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The dataset generation failed
Error code: DatasetGenerationError
Exception: TypeError
Message: int() argument must be a string, a bytes-like object or a real number, not 'NoneType'
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1531, in _prepare_split_single
for key, record in generator:
^^^^^^^^^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 613, in wrapped
for item in generator(*args, **kwargs):
~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 127, in _generate_examples
for example_idx, example in enumerate(self._get_pipeline_from_tar(tar_path, tar_iterator)):
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 32, in _get_pipeline_from_tar
for filename, f in tar_iterator:
^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/utils/track.py", line 49, in __iter__
for x in self.generator(*self.args):
~~~~~~~~~~~~~~^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 1405, in _iter_from_urlpath
with xopen(urlpath, "rb", download_config=download_config, block_size=0) as f:
~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 982, in xopen
file_obj = fs.open(paths[0], mode)
File "<string>", line 3, in open
File "/usr/local/lib/python3.14/unittest/mock.py", line 1176, in __call__
return self._mock_call(*args, **kwargs)
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/unittest/mock.py", line 1180, in _mock_call
return self._execute_mock_call(*args, **kwargs)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/unittest/mock.py", line 1247, in _execute_mock_call
result = effect(*args, **kwargs)
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 786, in wrapped
tracker.files[urlpath] = {"read": 0, "size": int(f.size)}
~~~^^^^^^^^
TypeError: int() argument must be a string, a bytes-like object or a real number, not 'NoneType'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1369, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
~~~~~~~~~~~~~~~~~~~~~~~~~^
builder, max_dataset_size_bytes=max_dataset_size_bytes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 948, in stream_convert_to_parquet
builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1393, in _prepare_split
for job_id, done, content in self._prepare_split_single(
~~~~~~~~~~~~~~~~~~~~~~~~~~^
gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
):
^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1571, in _prepare_split_single
raise DatasetGenerationError("An error occurred while generating the dataset") from e
datasets.exceptions.DatasetGenerationError: An error occurred while generating the datasetNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
bin unknown | frc unknown | nrg unknown | __key__ string | __url__ string |
|---|---|---|---|---|
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End of preview.
Many Peptides Forces
A fork of the ManyPeptidesMD single-frame WebDataset in which every frame carries AMBER14 + OBC1 implicit-solvent potential energies and forces in addition to the original atom coordinates.
Contents
Release Status
This dataset is being prepared. The first shard is an early preview, not a completed release. Full-dataset validation and upload are still in progress. The counts below describe the planned complete dataset.
Planned Contents
- 5,000 shard tars
single_frames_forces/0000.tar..4999.tar, one per source shard, identical member order and identical frame set. - 21,700 train peptide sequences (2..8 residues), 4 frames per sequence per shard, 86,800 frames per shard, 434,000,000 frames total.
- Every original member
SEQ_<fid>.bingains two siblings:SEQ_<fid>.bin— float32(N, 3)atom coordinates in nm, bytes identical to the source dataset.<fid>indexes the 200,000-frame source trajectorypositionsarray.SEQ_<fid>.frc— float32(N, 3)forces in kJ/(mol*nm), little-endian, same length in bytes as the.binmember.SEQ_<fid>.nrg— float64 scalar OBC1 potential energy in kJ/mol, little-endian.
Force field
All energies and forces use the same implicit-solvent model as the thermax importance-weight calculations on the many-peptides dataset:
- AMBER14 protein force field (
amber14-all.xml) - OBC1 implicit solvent (
implicit/obc1.xml) - CutoffNonPeriodic nonbonded method, 2.0 nm cutoff, no constraints
- Temperature 310 K
Forces are F = -dU/dx obtained by automatic differentiation of the JAX
energy implementation (thermax.energy.amber14), evaluated in float32,
i.e. the exact gradient of the float32 energy used for importance weights
(log w = -beta * U - log q).
Validation
- JAX energies and forces match the OpenMM Reference platform on real many-peptides frames (float64: < 1e-4 kJ/mol energies, < 1e-3 kJ/(molnm) forces; float32 stored precision: < 1e-2 kJ/mol energies, < 5e-2 kJ/(molnm) forces, < 1e-5 relative).
- The dataset-level QC procedure checks per shard: member trios, byte-identity of coordinates with the source, finiteness of forces and energies, and agreement of stored values with fresh evaluations and the independent OpenMM reference energies where available. These checks are not yet complete for the full dataset.
Attribution
Derived from the many-peptides MD dataset (Tong lab). AMBER14 and OBC1 parameters ship with OpenMM. This fork adds no new simulation data; all added values are deterministic functions of the stored coordinates.
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