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running error #114

Closed fglaser closed 1 month ago

fglaser commented 1 month ago

Dear RoseTTAFold-All-Atom community,

First thanks a lot for this Wonderfull tool. I am having some trouble running RFAA, although the installation seems done correctly. I paste the output below, maybe somebody can give a hand to find the problem.

Thanks! Fabian

python rf2aa/run_inference.py --config-name protein | grep protein Traceback (most recent call last): File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 15, in from rf2aa.model.RoseTTAFoldModel import RoseTTAFoldModule File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/model/RoseTTAFoldModel.py", line 6, in from rf2aa.model.layers.Embeddings import MSA_emb, Extra_emb, Bond_emb, Templ_emb, recycling_factory File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/model/layers/Embeddings.py", line 7, in from rf2aa.util_module import Dropout, get_clones, create_custom_forward, rbf, init_lecun_normal, get_res_atom_dist File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/util_module.py", line 7, in import dgl File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/init.py", line 16, in from . import ( File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/dataloading/init.py", line 13, in from .dataloader import File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/dataloading/dataloader.py", line 27, in from ..distributed import DistGraph File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/distributed/init.py", line 5, in from .dist_graph import DistGraph, DistGraphServer, edge_split, node_split File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/distributed/dist_graph.py", line 11, in from .. import backend as F, graphbolt as gb, heterograph_index File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/graphbolt/init.py", line 8, in from .base import File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/graphbolt/base.py", line 8, in from torchdata.datapipes.iter import IterDataPipe File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torchdata/init.py", line 9, in from . import datapipes File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torchdata/datapipes/init.py", line 9, in from . import iter, map, utils File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torchdata/datapipes/iter/init.py", line 79, in from torchdata.datapipes.iter.util.cacheholder import ( File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torchdata/datapipes/iter/util/cacheholder.py", line 24, in from torch.utils.data.datapipes.utils.common import _check_unpickable_fn, DILL_AVAILABLE ImportError: cannot import name 'DILL_AVAILABLE' from 'torch.utils.data.datapipes.utils.common' (/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/utils/data/datapipes/utils/common.py)

fglaser commented 1 month ago

Hi, it seems I solved most problems,

My test run starts to run correctly, but it dies after hhblit and hhfilter end, I installed everything as suggested and added all missing packages, but some where missing and I installed manually, like hydra and dgl.

Maybe dgl package it's not the correct version?

How should I try to install it exactly?

Thanks A lot, Fabian

python -m rf2aa.run_inference --config-name protein.yaml /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/hydra/_internal/defaults_list.py:251: UserWarning: In 'protein.yaml': Defaults list is missing _self_. See https://hydra.cc/docs/1.2/upgrades/1.0_to_1.1/default_composition_order for more information warnings.warn(msg, UserWarning) Using the cif atom ordering for TRP. /home/fabian/RoseTTAFold-All-Atom/rf2aa/chemical.py:20: UserWarning: Using torch.cross without specifying the dim arg is deprecated. Please either pass the dim explicitly or simply use torch.linalg.cross. The default value of dim will change to agree with that of linalg.cross in a future release. (Triggered internally at ../aten/src/ATen/native/Cross.cpp:62.) Z = torch.cross(Xn,Yn) ./make_msa.sh examples/protein/7u7w_A.fasta 7u7w_protein/A 4 64 pdb100_2021Mar03/pdb100_2021Mar03 signalp6 6.0g has not been installed yet.

Due to license restrictions, this recipe cannot distribute signalp6 directly. Please download signalp-6.0g.fast.tar.gz from: https://services.healthtech.dtu.dk/services/SignalP-6.0g/9-Downloads.php#

and run the following command to complete the installation: $ signalp6-register signalp-6.0g.fast.tar.gz

This will copy signalp6 into your conda environment. Running HHblits against UniRef30 with E-value cutoff 1e-10

Running PSIPRED Running hhsearch cat: 7u7wprotein/A/t000.ss2: No such file or directory Error executing job with overrides: [] Traceback (most recent call last): File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 206, in main runner.infer() File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 155, in infer outputs = self.run_model_forward(input_feats) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 121, in run_model_forward outputs = recycle_step_legacy(self.model, File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/training/recycling.py", line 30, in recycle_step_legacy output_i = ddp_model(input_i) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(*args, *kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(args, kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/model/RoseTTAFoldModel.py", line 368, in forward msa, pair, xyz, alpha_s, xyz_allatom, state, symmsub, quat = self.simulator( File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(*args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(*args, *kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/model/Track_module.py", line 1109, in forward msa_full, pair, xyz, state, alpha, symmsub, quat = self.extra_block[i_m](msa_full, pair, File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(*args, kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/model/Track_module.py", line 963, in forward xyz, state, alpha, quat = self.str2str( File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(*args, *kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 16, in decorate_autocast return func(*args, kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/model/Track_module.py", line 545, in forward shift = self.se3(G, node.reshape(BL, -1, 1), l1_feats, edge_feats) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(*args, kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/model/layers/SE3_network.py", line 99, in forward return self.se3(G, node_features, edge_features) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(*args, *kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(args, kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/SE3Transformer/se3_transformer/model/transformer.py", line 185, in forward node_feats = self.graph_modules(node_feats, edge_feats, graph=graph, basis=basis) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(*args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(*args, *kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/SE3Transformer/se3_transformer/model/transformer.py", line 47, in forward input = module(input, args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(*args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(*args, *kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/SE3Transformer/se3_transformer/model/layers/attention.py", line 162, in forward fused_key_value = self.to_key_value(node_features, edge_features, graph, basis) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl return self._call_impl(args, kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl return forward_call(*args, *kwargs) File "/home/fabian/RoseTTAFold-All-Atom/rf2aa/SE3Transformer/se3_transformer/model/layers/convolution.py", line 319, in forward src, dst = graph.edges() File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/view.py", line 166, in call return self._graph.all_edges(args, **kwargs) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/heterograph.py", line 3417, in all_edges src, dst, eid = self._graph.edges(self.get_etype_id(etype), order) File "/home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/heterograph_index.py", line 609, in edges edge_array = _CAPI_DGLHeteroEdges(self, int(etype), order) File "dgl/_ffi/_cython/./function.pxi", line 293, in dgl._ffi._cy3.core.FunctionBase.call File "dgl/_ffi/_cython/./function.pxi", line 225, in dgl._ffi._cy3.core.FuncCall File "dgl/_ffi/_cython/./function.pxi", line 215, in dgl._ffi._cy3.core.FuncCall3 dgl._ffi.base.DGLError: [21:39:54] /opt/dgl/src/array/array.cc:34: Operator Range does not support cuda device. Stack trace: [bt] (0) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/libdgl.so(dmlc::LogMessageFatal::~LogMessageFatal()+0x4f) [0x7f58be7686ef] [bt] (1) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/libdgl.so(dgl::aten::Range(long, long, unsigned char, DLContext)+0xc1) [0x7f58be740b61] [bt] (2) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/libdgl.so(dgl::UnitGraph::COO::Edges(unsigned long, std::string const&) const+0x9b) [0x7f58bebaa22b] [bt] (3) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/libdgl.so(dgl::UnitGraph::Edges(unsigned long, std::string const&) const+0xa1) [0x7f58beba4f31] [bt] (4) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/libdgl.so(dgl::HeteroGraph::Edges(unsigned long, std::string const&) const+0x2a) [0x7f58beaa44ba] [bt] (5) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/libdgl.so(+0x4e6e2c) [0x7f58beaade2c] [bt] (6) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/libdgl.so(DGLFuncCall+0x48) [0x7f58bea30118] [bt] (7) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/_ffi/_cy3/core.cpython-310-x86_64-linux-gnu.so(+0x1525c) [0x7f58be1bf25c] [bt] (8) /home/fabian/localcolabfold/colabfold-conda/lib/python3.10/site-packages/dgl/_ffi/_cy3/core.cpython-310-x86_64-linux-gnu.so(+0x1578b) [0x7f58be1bf78b]

Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.

fglaser commented 1 month ago

Solved by repeating the installation without SignalP

Thanks, Fabian