Error after GPU part - Githubissues

Hi, after installation the "CPU part" (jackhammer and hhblits) work well. But when i start the gpu part, i've got this error message: TypeError: take requires ndarray or scalar arguments, got <class 'list'> at position 0.

1st part: ./run_feature.sh -d data -o ./tmp -m model_1,model_2,model_3,model_4,model_5 -f ./query/1crn.fasta -t 2021-07-27 2st part: ./run_alphafold.sh -d data -o ./tmp -m model_1,model_2,model_3,model_4,model_5 -f ./query/1crn.fasta -t 2021-07-27

Full error message: File "/softwares/alphafold/run_alphafold.py", line 316, in app.run(main) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/softwares/alphafold/run_alphafold.py", line 289, in main predict_structure( File "/softwares/alphafold/run_alphafold.py", line 188, in predict_structure relaxed_pdbstr, , _ = amber_relaxer.process(prot=unrelaxed_protein) File "/softwares/alphafold/alphafold/relax/relax.py", line 58, in process out = amber_minimize.run_pipeline( File "/softwares/alphafold/alphafold/relax/amber_minimize.py", line 482, in run_pipeline ret.update(get_violation_metrics(prot)) File "/softwares/alphafold/alphafold/relax/amber_minimize.py", line 356, in get_violation_metrics structural_violations, struct_metrics = find_violations(prot) File "/softwares/alphafold/alphafold/relax/amber_minimize.py", line 338, in find_violations violations = folding.find_structural_violations( File "/softwares/alphafold/alphafold/model/folding.py", line 757, in find_structural_violations atom14_atom_radius = batch['atom14_atom_exists'] utils.batched_gather( File "/softwares/alphafold/alphafold/model/utils.py", line 39, in batched_gather return take_fn(params, indices) File "/softwares/alphafold/alphafold/model/utils.py", line 36, in take_fn = lambda p, i: jnp.take(p, i, axis=axis) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/_src/numpy/lax_numpy.py", line 5383, in take return _take(a, indices, None if axis is None else operator.index(axis), out, File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/_src/traceback_util.py", line 162, in reraise_with_filtered_traceback return fun(args, kwargs) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/_src/api.py", line 411, in cache_miss out_flat = xla.xla_call( File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/core.py", line 1618, in bind return call_bind(self, fun, *args, *params) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/core.py", line 1609, in call_bind outs = primitive.process(top_trace, fun, tracers, params) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/core.py", line 1621, in process return trace.process_call(self, fun, tracers, params) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/core.py", line 615, in process_call return primitive.impl(f, tracers, params) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/interpreters/xla.py", line 622, in _xla_call_impl compiled_fun = _xla_callable(fun, device, backend, name, donated_invars, File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/linear_util.py", line 262, in memoized_fun ans = call(fun, args) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/interpreters/xla.py", line 694, in _xla_callable return lower_xla_callable(fun, device, backend, name, donated_invars, arg_specs).compile().unsafe_call File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/interpreters/xla.py", line 702, in lower_xla_callable jaxpr, out_avals, consts = pe.trace_to_jaxpr_final( File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/interpreters/partial_eval.py", line 1522, in trace_to_jaxpr_final jaxpr, out_avals, consts = trace_to_subjaxpr_dynamic(fun, main, in_avals) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/interpreters/partial_eval.py", line 1500, in trace_to_subjaxpr_dynamic ans = fun.call_wrapped(in_tracers) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/linear_util.py", line 166, in call_wrapped ans = self.f(args, dict(self.params, kwargs)) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/_src/numpy/lax_numpy.py", line 5390, in _take _check_arraylike("take", a) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/_src/numpy/lax_numpy.py", line 559, in _check_arraylike raise TypeError(msg.format(fun_name, type(arg), pos)) jax._src.traceback_util.UnfilteredStackTrace: TypeError: take requires ndarray or scalar arguments, got <class 'list'> at position 0.

The stack trace below excludes JAX-internal frames. The preceding is the original exception that occurred, unmodified.

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/softwares/alphafold/run_alphafold.py", line 316, in app.run(main) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/softwares/alphafold/run_alphafold.py", line 289, in main predict_structure( File "/softwares/alphafold/run_alphafold.py", line 188, in predict_structure relaxed_pdbstr, , _ = amber_relaxer.process(prot=unrelaxed_protein) File "/softwares/alphafold/alphafold/relax/relax.py", line 58, in process out = amber_minimize.run_pipeline( File "/softwares/alphafold/alphafold/relax/amber_minimize.py", line 482, in run_pipeline ret.update(get_violation_metrics(prot)) File "/softwares/alphafold/alphafold/relax/amber_minimize.py", line 356, in get_violation_metrics structural_violations, struct_metrics = find_violations(prot) File "/softwares/alphafold/alphafold/relax/amber_minimize.py", line 338, in find_violations violations = folding.find_structural_violations( File "/softwares/alphafold/alphafold/model/folding.py", line 757, in find_structural_violations atom14_atom_radius = batch['atom14_atom_exists'] * utils.batched_gather( File "/softwares/alphafold/alphafold/model/utils.py", line 39, in batched_gather return take_fn(params, indices) File "/softwares/alphafold/alphafold/model/utils.py", line 36, in take_fn = lambda p, i: jnp.take(p, i, axis=axis) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/_src/numpy/lax_numpy.py", line 5383, in take return _take(a, indices, None if axis is None else operator.index(axis), out, File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/_src/numpy/lax_numpy.py", line 5390, in _take _check_arraylike("take", a) File "/softwares/alphafold/envs/alphafold/lib/python3.8/site-packages/jax/_src/numpy/lax_numpy.py", line 559, in _check_arraylike raise TypeError(msg.format(fun_name, type(arg), pos)) TypeError: take requires ndarray or scalar arguments, got <class 'list'> at position 0.

Zuricho / ParallelFold

Error after GPU part #4