 2026•

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The very specific combination of using libmesh and not using mpi makes openmc crash when trying to write to hdf5 from c-api.

I cannot reproduce this behavior locally because when I install libmesh from the moose channel it comes compiled with mpi and I still did not manage to compile libmesh myself.
paulromano
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Thanks @yrrepy for the PR here and @GuySten for reviewing. I'd like to take a look at this one before merging so putting a placeholder review for now. Will provide actual comments shortly.
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mentioned this pull request
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, 'i');
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// Strip utm_, fbclid, gclid, etc. from all links on page
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var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
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observer.observe(document.body, { childList: true, subtree: true });
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}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach by yrrepy · Pull Request #3951 · openmc-dev/openmc · GitHub
Skip to content
wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach - #3951
Open
yrrepy wants to merge 44 commits into
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Open
wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach#3951
yrrepy wants to merge 44 commits into
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@yrrepy
@yrrepyyrrepy
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Closed#3942

in favor of the alternative approach, (this PR).
Switching to the per-mesh Mesh.to_hdf5 design, each mesh subclass serializes itself, mirroring the existing to_xml_element super-call pattern) instead of a central dispatch helper.
This PR:
  1. Fixes: openmc.WeightWindowsList.from_wwinp('wwinp') fails when processing wwinp files that are larger than ~2GB
  2. Speeds-up WeightWindowsList processing (which gets to be slow with multi-GB wwinp).
This enables support for many-GB wwinp files and faster processing of them.
Checklist
  •  I have performed a self-review of my own code
  •  I have run clang-format (version 18) on any C++ source files (if applicable)
  •  I have followed the style guidelines for Python source files (if applicable)
  •  I have made corresponding changes to the documentation (if applicable)
  •  I have added tests that prove my fix is effective or that my feature works (if applicable)
yrrepy
added 5 commits
May 22, 2026 14:02
@yrrepy
Speed up check_iterable_type for numpy float/complex arrays
aa90915
Float/complex ndarrays are dtype-validated, so the per-element
isinstance() scan is redundant. Also construct upper_ww_bounds in
WeightWindows.__init__ as an ndarray multiplication (not a list
comprehension) so the upper-bounds setter benefits too. ~11x speedup
on 172M-element wwinp inputs (397 s -> 35 s).
@yrrepy
Bypass XML round-trip in WeightWindowsList.export_to_hdf5
6c4ad09
The XML serialization raised MemoryError on bound arrays >~200M
elements -- lxml's intermediate ASCII allocation fails before the
text node can be built. Write HDF5 directly via h5py, mirroring
the C++ WeightWindows::to_hdf5 writer.
Critical details for C++ compatibility:
- Bounds are 2D (ne, n_voxels) on disk (4D would segfault the
C++ tensor::Tensor<double> reader).
- max_lower_bound_ratio is written unconditionally (default 1.0).
- Root attrs filetype and version are required by
openmc_weight_windows_import.
Adds Mesh.to_hdf5 on each structured mesh subclass, mirroring the
existing Mesh.to_xml_element pattern. UnstructuredMesh raises
NotImplementedError (wwinp cannot produce one).
@yrrepy
Tighten check_iterable_type fast path: validate expected_type
9817c8e
The dtype-trust fast path returned for any float/complex ndarray of
matching depth, even when expected_type was int or another class --
the docstring promised element-type validation but the fast path
skipped it. Gate the fast path on expected_type in (Real, float,
complex) so it only fires when dtype.kind in 'fc' actually satisfies
the contract.
@yrrepy
Restore UnstructuredMesh support via TemporarySession fallback
cf1c44f
The direct-h5py writer cannot serialize an UnstructuredMesh from pure
Python: vertex and connectivity data live in the external .exo/.h5m
file and only exist in memory after LibMesh/MOAB loads them via
openmc.lib.init. Dispatch on mesh type up front: structured meshes
take the new fast path; UnstructuredMesh falls back to the previous
TemporarySession + openmc.lib.export_weight_windows route, which also
restores honoring of init_kwargs on that path.
Removes the dead NotImplementedError branch from _write_mesh_group.
@yrrepy
Comment cleanup
40539f1
@yrrepy
yrrepy
requested a review
from pshriwise
as a code ownerMay 30, 2026 15:10
@yrrepyyrrepy
mentioned this pull request
May 30, 2026
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5 tasks
GuySten
GuySten
reviewed
May 30, 2026
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Comment threadopenmc/checkvalue.py
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Comment threadopenmc/mesh.py
Comment threadopenmc/mesh.py
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Comment threadopenmc/weight_windows.py
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@GuySten
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Looks good to me.
@yrrepy, if you agree with my changes and no one else objects, I will merge tomorrow.
@GuyStenGuySten
added
the 
Merging Soon
PR will be merged in < 24 hrs if no further comments are made.
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@yrrepy
yrrepy
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Jun 3, 2026

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I'm swamped with other work right now, so I can't follow up on this right now. Can only pivot back in a week or 10 days unfortunately.

Can you TLDR what the current problems are that you trying to overcome?
@GuySten
GuySten
commented
Jun 4, 2026•

edited

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The very specific combination of using libmesh and not using mpi makes openmc crash when trying to write to hdf5 from c-api.

I cannot reproduce this behavior locally because when I install libmesh from the moose channel it comes compiled with mpi and I still did not manage to compile libmesh myself.
paulromano
paulromano
requested changes
Jun 5, 2026
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Thanks @yrrepy for the PR here and @GuySten for reviewing. I'd like to take a look at this one before merging so putting a placeholder review for now. Will provide actual comments shortly.
@paulromanopaulromano
mentioned this pull request
Aug 7, 2026
 Open

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@yrrepy@GuySten@paulromano

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
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var lastUrl = location.href;
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if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
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}, 1000);
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var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach by yrrepy · Pull Request #3951 · openmc-dev/openmc · GitHub
Skip to content
wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach - #3951
Open
yrrepy wants to merge 44 commits into
openmc-dev:developfrom 
yrrepy:wwinp_2GB_faster
Open
wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach#3951
yrrepy wants to merge 44 commits into
openmc-dev:developfrom 
yrrepy:wwinp_2GB_faster
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@yrrepy
@yrrepyyrrepy
commented
May 30, 2026•

edited

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Closed#3942

in favor of the alternative approach, (this PR).
Switching to the per-mesh Mesh.to_hdf5 design, each mesh subclass serializes itself, mirroring the existing to_xml_element super-call pattern) instead of a central dispatch helper.
This PR:
  1. Fixes: openmc.WeightWindowsList.from_wwinp('wwinp') fails when processing wwinp files that are larger than ~2GB
  2. Speeds-up WeightWindowsList processing (which gets to be slow with multi-GB wwinp).
This enables support for many-GB wwinp files and faster processing of them.
Checklist
  •  I have performed a self-review of my own code
  •  I have run clang-format (version 18) on any C++ source files (if applicable)
  •  I have followed the style guidelines for Python source files (if applicable)
  •  I have made corresponding changes to the documentation (if applicable)
  •  I have added tests that prove my fix is effective or that my feature works (if applicable)
yrrepy
added 5 commits
May 22, 2026 14:02
@yrrepy
Speed up check_iterable_type for numpy float/complex arrays
aa90915
Float/complex ndarrays are dtype-validated, so the per-element
isinstance() scan is redundant. Also construct upper_ww_bounds in
WeightWindows.__init__ as an ndarray multiplication (not a list
comprehension) so the upper-bounds setter benefits too. ~11x speedup
on 172M-element wwinp inputs (397 s -> 35 s).
@yrrepy
Bypass XML round-trip in WeightWindowsList.export_to_hdf5
6c4ad09
The XML serialization raised MemoryError on bound arrays >~200M
elements -- lxml's intermediate ASCII allocation fails before the
text node can be built. Write HDF5 directly via h5py, mirroring
the C++ WeightWindows::to_hdf5 writer.
Critical details for C++ compatibility:
- Bounds are 2D (ne, n_voxels) on disk (4D would segfault the
C++ tensor::Tensor<double> reader).
- max_lower_bound_ratio is written unconditionally (default 1.0).
- Root attrs filetype and version are required by
openmc_weight_windows_import.
Adds Mesh.to_hdf5 on each structured mesh subclass, mirroring the
existing Mesh.to_xml_element pattern. UnstructuredMesh raises
NotImplementedError (wwinp cannot produce one).
@yrrepy
Tighten check_iterable_type fast path: validate expected_type
9817c8e
The dtype-trust fast path returned for any float/complex ndarray of
matching depth, even when expected_type was int or another class --
the docstring promised element-type validation but the fast path
skipped it. Gate the fast path on expected_type in (Real, float,
complex) so it only fires when dtype.kind in 'fc' actually satisfies
the contract.
@yrrepy
Restore UnstructuredMesh support via TemporarySession fallback
cf1c44f
The direct-h5py writer cannot serialize an UnstructuredMesh from pure
Python: vertex and connectivity data live in the external .exo/.h5m
file and only exist in memory after LibMesh/MOAB loads them via
openmc.lib.init. Dispatch on mesh type up front: structured meshes
take the new fast path; UnstructuredMesh falls back to the previous
TemporarySession + openmc.lib.export_weight_windows route, which also
restores honoring of init_kwargs on that path.
Removes the dead NotImplementedError branch from _write_mesh_group.
@yrrepy
Comment cleanup
40539f1
@yrrepy
yrrepy
requested a review
from pshriwise
as a code ownerMay 30, 2026 15:10
@yrrepyyrrepy
mentioned this pull request
May 30, 2026
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GuySten
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Comment threadopenmc/mesh.py
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GuySten
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Looks good to me.
@yrrepy, if you agree with my changes and no one else objects, I will merge tomorrow.
@GuyStenGuySten
added
the 
Merging Soon
PR will be merged in < 24 hrs if no further comments are made.
label
Jun 2, 2026
@yrrepy
yrrepy
commented
Jun 3, 2026

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I'm swamped with other work right now, so I can't follow up on this right now. Can only pivot back in a week or 10 days unfortunately.

Can you TLDR what the current problems are that you trying to overcome?
@GuySten
GuySten
commented
Jun 4, 2026•

edited

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The very specific combination of using libmesh and not using mpi makes openmc crash when trying to write to hdf5 from c-api.

I cannot reproduce this behavior locally because when I install libmesh from the moose channel it comes compiled with mpi and I still did not manage to compile libmesh myself.
paulromano
paulromano
requested changes
Jun 5, 2026
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Thanks @yrrepy for the PR here and @GuySten for reviewing. I'd like to take a look at this one before merging so putting a placeholder review for now. Will provide actual comments shortly.
@paulromanopaulromano
mentioned this pull request
Aug 7, 2026
 Open

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@GuyStenGuyStenGuySten approved these changes
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@pshriwisepshriwiseAwaiting requested review from pshriwisepshriwise is a code owner

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, 'i');
if (__m === '*' || __re.test(location.href)) {
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})();
})();
wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach by yrrepy · Pull Request #3951 · openmc-dev/openmc · GitHub
Skip to content
wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach - #3951
Open
yrrepy wants to merge 44 commits into
openmc-dev:developfrom 
yrrepy:wwinp_2GB_faster
Open
wwinp files: Fix MemoryError in WeightWindowsList.export_to_hdf5 and speed up from_wwinp. Alternative Approach#3951
yrrepy wants to merge 44 commits into
openmc-dev:developfrom 
yrrepy:wwinp_2GB_faster
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@yrrepy
@yrrepyyrrepy
commented
May 30, 2026•

edited

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Closed#3942

in favor of the alternative approach, (this PR).
Switching to the per-mesh Mesh.to_hdf5 design, each mesh subclass serializes itself, mirroring the existing to_xml_element super-call pattern) instead of a central dispatch helper.
This PR:
  1. Fixes: openmc.WeightWindowsList.from_wwinp('wwinp') fails when processing wwinp files that are larger than ~2GB
  2. Speeds-up WeightWindowsList processing (which gets to be slow with multi-GB wwinp).
This enables support for many-GB wwinp files and faster processing of them.
Checklist
  •  I have performed a self-review of my own code
  •  I have run clang-format (version 18) on any C++ source files (if applicable)
  •  I have followed the style guidelines for Python source files (if applicable)
  •  I have made corresponding changes to the documentation (if applicable)
  •  I have added tests that prove my fix is effective or that my feature works (if applicable)
yrrepy
added 5 commits
May 22, 2026 14:02
@yrrepy
Speed up check_iterable_type for numpy float/complex arrays
aa90915
Float/complex ndarrays are dtype-validated, so the per-element
isinstance() scan is redundant. Also construct upper_ww_bounds in
WeightWindows.__init__ as an ndarray multiplication (not a list
comprehension) so the upper-bounds setter benefits too. ~11x speedup
on 172M-element wwinp inputs (397 s -> 35 s).
@yrrepy
Bypass XML round-trip in WeightWindowsList.export_to_hdf5
6c4ad09
The XML serialization raised MemoryError on bound arrays >~200M
elements -- lxml's intermediate ASCII allocation fails before the
text node can be built. Write HDF5 directly via h5py, mirroring
the C++ WeightWindows::to_hdf5 writer.
Critical details for C++ compatibility:
- Bounds are 2D (ne, n_voxels) on disk (4D would segfault the
C++ tensor::Tensor<double> reader).
- max_lower_bound_ratio is written unconditionally (default 1.0).
- Root attrs filetype and version are required by
openmc_weight_windows_import.
Adds Mesh.to_hdf5 on each structured mesh subclass, mirroring the
existing Mesh.to_xml_element pattern. UnstructuredMesh raises
NotImplementedError (wwinp cannot produce one).
@yrrepy
Tighten check_iterable_type fast path: validate expected_type
9817c8e
The dtype-trust fast path returned for any float/complex ndarray of
matching depth, even when expected_type was int or another class --
the docstring promised element-type validation but the fast path
skipped it. Gate the fast path on expected_type in (Real, float,
complex) so it only fires when dtype.kind in 'fc' actually satisfies
the contract.
@yrrepy
Restore UnstructuredMesh support via TemporarySession fallback
cf1c44f
The direct-h5py writer cannot serialize an UnstructuredMesh from pure
Python: vertex and connectivity data live in the external .exo/.h5m
file and only exist in memory after LibMesh/MOAB loads them via
openmc.lib.init. Dispatch on mesh type up front: structured meshes
take the new fast path; UnstructuredMesh falls back to the previous
TemporarySession + openmc.lib.export_weight_windows route, which also
restores honoring of init_kwargs on that path.
Removes the dead NotImplementedError branch from _write_mesh_group.
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Looks good to me.
@yrrepy, if you agree with my changes and no one else objects, I will merge tomorrow.
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I'm swamped with other work right now, so I can't follow up on this right now. Can only pivot back in a week or 10 days unfortunately.

Can you TLDR what the current problems are that you trying to overcome?
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The very specific combination of using libmesh and not using mpi makes openmc crash when trying to write to hdf5 from c-api.

I cannot reproduce this behavior locally because when I install libmesh from the moose channel it comes compiled with mpi and I still did not manage to compile libmesh myself.
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Thanks @yrrepy for the PR here and @GuySten for reviewing. I'd like to take a look at this one before merging so putting a placeholder review for now. Will provide actual comments shortly.
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