af2_complex running error

/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/Bio/Data/SCOPData.py:18: BiopythonDeprecationWarning: The 'Bio. Data.SCOPData' module will be deprecated in a future release of Biopython in favor of 'Bio.Data.PDBData. warnings.warn( /scratch/valiente/dl_binder_design/af2_initial_guess/af2_util.py:14: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'. from rosetta import * No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.) WARNING:tensorflow:From /scratch/valiente/dl_binder_design/af2_initial_guess/alphafold/model/tf/input_pipeline.py:151: calling map_fn (from t ensorflow.python.ops.map_fn) with dtype is deprecated and will be removed in a future version. Instructions for updating: Use fn_output_signature instead PyRosetta-4 2023 [Rosetta PyRosetta4.conda.linux.cxx11thread.serialization.CentOS.python39.Release 2023.33+release.9c16e13c3cc4d3ef76e5869e0a 5b44da70cff686 2023-08-18T11:32:04] retrieved from: http://www.pyrosetta.org (C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team. //////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////// WARNING! No GPU detected running AF2 on CPU //////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////

Processing struct with tag: design_ppi_0_dldesign_0_cycle1 The distance between residues 95 and 96 is 57.33 A > limit 3.0 A. I'm going to insert a chainbreak after residue 95 Running model_1_ptm Traceback (most recent call last): File "/scratch/valiente/dl_binder_design/af2_initial_guess/predict.py", line 546, in if args.debug: af2_runner.process_struct(pdb) File "/scratch/valiente/dl_binder_design/af2_initial_guess/predict.py", line 282, in process_struct prediction_result = self.model_runner.apply( self.model_runner.params, File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/traceback_util.py", line 166, in reraisewith filtered_traceback return fun(*args, kwargs) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/pjit.py", line 253, in cache_miss outs, out_flat, out_tree, args_flat, jaxpr = _python_pjit_helper( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/pjit.py", line 161, in _python_pjit_helper argsflat, , params, in_tree, outtree, = infer_params_fn( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/api.py", line 324, in infer_params return pjit.common_infer_params(pjit_info_args, *args, kwargs) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/pjit.py", line 491, in common_infer_params jaxpr, consts, canonicalized_out_shardings_flat = _pjit_jaxpr( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/pjit.py", line 969, in _pjit_jaxpr jaxpr, final_consts, out_type = _create_pjit_jaxpr( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/linear_util.py", line 345, in memoized_fun ans = call(fun, args) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/pjit.py", line 922, in _create_pjit_jaxpr jaxpr, global_out_avals, consts = pe.trace_to_jaxpr_dynamic( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/profiler.py", line 314, in wrapper return func(args, kwargs) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/interpreters/partial_eval.py", line 2155, in t race_to_jaxpr_dynamic jaxpr, out_avals, consts = trace_to_subjaxpr_dynamic( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/interpreters/partial_eval.py", line 2177, in t race_to_subjaxpr_dynamic ans = fun.call_wrapped(intracers) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/linear_util.py", line 188, in call_wrapped ans = self.f(args, dict(self.params, kwargs)) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/transform.py", line 127, in apply_fn out, state = f.apply(params, {}, *args, kwargs) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/transform.py", line 383, in apply_fn out = f(*args, kwargs) File "/scratch/valiente/dl_binder_design/af2_initial_guess/alphafold/model/model.py", line 60, in _forward_fn return model( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/module.py", line 428, in wrapped out = f(*args, *kwargs) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/module.py", line 279, in run_interceptors return bound_method(args, kwargs) File "/scratch/valiente/dl_binder_design/af2_initialguess/alphafold/model/modules.py", line 385, in call , prev = hk.while_loop( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/stateful.py", line 621, in while_loop val, state = jax.lax.while_loop(pure_cond_fun, pure_body_fun, init_val) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/traceback_util.py", line 166, in reraisewith filtered_traceback return fun(*args, kwargs) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/lax/control_flow/loops.py", line 1210, in whil e_loop init_vals, init_avals, body_jaxpr, in_tree, rest = _create_jaxpr(init_val) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/lax/control_flow/loops.py", line 1193, in _cre ate_jaxpr body_jaxpr, body_consts, body_tree = _initial_style_jaxpr( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/lax/control_flow/common.py", line 65, in _init ial_style_jaxpr jaxpr, consts, out_tree = _initial_style_open_jaxpr( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/lax/control_flow/common.py", line 59, in _init ial_style_openjaxpr jaxpr, , consts = pe.trace_to_jaxpr_dynamic(wrapped_fun, in_avals, debug) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/profiler.py", line 314, in wrapper return func(args, kwargs) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/interpreters/partial_eval.py", line 2155, in t race_to_jaxpr_dynamic jaxpr, out_avals, consts = trace_to_subjaxpr_dynamic( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/interpreters/partial_eval.py", line 2177, in t race_to_subjaxpr_dynamic ans = fun.call_wrapped(intracers) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/linear_util.py", line 188, in call_wrapped ans = self.f(args, dict(self.params, kwargs)) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/stateful.py", line 616, in pure_body_fun val = body_fun(val) File "/scratch/valiente/dl_binder_design/af2_initial_guess/alphafold/model/modules.py", line 377, in get_prev(do_call(x[1], recycle_idx=x[0], File "/scratch/valiente/dl_binder_design/af2_initial_guess/alphafold/model/modules.py", line 339, in do_call return impl( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/module.py", line 428, in wrapped out = f(*args, kwargs) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/module.py", line 279, in run_interceptors return bound_method(*args, *kwargs) File "/scratch/valiente/dl_binder_design/af2_initial_guess/alphafold/model/modules.py", line 165, in call representations = evoformer_module(batch0, is_training) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/module.py", line 428, in wrapped out = f(args, kwargs) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/module.py", line 279, in run_interceptors return bound_method(*args, kwargs) File "/scratch/valiente/dl_binder_design/af2_initial_guess/alphafold/model/modules.py", line 1771, in call template_pair_representation = TemplateEmbedding(c.template, gc)( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/module.py", line 428, in wrapped out = f(*args, *kwargs) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/module.py", line 279, in run_interceptors return bound_method(args, kwargs) File "/scratch/valiente/dl_binder_design/af2_initial_guess/alphafold/model/modules.py", line 2066, in call template_pair_representation = mapping.sharded_map(map_fn, in_axes=0)( File "/scratch/valiente/dl_binder_design/af2_initial_guess/alphafold/model/mapping.py", line 141, in mapped_fn remainder_shape_dtype = hk.eval_shape( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/stateful.py", line 688, in eval_shape out_shape = jax.eval_shape(stateless_fun, internal_state(), *args, kwargs) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/traceback_util.py", line 166, in reraisewith filtered_traceback return fun(*args, *kwargs) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/api.py", line 2807, in eval_shape out = pe.abstract_eval_fun(wrapped_fun.call_wrapped, File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/interpreters/partial_eval.py", line 670, in ab stract_evalfun , avalsout, = trace_to_jaxpr_dynamic( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/profiler.py", line 314, in wrapper return func(args, kwargs) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/interpreters/partial_eval.py", line 2155, in t race_to_jaxpr_dynamic jaxpr, out_avals, consts = trace_to_subjaxpr_dynamic( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/interpreters/partial_eval.py", line 2177, in t race_to_subjaxpr_dynamic ans = fun.call_wrapped(intracers) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/linear_util.py", line 188, in call_wrapped ans = self.f(args, dict(self.params, kwargs)) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/linear_util.py", line 188, in call_wrapped ans = self.f(args, dict(self.params, kwargs)) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/stateful.py", line 684, in stateless_fun out = fun(args, kwargs) File "/scratch/valiente/dl_binder_design/af2_initial_guess/alphafold/model/mapping.py", line 139, in apply_fun_to_slice return fun(input_slice) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/stateful.py", line 576, in mapped_fun out, state = mapped_pure_fun(args, state) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/traceback_util.py", line 166, in reraisewith filtered_traceback return fun(args, kwargs) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/api.py", line 1258, in vmap_f out_flat = batching.batch( File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/linear_util.py", line 188, in call_wrapped ans = self.f(*args, dict(self.params, kwargs)) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/stateful.py", line 568, in pure_fun state_out = difference(state_in, internal_state()) File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/haiku/_src/stateful.py", line 313, in difference params_after = jax.tree_multimap(functools.partial(if_changed, is_new_param), File "/scratch/valiente/anaconda3/envs/dl_binder_design/lib/python3.9/site-packages/jax/_src/deprecations.py", line 53, in getattr raise AttributeError(f"module {module!r} has no attribute {name!r}") jax._src.traceback_util.UnfilteredStackTrace: AttributeError: module 'jax' has no attribute 'tree_multimap'

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

nrbennet / dl_binder_design

af2_complex running error #40