AttributeError: 'MMseqs2' object has no attribute 'gpu_db'

[gha2012]

Hi,
thanks for sharing this. I am getting the error below when I try the example. Can you give me a tip how to fix this problem?
Thank you!

I0227 20:24:14.755610 23059727255360 folding_input.py:1044] Detected AF3_mmseqs2/examples/alphafold_input.json is an AlphaFold 3 JSON since the top-level is not a list.
I0227 20:24:15.572278 23059727255360 xla_bridge.py:895] Unable to initialize backend 'rocm': module 'jaxlib.xla_extension' has no attribute 'GpuAllocatorConfig'
I0227 20:24:15.578581 23059727255360 xla_bridge.py:895] Unable to initialize backend 'tpu': INTERNAL: Failed to open libtpu.so: libtpu.so: cannot open shared object file: No such file or directory
I0227 20:24:15.619319 23059727255360 run_alphafold.py:676] Using all available GPU devices: ['0']
2025-02-27 20:24:16.004208: W external/xla/xla/service/gpu/nvptx_compiler.cc:930] The NVIDIA driver's CUDA version is 12.2 which is older than the PTX compiler version 12.6.77. Because the driver is older than the PTX compiler version, XLA is disabling parallel compilation, which may slow down compilation. You should update your NVIDIA driver or use the NVIDIA-provided CUDA forward compatibility packages.
I0227 20:24:19.352719 23050651166272 mmseqs2.py:317] Query sequence: GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQG
I0227 20:24:19.353253 23050649065024 mmseqs2.py:317] Query sequence: GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQG
I0227 20:24:19.353365 23050644862528 mmseqs2.py:317] Query sequence: GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQG
I0227 20:24:19.353436 23050646963776 mmseqs2.py:317] Query sequence: GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQG
I0227 20:24:19.381951 23050649065024 mmseqs2.py:340] Found 1 GPU devices
I0227 20:24:19.391250 23050651166272 mmseqs2.py:340] Found 1 GPU devices
I0227 20:24:19.394526 23050644862528 mmseqs2.py:340] Found 1 GPU devices
I0227 20:24:19.398210 23050646963776 mmseqs2.py:340] Found 1 GPU devices
Running AlphaFold 3. Please note that standard AlphaFold 3 model parameters are
only available under terms of use provided at
https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md.
If you do not agree to these terms and are using AlphaFold 3 derived model
parameters, cancel execution of AlphaFold 3 inference with CTRL-C, and do not
use the model parameters.
Found local devices: [CudaDevice(id=0)]
Building model from scratch...
Processing 1 fold inputs.
Processing fold input 2PV7
Checking we can load the model parameters...
Running data pipeline...
Processing chain A
Traceback (most recent call last):
  File "/AF3_mmseqs2/run_alphafold.py", line 781, in <module>
    app.run(main)
  File "/af3_mmseq_env/lib/python3.11/site-packages/absl/app.py", line 308, in run
    _run_main(main, args)
  File "/af3_mmseq_env/lib/python3.11/site-packages/absl/app.py", line 254, in _run_main
    sys.exit(main(argv))
             ^^^^^^^^^^
  File "/AF3_mmseqs2/run_alphafold.py", line 766, in main
    process_fold_input(
  File "/AF3_mmseqs2/run_alphafold.py", line 580, in process_fold_input
    fold_input = pipeline.DataPipeline(data_pipeline_config).process(fold_input)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/af3_mmseq_env/lib/python3.11/site-packages/alphafold3/data/pipeline.py", line 394, in process
    processed_chains.append(self.process_protein_chain(chain))
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/af3_mmseq_env/lib/python3.11/site-packages/alphafold3/data/pipeline.py", line 343, in process_protein_chain
    unpaired_msa, _, template_hits = _get_protein_msa_and_templates(
                                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/af3_mmseq_env/lib/python3.11/site-packages/alphafold3/data/pipeline.py", line 57, in _get_protein_msa_and_templates
    uniref90_msa = uniref90_msa_future.result()
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/af3_mmseq_env/lib/python3.11/concurrent/futures/_base.py", line 449, in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
  File "/af3_mmseq_env/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
  File "/af3_mmseq_env/lib/python3.11/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/af3_mmseq_env/lib/python3.11/site-packages/alphafold3/data/msa.py", line 195, in get_msa
    a3m=get_msa_tool(run_config.config).query(target_sequence).a3m,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/af3_mmseq_env/lib/python3.11/site-packages/alphafold3/data/tools/mmseqs2.py", line 346, in query
    gpu_db = self.gpu_db
             ^^^^^^^^^^^
AttributeError: 'MMseqs2' object has no attribute 'gpu_db'

[t9lex]

root@61f9745bd8e9:/data2/home_data/ycli/antibody_software/AF3_mmseqs2# python run_alphafold.py --buckets '256,512,768,1024' --mmseqs_gpu_devices 1 --flash_attention_implementation xla --json_path /data2/home_data/ycli/antibody_software/alf_test/alphafold_input.json --db_dir /data2/home_data/tangyike/database/af3_db/ --model_dir /data2/home_data/tangyike/database/af3_model/ --output_dir /data2/home_data/ycli/antibody_software/alf_test
I0311 01:45:15.887406 139892533239808 folding_input.py:1044] Detected /data2/home_data/ycli/antibody_software/alf_test/alphafold_input.json is an AlphaFold 3 JSON since the top-level is not a list.
I0311 01:45:16.272857 139892533239808 xla_bridge.py:895] Unable to initialize backend 'rocm': module 'jaxlib.xla_extension' has no attribute 'GpuAllocatorConfig'
I0311 01:45:16.273875 139892533239808 xla_bridge.py:895] Unable to initialize backend 'tpu': INTERNAL: Failed to open libtpu.so: libtpu.so: cannot open shared object file: No such file or directory
I0311 01:45:16.318140 139892533239808 run_alphafold.py:676] Using all available GPU devices: ['0', '1']
Running AlphaFold 3. Please note that standard AlphaFold 3 model parameters are
only available under terms of use provided at
https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md.
If you do not agree to these terms and are using AlphaFold 3 derived model
parameters, cancel execution of AlphaFold 3 inference with CTRL-C, and do not
use the model parameters.
I0311 01:45:16.321006 139892533239808 run_alphafold.py:726] MMseqs2 will use GPU devices: ('1',)
Traceback (most recent call last):
File "/data2/home_data/ycli/antibody_software/AF3_mmseqs2/run_alphafold.py", line 781, in
app.run(main)
File "/alphafold3_venv/lib/python3.11/site-packages/absl/app.py", line 308, in run
_run_main(main, args)
File "/alphafold3_venv/lib/python3.11/site-packages/absl/app.py", line 254, in _run_main
sys.exit(main(argv))
^^^^^^^^^^
File "/data2/home_data/ycli/antibody_software/AF3_mmseqs2/run_alphafold.py", line 729, in main
data_pipeline_config = pipeline.DataPipelineConfig(**pipeline_config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: DataPipelineConfig.init() got an unexpected keyword argument 'mmseqs2_binary_path'

[t9lex]

i have this problem

[yuanfu-bio]

I got this error as well, has anyone solved this problem yet?
AttributeError: 'MMseqs2' object has no attribute 'gpu_db'

Hi, thanks for sharing this. I am getting the error below when I try the example. Can you give me a tip how to fix this problem? Thank you!

I0227 20:24:14.755610 23059727255360 folding_input.py:1044] Detected AF3_mmseqs2/examples/alphafold_input.json is an AlphaFold 3 JSON since the top-level is not a list.
I0227 20:24:15.572278 23059727255360 xla_bridge.py:895] Unable to initialize backend 'rocm': module 'jaxlib.xla_extension' has no attribute 'GpuAllocatorConfig'
I0227 20:24:15.578581 23059727255360 xla_bridge.py:895] Unable to initialize backend 'tpu': INTERNAL: Failed to open libtpu.so: libtpu.so: cannot open shared object file: No such file or directory
I0227 20:24:15.619319 23059727255360 run_alphafold.py:676] Using all available GPU devices: ['0']
2025-02-27 20:24:16.004208: W external/xla/xla/service/gpu/nvptx_compiler.cc:930] The NVIDIA driver's CUDA version is 12.2 which is older than the PTX compiler version 12.6.77. Because the driver is older than the PTX compiler version, XLA is disabling parallel compilation, which may slow down compilation. You should update your NVIDIA driver or use the NVIDIA-provided CUDA forward compatibility packages.
I0227 20:24:19.352719 23050651166272 mmseqs2.py:317] Query sequence: GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQG
I0227 20:24:19.353253 23050649065024 mmseqs2.py:317] Query sequence: GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQG
I0227 20:24:19.353365 23050644862528 mmseqs2.py:317] Query sequence: GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQG
I0227 20:24:19.353436 23050646963776 mmseqs2.py:317] Query sequence: GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQG
I0227 20:24:19.381951 23050649065024 mmseqs2.py:340] Found 1 GPU devices
I0227 20:24:19.391250 23050651166272 mmseqs2.py:340] Found 1 GPU devices
I0227 20:24:19.394526 23050644862528 mmseqs2.py:340] Found 1 GPU devices
I0227 20:24:19.398210 23050646963776 mmseqs2.py:340] Found 1 GPU devices
Running AlphaFold 3. Please note that standard AlphaFold 3 model parameters are
only available under terms of use provided at
https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md.
If you do not agree to these terms and are using AlphaFold 3 derived model
parameters, cancel execution of AlphaFold 3 inference with CTRL-C, and do not
use the model parameters.
Found local devices: [CudaDevice(id=0)]
Building model from scratch...
Processing 1 fold inputs.
Processing fold input 2PV7
Checking we can load the model parameters...
Running data pipeline...
Processing chain A
Traceback (most recent call last):
  File "/AF3_mmseqs2/run_alphafold.py", line 781, in <module>
    app.run(main)
  File "/af3_mmseq_env/lib/python3.11/site-packages/absl/app.py", line 308, in run
    _run_main(main, args)
  File "/af3_mmseq_env/lib/python3.11/site-packages/absl/app.py", line 254, in _run_main
    sys.exit(main(argv))
             ^^^^^^^^^^
  File "/AF3_mmseqs2/run_alphafold.py", line 766, in main
    process_fold_input(
  File "/AF3_mmseqs2/run_alphafold.py", line 580, in process_fold_input
    fold_input = pipeline.DataPipeline(data_pipeline_config).process(fold_input)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/af3_mmseq_env/lib/python3.11/site-packages/alphafold3/data/pipeline.py", line 394, in process
    processed_chains.append(self.process_protein_chain(chain))
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/af3_mmseq_env/lib/python3.11/site-packages/alphafold3/data/pipeline.py", line 343, in process_protein_chain
    unpaired_msa, _, template_hits = _get_protein_msa_and_templates(
                                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/af3_mmseq_env/lib/python3.11/site-packages/alphafold3/data/pipeline.py", line 57, in _get_protein_msa_and_templates
    uniref90_msa = uniref90_msa_future.result()
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/af3_mmseq_env/lib/python3.11/concurrent/futures/_base.py", line 449, in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
  File "/af3_mmseq_env/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
  File "/af3_mmseq_env/lib/python3.11/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/af3_mmseq_env/lib/python3.11/site-packages/alphafold3/data/msa.py", line 195, in get_msa
    a3m=get_msa_tool(run_config.config).query(target_sequence).a3m,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/af3_mmseq_env/lib/python3.11/site-packages/alphafold3/data/tools/mmseqs2.py", line 346, in query
    gpu_db = self.gpu_db
             ^^^^^^^^^^^
AttributeError: 'MMseqs2' object has no attribute 'gpu_db'