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dgl error? #115

Open fglaser opened 4 months ago

fglaser commented 4 months ago

Hi,

I installed RoseTTAFold-All-Atom exactly as instructed, and then completed missing packages,

2005 pip install hydra-core --upgrade 2007 pip install icecream 2009 pip install assertpy 2011 pip install openbabel 2014 pip3 install openbabel 2015 pip install openbabel-wheel 2017 pip install dgl==0.9.1 2019 pip install deepdiff

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 4 months ago

Can somebody please send a protocol of how exactly to install hydra and dgl? I don't understand why is trying to run hydra from colabfold environment...

Thanks! Fabian

kimdn commented 2 months ago

I met "dgl._ffi.base.DGLError: [21:39:54] /opt/dgl/src/array/array.cc:34: Operator Range does not support cuda device." error as well.

My solution was pip install dgl==1.1.3+cu118 -f https://data.dgl.ai/wheels/cu118/repo.html

This is logical given that the error concerns DGL’s lack of support for CUDA. The specification dgl==1.1.3+cu118 indicates that this version of DGL is intended to be installed with CUDA support, unlike the general pip install dgl==1.1.3 which installs the version without CUDA enhancements.