google-deepmind / google-deepmind/alphafold

alphafold2 doesn't work on RTX4090?

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Description

I followed everything every step of the instruction

I0605 11:20:06.397100 140157971002496 run_docker.py:235] Traceback (most recent call last):
I0605 11:20:06.397124 140157971002496 run_docker.py:235] File "/app/alphafold/run_alphafold.py", line 459, in
I0605 11:20:06.397146 140157971002496 run_docker.py:235] app.run(main)
I0605 11:20:06.397182 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run
I0605 11:20:06.397204 140157971002496 run_docker.py:235] _run_main(main, args)
I0605 11:20:06.397226 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main
I0605 11:20:06.397248 140157971002496 run_docker.py:235] sys.exit(main(argv))
I0605 11:20:06.397271 140157971002496 run_docker.py:235] File "/app/alphafold/run_alphafold.py", line 444, in main
I0605 11:20:06.397292 140157971002496 run_docker.py:235] models_to_relax=FLAGS.models_to_relax)
I0605 11:20:06.397313 140157971002496 run_docker.py:235] File "/app/alphafold/run_alphafold.py", line 222, in predict_structure
I0605 11:20:06.397335 140157971002496 run_docker.py:235] random_seed=model_random_seed)
I0605 11:20:06.397356 140157971002496 run_docker.py:235] File "/app/alphafold/alphafold/model/model.py", line 167, in predict
I0605 11:20:06.397378 140157971002496 run_docker.py:235] result = self.apply(self.params, jax.random.PRNGKey(random_seed), feat)
I0605 11:20:06.397400 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/_src/random.py", line 132, in PRNGKey
I0605 11:20:06.397438 140157971002496 run_docker.py:235] key = prng.seed_with_impl(impl, seed)
I0605 11:20:06.397461 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/_src/prng.py", line 267, in seed_with_impl
I0605 11:20:06.397483 140157971002496 run_docker.py:235] return random_seed(seed, impl=impl)
I0605 11:20:06.397505 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/_src/prng.py", line 580, in random_seed
I0605 11:20:06.397528 140157971002496 run_docker.py:235] return random_seed_p.bind(seeds_arr, impl=impl)
I0605 11:20:06.397550 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/core.py", line 329, in bind
I0605 11:20:06.397573 140157971002496 run_docker.py:235] return self.bind_with_trace(find_top_trace(args), args, params)
I0605 11:20:06.397596 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/core.py", line 332, in bind_with_trace
I0605 11:20:06.397617 140157971002496 run_docker.py:235] out = trace.process_primitive(self, map(trace.full_raise, args), params)
I0605 11:20:06.397639 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/core.py", line 712, in process_primitive
I0605 11:20:06.397660 140157971002496 run_docker.py:235] return primitive.impl(*tracers, **params)
I0605 11:20:06.397680 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/_src/prng.py", line 592, in random_seed_impl
I0605 11:20:06.397703 140157971002496 run_docker.py:235] base_arr = random_seed_impl_base(seeds, impl=impl)
I0605 11:20:06.397723 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/_src/prng.py", line 597, in random_seed_impl_base
I0605 11:20:06.397745 140157971002496 run_docker.py:235] return seed(seeds)
I0605 11:20:06.397766 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/_src/prng.py", line 832, in threefry_seed
I0605 11:20:06.397787 140157971002496 run_docker.py:235] lax.shift_right_logical(seed, lax_internal._const(seed, 32)))
I0605 11:20:06.397808 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/_src/lax/lax.py", line 515, in shift_right_logical
I0605 11:20:06.397829 140157971002496 run_docker.py:235] return shift_right_logical_p.bind(x, y)
I0605 11:20:06.397851 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/core.py", line 329, in bind
I0605 11:20:06.397871 140157971002496 run_docker.py:235] return self.bind_with_trace(find_top_trace(args), args, params)
I0605 11:20:06.397893 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/core.py", line 332, in bind_with_trace
I0605 11:20:06.397914 140157971002496 run_docker.py:235] out = trace.process_primitive(self, map(trace.full_raise, args), params)
I0605 11:20:06.397935 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/core.py", line 712, in process_primitive
I0605 11:20:06.397955 140157971002496 run_docker.py:235] return primitive.impl(*tracers, **params)
I0605 11:20:06.397976 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/_src/dispatch.py", line 115, in apply_primitive
I0605 11:20:06.397998 140157971002496 run_docker.py:235] return compiled_fun(*args)
I0605 11:20:06.398021 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/_src/dispatch.py", line 200, in
I0605 11:20:06.398042 140157971002496 run_docker.py:235] return lambda *args, **kw: compiled(*args, **kw)[0]
I0605 11:20:06.398062 140157971002496 run_docker.py:235] File "/opt/conda/lib/python3.7/site-packages/jax/_src/dispatch.py", line 895, in _execute_compiled
I0605 11:20:06.398084 140157971002496 run_docker.py:235] out_flat = compiled.execute(in_flat)
I0605 11:20:06.398105 140157971002496 run_docker.py:235] jaxlib.xla_extension.XlaRuntimeError: INTERNAL: Could not find the corresponding function

and this is my docker image:
(af2) bulat@AuroraR15:~/apps/AF230multimer/alphafold$ docker image inspect alphafold
[
{
"Id": "sha256:fcb14e253899d17d14b0b094c03db3262352ac946df6e6ccd75d8feed624fecf",
"RepoTags": [
"alphafold:latest"
],
"RepoDigests": [],
"Parent": "",
"Comment": "buildkit.dockerfile.v0",
"Created": "2023-06-05T11:11:19.751298916-04:00",
"Container": "",
"ContainerConfig": {
"Hostname": "",
"Domainname": "",
"User": "",
"AttachStdin": false,
"AttachStdout": false,
"AttachStderr": false,
"Tty": false,
"OpenStdin": false,
"StdinOnce": false,
"Env": null,
"Cmd": null,
"Image": "",
"Volumes": null,
"WorkingDir": "",
"Entrypoint": null,
"OnBuild": null,
"Labels": null
},
"DockerVersion": "",
"Author": "",
"Config": {
"Hostname": "",
"Domainname": "",
"User": "",
"AttachStdin": false,
"AttachStdout": false,
"AttachStderr": false,
"Tty": false,
"OpenStdin": false,
"StdinOnce": false,
"Env": [
"PATH=/opt/conda/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
"NVARCH=x86_64",
"NVIDIA_REQUIRE_CUDA=cuda>=11.1 brand=tesla,driver>=418,driver<419 brand=tesla,driver>=450,driver<451",
"NV_CUDA_CUDART_VERSION=11.1.74-1",
"NV_CUDA_COMPAT_PACKAGE=cuda-compat-11-1",
"CUDA_VERSION=11.1.1",
"LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64",
"NVIDIA_VISIBLE_DEVICES=all",
"NVIDIA_DRIVER_CAPABILITIES=compute,utility",
"NV_CUDA_LIB_VERSION=11.1.1-1",
"NV_NVTX_VERSION=11.1.74-1",
"NV_LIBNPP_VERSION=11.1.2.301-1",
"NV_LIBNPP_PACKAGE=libnpp-11-1=11.1.2.301-1",
"NV_LIBCUSPARSE_VERSION=11.3.0.10-1",
"NV_LIBCUBLAS_PACKAGE_NAME=libcublas-11-1",
"NV_LIBCUBLAS_VERSION=11.3.0.106-1",
"NV_LIBCUBLAS_PACKAGE=libcublas-11-1=11.3.0.106-1",
"NV_LIBNCCL_PACKAGE_NAME=libnccl2",
"NV_LIBNCCL_PACKAGE_VERSION=2.8.4-1",
"NCCL_VERSION=2.8.4-1",
"NV_LIBNCCL_PACKAGE=libnccl2=2.8.4-1+cuda11.1",
"NV_CUDNN_VERSION=8.0.5.39",
"NV_CUDNN_PACKAGE_NAME=libcudnn8",
"NV_CUDNN_PACKAGE=libcudnn8=8.0.5.39-1+cuda11.1"
],
"Cmd": null,
"Image": "",
"Volumes": null,
"WorkingDir": "/app/alphafold",
"Entrypoint": [
"/app/run_alphafold.sh"
],
"OnBuild": null,
"Labels": {
"com.nvidia.cudnn.version": "8.0.5.39",
"maintainer": "NVIDIA CORPORATION "
},
"Shell": [
"/bin/bash",
"-o",
"pipefail",
"-c"
]
},
"Architecture": "amd64",
"Os": "linux",
"Size": 9924197318,
"VirtualSize": 9924197318,
"GraphDriver": {
"Data": {
"LowerDir": "/var/lib/docker/overlay2/sbxmecbsjt11l3qyccji7l5kf/diff:/var/lib/docker/overlay2/u5kuh6plaibllh9jpuomdyjhn/diff:/var/lib/docker/overlay2/t49o4ey3s5b7ekg1zxidppxbb/diff:/var/lib/docker/overlay2/xmtjesixrlc1mg14cowazbk0m/diff:/var/lib/docker/overlay2/irr673954hnwg04pfp20vq8lz/diff:/var/lib/docker/overlay2/l0vuaq33gpdbn7fzulqngf2kx/diff:/var/lib/docker/overlay2/suhsvcnbzjxh1peozvhn58noz/diff:/var/lib/docker/overlay2/50elvoyrfa07nd835wravqkbl/diff:/var/lib/docker/overlay2/kbmsqxhwpwyqmsj27pvb3ak43/diff:/var/lib/docker/overlay2/y266fduk6jzb7dd3sf1v7dbf9/diff:/var/lib/docker/overlay2/u15ulcsr1gdp7ok28cek67cg0/diff:/var/lib/docker/overlay2/16801172f93f69d9e0d740f62371ca7ba0bee729769a731b7d33c914651ae460/diff:/var/lib/docker/overlay2/f02078794c77293e590608047d0febff6f7dcf4d51e2404ea61e44c46b614017/diff:/var/lib/docker/overlay2/e8d3910161e3e31d142e6f458ea98a78e95fd34053da8a611aaf3c93e54e3289/diff:/var/lib/docker/overlay2/e1c4a091c1795ba8d134f7eaa59e83aff45105578a8b71f04d128753d1b57211/diff:/var/lib/docker/overlay2/691a7bdc38fb271d19270bfc90e903dcf73e8793819ece86b2aeba8d02df91a7/diff:/var/lib/docker/overlay2/0f852a4c5ac28097307f18e42b9c6967d35d5aa322290ab59fb34080b7b2e918/diff:/var/lib/docker/overlay2/7e7f687fede356633f48844f4f09572d730a8e21b2814b1bd00dae3974ee2821/diff:/var/lib/docker/overlay2/2a568af471f4f6a2bca78c0002c18d4baf5379e5838e8aaa8422761d5766e69e/diff",
"MergedDir": "/var/lib/docker/overlay2/whe6wf7mkchy8fvyt3m34yuc2/merged",
"UpperDir": "/var/lib/docker/overlay2/whe6wf7mkchy8fvyt3m34yuc2/diff",
"WorkDir": "/var/lib/docker/overlay2/whe6wf7mkchy8fvyt3m34yuc2/work"
},
"Name": "overlay2"
},
"RootFS": {
"Type": "layers",
"Layers": [
"sha256:69f57fbceb1b420d7e4697e0f6514887b0805ee0059bea7d51e0a832962e74bf",
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"sha256:a7e9e4c7cd5e0e43cfeee24a85ab8194aefd7f0f8b2bf04fd6fd88b2ee89a37f",
"sha256:b8074f4e7d22b866fcd09d60c5262b6b0f7f691d592c98fadf9514d9cf8b9839",
"sha256:a827e81751a7b3c72c87fdf4a160a746085ca77ae10fc4307a0d0b5d03d0bc54",
"sha256:5f70bf18a086007016e948b04aed3b82103a36bea41755b6cddfaf10ace3c6ef",
"sha256:756e5317e1d484ad1e77862430ec8150875a1e49ef66bc6f3b6b9a8523e85c7a",
"sha256:213a79d7456b950ae34c364a88ceb3c6600354cb852fdc605d59528e34dc71c1",
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"sha256:f9f35834bc449ef3071cb17822df1748888e683c98a484372859f0f4984c184a"
]
},
"Metadata": {
"LastTagTime": "0001-01-01T00:00:00Z"
}
}
]

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