Dear ChimeraX users!
I am testing the Boltz-2 on Mac in the ChimeraX-daily: for one receptor
(provided fasta sequence) and 5 ligands (provided smiles strings for each
compound). My calculations are running on GPUs and I see the Boltz-2 folder
with the results. However, the ChimeraX send the following error message
(copied directly from log):
Running Boltz prediction of 5 ligands on gpu
Using cached multiple sequence alignment
Running boltz prediction failed with exit code 1:
command:
/Users/enrico/boltz22/bin/boltz predict /Users/enrico/Desktop/boltz_2
--accelerator gpu --no_kernels
stdout:
Boltz version 2.2.0
Checking input data.
Processing 5 inputs with 5 threads.
Running structure prediction for 5 inputs.
Predicting: | | 0/? [00:00<?, ?it/s] Predicting: 0%| | 0/5 [00:00<?, ?it/s]
Predicting DataLoader 0: 0%| | 0/5 [00:00<?, ?it/s] Predicting DataLoader
0: 20%|██ | 1/5 [01:55<07:42, 0.01it/s] Predicting DataLoader 0: 40%|████ |
2/5 [03:55<05:53, 0.01it/s] Predicting DataLoader 0: 60%|██████ | 3/5
[05:53<03:55, 0.01it/s] Predicting DataLoader 0: 80%|████████ | 4/5
[07:56<01:59, 0.01it/s] Predicting DataLoader 0: 100%|██████████| 5/5
[09:59<00:00, 0.01it/s]Number of failed examples: 0
Predicting DataLoader 0: 100%|██████████| 5/5 [09:59<00:00, 0.01it/s]
Predicting property: affinity
Checking input data for affinity.
Running affinity prediction for 5 inputs.
stderr:
0%| | 0/5 [00:00<?, ?it/s] 20%|██ | 1/5 [00:05<00:23, 5.78s/it]
100%|██████████| 5/5 [00:05<00:00, 1.17s/it]
GPU available: True (mps), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/Users/enrico/boltz22/lib/python3.11/site-packages/pytorch_lightning/trainer/connectors/logger_connector/logger_connector.py:76:
Starting from v1.9.0, `tensorboardX` has been removed as a dependency of
the `pytorch_lightning` package, due to potential conflicts with other
packages in the ML ecosystem. For this reason, `logger=True` will use
`CSVLogger` as the default logger, unless the `tensorboard` or
`tensorboardX` packages are found. Please `pip install lightning[extra]` or
one of them to enable TensorBoard support by default
Mon Sep 1 14:38:24 2025: Loading Boltz structure prediction weights
/Users/enrico/boltz22/lib/python3.11/site-packages/pytorch_lightning/utilities/migration/utils.py:56:
The loaded checkpoint was produced with Lightning v2.5.0.post0, which is
newer than your current Lightning version: v2.5.0
Mon Sep 1 14:38:35 2025: Finished loading Boltz structure prediction weights
Mon Sep 1 14:38:35 2025: Starting structure inference
/Users/enrico/boltz22/lib/python3.11/site-packages/pytorch_lightning/trainer/connectors/data_connector.py:420:
Consider setting `persistent_workers=True` in 'predict_dataloader' to speed
up the dataloader worker initialization.
/Users/enrico/boltz22/lib/python3.11/site-packages/torch/utils/data/dataloader.py:684:
UserWarning: 'pin_memory' argument is set as true but not supported on MPS
now, then device pinned memory won't be used.
warnings.warn(warn_msg)
Mon Sep 1 14:38:44 2025: Begin structure inference ligand4 (1 of 5)
/Users/enrico/boltz22/lib/python3.11/site-packages/boltz/model/loss/diffusionv2.py:51:
UserWarning: The operator 'aten::linalg_svd' is not currently supported on
the MPS backend and will fall back to run on the CPU. This may have
performance implications. (Triggered internally at
/Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/mps/MPSFallback.mm:15.)
U, S, V = torch.linalg.svd(
Mon Sep 1 14:40:40 2025: End structure inference ligand4 (1 of 5)
Mon Sep 1 14:40:40 2025: Begin structure inference ligand5 (2 of 5)
Mon Sep 1 14:42:40 2025: End structure inference ligand5 (2 of 5)
Mon Sep 1 14:42:40 2025: Begin structure inference ligand2 (3 of 5)
Mon Sep 1 14:44:38 2025: End structure inference ligand2 (3 of 5)
Mon Sep 1 14:44:38 2025: Begin structure inference ligand3 (4 of 5)
Mon Sep 1 14:46:41 2025: End structure inference ligand3 (4 of 5)
Mon Sep 1 14:46:41 2025: Begin structure inference ligand1 (5 of 5)
Mon Sep 1 14:48:44 2025: End structure inference ligand1 (5 of 5)
Mon Sep 1 14:48:57 2025: Finished structure inference
Mon Sep 1 14:48:57 2025: Loading affinity prediction weights
Traceback (most recent call last):
File "/Users/enrico/boltz22/bin/boltz", line 8, in <module>
sys.exit(cli())
^^^^^
File "/Users/enrico/boltz22/lib/python3.11/site-packages/click/core.py",
line 1157, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/enrico/boltz22/lib/python3.11/site-packages/click/core.py",
line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/Users/enrico/boltz22/lib/python3.11/site-packages/click/core.py",
line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/enrico/boltz22/lib/python3.11/site-packages/click/core.py",
line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/enrico/boltz22/lib/python3.11/site-packages/click/core.py",
line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/enrico/boltz22/lib/python3.11/site-packages/boltz/main.py",
line 1419, in predict
model_module = Boltz2.load_from_checkpoint(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/enrico/boltz22/lib/python3.11/site-packages/pytorch_lightning/utilities/model_helpers.py",
line 125, in wrapper
return self.method(cls, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/enrico/boltz22/lib/python3.11/site-packages/pytorch_lightning/core/module.py",
line 1581, in load_from_checkpoint
loaded = _load_from_checkpoint(
^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/enrico/boltz22/lib/python3.11/site-packages/pytorch_lightning/core/saving.py",
line 63, in _load_from_checkpoint
checkpoint = pl_load(checkpoint_path, map_location=map_location)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/enrico/boltz22/lib/python3.11/site-packages/lightning_fabric/utilities/cloud_io.py",
line 60, in _load
return torch.load(
^^^^^^^^^^^
File
"/Users/enrico/boltz22/lib/python3.11/site-packages/torch/serialization.py",
line 1491, in load
with _open_zipfile_reader(opened_file) as opened_zipfile:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/enrico/boltz22/lib/python3.11/site-packages/torch/serialization.py",
line 771, in __init__
super().__init__(torch._C.PyTorchFileReader(name_or_buffer))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: PytorchStreamReader failed reading zip archive: failed
finding central directory
Could you precise which package causes this issue and how would the problem
be solved in the ChimeraX update?
Many thanks for help!!
Enrico
