google-deepmind / google-deepmind/alphafold

error running with a nvidia blackwell RTX5090

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Description

Hi all
I installed AF without a problem in the following computer:

ASUS PRIME X870-P WIFI
AMD Ryzen 9 7950X 16-Core Processor
OS: AlmaLinux 8.10 (Cerulean Leopard)
nvidia-smi: NVIDIA-SMI 575.57.08 Driver Version: 575.57.08 CUDA Version: 12.9
I have cuda 12.9 12.8 12.2 and 12.0 installed.
Since this is a blackwell GPU only the nvidia-open driver flavor is supported (the one that I installed)

this is my python env for af runs:
Python 3.11.11
absl-py==1.0.0
certifi==2025.4.26
charset-normalizer==2.1.1
docker==5.0.0
idna==3.10
requests==2.28.1
six==1.17.0
urllib3==1.26.20
websocket-client==1.8.0

when I run a alphafold job it starts. I can see jackhmmer running.

Here is the command:
```
JAX_TRACEBACK_FILTERING=off python3 /path_to_my_dir/ALPHAFOLD_GITHUB/alphafold/docker/run_docker.py --fasta_paths=/path_to_my_dir/ALPHAFOLD/TEST/Rpff2_toAlphF.fst --output_dir=/path_to_my_dir/ALPHAFOLD/TEST/A
FOUT/REDUCED-20250606_162608 --data_dir=/path_to_my_dir/ALPHAFOLD/DOWN_DBS --max_template_date=2024-12-31 --db_preset=reduced_dbs --model_preset=monomer_ptm
```

But when it starts generating the first model I get the following error:

`I0606 15:08:19.539341 139629339072320 run_docker.py:258] Traceback (most recent call last):
I0606 15:08:19.539410 139629339072320 run_docker.py:258] File "/app/alphafold/run_alphafold.py", line 570, in
I0606 15:08:19.539434 139629339072320 run_docker.py:258] app.run(main)
I0606 15:08:19.539455 139629339072320 run_docker.py:258] File "/opt/conda/lib/python3.11/site-packages/absl/app.py", line 312, in run
I0606 15:08:19.539471 139629339072320 run_docker.py:258] _run_main(main, args)
I0606 15:08:19.539486 139629339072320 run_docker.py:258] File "/opt/conda/lib/python3.11/site-packages/absl/app.py", line 258, in _run_main
I0606 15:08:19.539502 139629339072320 run_docker.py:258] sys.exit(main(argv))
I0606 15:08:19.539515 139629339072320 run_docker.py:258] ^^^^^^^^^^
I0606 15:08:19.539530 139629339072320 run_docker.py:258] File "/app/alphafold/run_alphafold.py", line 543, in main
I0606 15:08:19.539554 139629339072320 run_docker.py:258] predict_structure(
I0606 15:08:19.539569 139629339072320 run_docker.py:258] File "/app/alphafold/run_alphafold.py", line 284, in predict_structure
I0606 15:08:19.539583 139629339072320 run_docker.py:258] prediction_result = model_runner.predict(processed_feature_dict,
I0606 15:08:19.539597 139629339072320 run_docker.py:258] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
I0606 15:08:19.539610 139629339072320 run_docker.py:258] File "/app/alphafold/alphafold/model/model.py", line 167, in predict
I0606 15:08:19.539624 139629339072320 run_docker.py:258] result = self.apply(self.params, jax.random.PRNGKey(random_seed), feat)
I0606 15:08:19.539638 139629339072320 run_docker.py:258] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
I0606 15:08:19.539651 139629339072320 run_docker.py:258] File "/opt/conda/lib/python3.11/site-packages/jax/_src/random.py", line 241, in PRNGKey
I0606 15:08:19.539664 139629339072320 run_docker.py:258] return _return_prng_keys(True, _key('PRNGKey', seed, impl))
I0606 15:08:19.539682 139629339072320 run_docker.py:258] ^^^^^^^^^^^^^^^^^^^^^^^^^^^
I0606 15:08:19.539695 139629339072320 run_docker.py:258] File "/opt/conda/lib/python3.11/site-packages/jax/_src/random.py", line 203, in _key
I0606 15:08:19.539713 139629339072320 run_docker.py:258] return prng.random_seed(seed, impl=impl)
I0606 15:08:19.539726 139629339072320 run_docker.py:258] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
I0606 15:08:19.539738 139629339072320 run_docker.py:258] File "/opt/conda/lib/python3.11/site-packages/jax/_src/prng.py", line 639, in random_seed
I0606 15:08:19.539750 139629339072320 run_docker.py:258] return random_seed_p.bind(seeds_arr, impl=impl)
I0606 15:08:19.539766 139629339072320 run_docker.py:258] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
I0606 15:08:19.539779 139629339072320 run_docker.py:258] File "/opt/conda/lib/python3.11/site-packages/jax/_src/core.py", line 387, in bind
I0606 15:08:19.539791 139629339072320 run_docker.py:258] return self.bind_with_trace(find_top_trace(args), args, params)
I0606 15:08:19.539805 139629339072320 run_docker.py:258] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
I0606 15:08:19.539818 139629339072320 run_docker.py:258] File "/opt/conda/lib/python3.11/site-packages/jax/_src/core.py", line 391, in bind_with_trace
I0606 15:08:19.539832 139629339072320 run_docker.py:258] out = trace.process_primitive(self, map(trace.full_raise, args), params)
I0606 15:08:19.539847 139629339072320 run_docker.py:258] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
I0606 15:08:19.539859 139629339072320 run_docker.py:258] File "/opt/conda/lib/python3.11/site-packages/jax/_src/core.py", line 879, in process_primitive
I0606 15:08:19.539913 139629339072320 run_docker.py:258] return primitive.impl(*tracers, **params)
I0606 15:08:19.539929 139629339072320 run_docker.py:258] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
I0606 15:08:19.539941 139629339072320 run_docker.py:258] File "/opt/conda/lib/python3.11/site-packages/jax/_src/prng.py", line 651, in random_seed_impl
I0606 15:08:19.539990 139629339072320 run_docker.py:258] base_arr = random_seed_impl_base(seeds, impl=impl)
I0606 15:08:19.540006 139629339072320 run_docker.py:258] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
I0606 15:08:19.540019 139629339072320 run_docker.py:258] File "/opt/conda/lib/python3.11/site-packages/jax/_src/prng.py", line 656, in random_seed_impl_base
I0606 15:08:19.540048 139629339072320 run_docker.py:258] return seed(seeds)
I0606 15:08:19.540071 139629339072320 run_docker.py:258] ^^^^^^^^^^^
I0606 15:08:19.540085 139629339072320 run_docker.py:258] File "/opt/conda/lib/python3.11/site-packages/jax/_src/prng.py", line 885, in threefry_seed
I0606 15:08:19.540120 139629339072320 run_docker.py:258] return _threefry_seed(seed)
I0606 15:08:19.540134 139629339072320 run_docker.py:258] ^^^^^^^^^^^^^^^^^^^^
I0606 15:08:19.540149 139629339072320 run_docker.py:258] jaxlib.xla_extension.XlaRuntimeError: INTERNAL: ptxas exited with non-zero error code 65280, output: ptxas fatal : Program with .target 'sm_90a' cannot be compiled to future architecture
I0606 15:08:19.540164 139629339072320 run_docker.py:258] : If the error message indicates that a file could not be written, please verify that sufficient filesystem space is provided.
I0606 15:08:19.540177 139629339072320 run_docker.py:258] --------------------
I0606 15:08:19.540189 139629339072320 run_docker.py:258] For simplicity, JAX has removed its internal frames from the traceback of the following exception. Set JAX_TRACEBACK_FILTERING=off to include these.`

PS: I have installed and run alphafold without a problem in different computers, all with different hardware, but all of them with the same OS.

Any help will be much appreciated

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