(partial) EasyBuild log for failed build of /scratch/eb-ake-tmp/eb-cfax5r0s/files_pr20013/p/PyTorch-Geometric/PyTorch-Geometric-2.5.0-foss-2023a-PyTorch-2.1.2-CUDA-12.1.1.eb (PR(s) #20013)

PyTorch-Geometric-2.5.0-foss-2023a-PyTorch-2.1.2-CUDA-12.1.1_partial.log

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test/utils/test_spmm.py::test_spmm_basic[sum-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_basic[mean-cpu] PASSED
test/utils/test_spmm.py::test_spmm_basic[mean-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_reduce[min-cpu] PASSED
test/utils/test_spmm.py::test_spmm_reduce[min-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_reduce[max-cpu] PASSED
test/utils/test_spmm.py::test_spmm_reduce[max-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_layout[sum-layout0-cpu] PASSED
test/utils/test_spmm.py::test_spmm_layout[sum-layout0-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_layout[sum-layout1-cpu] PASSED
test/utils/test_spmm.py::test_spmm_layout[sum-layout1-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_layout[sum-layout2-cpu] PASSED
test/utils/test_spmm.py::test_spmm_layout[sum-layout2-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_layout[mean-layout0-cpu] PASSED
test/utils/test_spmm.py::test_spmm_layout[mean-layout0-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_layout[mean-layout1-cpu] PASSED
test/utils/test_spmm.py::test_spmm_layout[mean-layout1-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_layout[mean-layout2-cpu] PASSED
test/utils/test_spmm.py::test_spmm_layout[mean-layout2-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_layout[min-layout0-cpu] PASSED
test/utils/test_spmm.py::test_spmm_layout[min-layout0-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_layout[min-layout1-cpu] PASSED
test/utils/test_spmm.py::test_spmm_layout[min-layout1-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_layout[min-layout2-cpu] PASSED
test/utils/test_spmm.py::test_spmm_layout[min-layout2-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_layout[max-layout0-cpu] PASSED
test/utils/test_spmm.py::test_spmm_layout[max-layout0-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_layout[max-layout1-cpu] PASSED
test/utils/test_spmm.py::test_spmm_layout[max-layout1-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_layout[max-layout2-cpu] PASSED
test/utils/test_spmm.py::test_spmm_layout[max-layout2-cuda:0] PASSED
test/utils/test_spmm.py::test_spmm_jit[sum] PASSED
test/utils/test_spmm.py::test_spmm_jit[mean] PASSED
test/utils/test_subgraph.py::test_get_num_hops PASSED
test/utils/test_subgraph.py::test_subgraph PASSED
test/utils/test_subgraph.py::test_subgraph_large_index[cpu] PASSED
test/utils/test_subgraph.py::test_subgraph_large_index[cuda:0] PASSED
test/utils/test_subgraph.py::test_bipartite_subgraph PASSED
test/utils/test_subgraph.py::test_bipartite_subgraph_large_index[cpu] PASSED
test/utils/test_subgraph.py::test_bipartite_subgraph_large_index[cuda:0] PASSED
test/utils/test_subgraph.py::test_k_hop_subgraph PASSED
test/utils/test_to_dense_adj.py::test_to_dense_adj PASSED
test/utils/test_to_dense_adj.py::test_to_dense_adj_with_empty_edge_index PASSED
test/utils/test_to_dense_adj.py::test_to_dense_adj_with_duplicate_entries PASSED
test/utils/test_to_dense_batch.py::test_to_dense_batch[70.0] PASSED
test/utils/test_to_dense_batch.py::test_to_dense_batch[fill1] PASSED
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test/utils/test_to_dense_batch.py::test_to_dense_batch_jit SKIPPED (Fast test run)
test/utils/test_train_test_split_edges.py::test_train_test_split_edges PASSED
test/utils/test_tree_decomposition.py::test_tree_decomposition[F/C=C/F] SKIPPED (Package rdkit not found)
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found)
test/utils/test_trim_to_layer.py::test_trim_sparse_tensor PASSED
test/utils/test_trim_to_layer.py::test_trim_to_layer_basic PASSED
test/utils/test_trim_to_layer.py::test_trim_to_layer_hetero PASSED
test/utils/test_trim_to_layer.py::test_trim_to_layer_with_neighbor_loader SKIPPED (Package pyg_lib not found)
test/utils/test_trim_to_layer.py::test_trim_to_layer_filtering PASSED
test/utils/test_unbatch.py::test_unbatch PASSED
test/utils/test_unbatch.py::test_unbatch_edge_index PASSED
test/utils/test_undirected.py::test_is_undirected PASSED
test/utils/test_undirected.py::test_to_undirected PASSED
test/visualization/test_graph_visualization.py::test_visualize_graph_via_graphviz[None] SKIPPED (Graphviz not installed)
test/visualization/test_graph_visualization.py::test_visualize_graph_via_graphviz[graphviz] SKIPPED (Graphviz not installed)
test/visualization/test_graph_visualization.py::test_visualize_graph_via_graphviz_with_node_labels[None] SKIPPED (Graphviz not
installed)
test/visualization/test_graph_visualization.py::test_visualize_graph_via_graphviz_with_node_labels[graphviz] SKIPPED (Graphviz not
installed)
test/visualization/test_graph_visualization.py::test_visualize_graph_via_networkx[None] PASSED
test/visualization/test_graph_visualization.py::test_visualize_graph_via_networkx[networkx] PASSED
test/visualization/test_influence.py::test_influence PASSED

================================================================== FAILURES ==================================================================
____________________________________________________ test_multithreading_neighbor_loader _____________________________________________________

spawn_context = None

    @onlyLinux
    @onlyNeighborSampler
    def test_multithreading_neighbor_loader(spawn_context):
        loader = NeighborLoader(
            data=Data(x=torch.randn(1, 1)),
            num_neighbors=[-1],
            batch_size=1,
            num_workers=2,
            worker_init_fn=init_fn,
        )
    
>       with loader.enable_multithreading(2):

test/loader/test_mixin.py:52: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/hpc2n/eb/software/Python/3.11.3-GCCcore-12.3.0/lib/python3.11/contextlib.py:137: in __enter__
    return next(self.gen)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = NeighborLoader(), worker_threads = 2

    @contextmanager
    def enable_multithreading(
        self,
        worker_threads: Optional[int] = None,
    ) -> None:
        r"""Enables multithreading in worker subprocesses.
        This option requires to change the start method from :obj:`"fork"` to
        :obj:`"spawn"`.
    
        .. code-block:: python
    
            def run():
                loader = NeigborLoader(data, num_workers=3)
                with loader.enable_multithreading(10):
                    for batch in loader:
                        pass
    
            if __name__ == '__main__':
                torch.set_start_method('spawn')
                run()
    
        Args:
            worker_threads (int, optional): The number of threads to use in
                each worker process.
                By default, it uses half of all available CPU cores.
                (default: :obj:`torch.get_num_threads() // num_workers`)
        """
        if worker_threads is None:
            worker_threads = torch.get_num_threads() // self.num_workers
    
        self._worker_threads = worker_threads
    
        if not self.num_workers > 0:
            raise ValueError(f"'enable_multithreading' needs to be performed "
                             f"with at least one worker "
                             f"(got {self.num_workers})")
    
        if worker_threads > torch.get_num_threads():
>           raise ValueError(f"'worker_threads' should be smaller than the "
                             f"total available number of threads "
                             f"{torch.get_num_threads()} "
                             f"(got {worker_threads})")
E           ValueError: 'worker_threads' should be smaller than the total available number of threads 1 (got 2)

/scratch/eb-ake-tmp/eb-cfax5r0s/tmpll4yzsnu/lib/python3.11/site-packages/torch_geometric/loader/mixin.py:154: ValueError
============================================================== warnings summary ==============================================================
../../../../../../../../scratch/eb-ake-tmp/eb-cfax5r0s/tmpll4yzsnu/lib/python3.11/site-packages/torch_geometric/graphgym/imports.py:14
  /scratch/eb-ake-tmp/eb-cfax5r0s/tmpll4yzsnu/lib/python3.11/site-packages/torch_geometric/graphgym/imports.py:14: UserWarning: Please install 'pytorch_lightning' via  'pip install pytorch_lightning' in order to use GraphGym
    warnings.warn("Please install 'pytorch_lightning' via  "

test/explain/algorithm/test_graphmask_explainer.py: 12960 warnings
  /scratch/eb-ake-tmp/eb-cfax5r0s/tmpll4yzsnu/lib/python3.11/site-packages/torch_geometric/explain/algorithm/graphmask_explainer.py:165: DeprecationWarning: `np.math` is a deprecated alias for the standard library `math` module (Deprecated Numpy 1.25). Replace usages of `np.math` with `math`
    beta * np.math.log(-gamma / zeta))

test/loader/test_imbalanced_sampler.py: 2 warnings
test/loader/test_link_neighbor_loader.py: 34 warnings
test/loader/test_mixin.py: 3 warnings
test/loader/test_neighbor_loader.py: 22 warnings
test/loader/test_zip_loader.py: 2 warnings
test/nn/conv/test_pna_conv.py: 1 warning
test/nn/models/test_basic_gnn.py: 2 warnings
  /scratch/eb-ake-tmp/eb-cfax5r0s/tmpll4yzsnu/lib/python3.11/site-packages/torch_geometric/sampler/neighbor_sampler.py:61: UserWarning: Using 'NeighborSampler' without a 'pyg-lib' installation is deprecated and will be removed soon. Please install 'pyg-lib' for accelerated neighborhood sampling
    warnings.warn(f"Using '{self.__class__.__name__}' without a "

test/nn/test_fx.py::test_dropout
  /hpc2n/eb/software/PyTorch/2.1.2-foss-2023a-CUDA-12.1.1/lib/python3.11/site-packages/torch/overrides.py:110: UserWarning: 'has_cuda' is deprecated, please use 'torch.backends.cuda.is_built()'
    torch.has_cuda,

test/nn/test_fx.py::test_dropout
  /hpc2n/eb/software/PyTorch/2.1.2-foss-2023a-CUDA-12.1.1/lib/python3.11/site-packages/torch/overrides.py:111: UserWarning: 'has_cudnn' is deprecated, please use 'torch.backends.cudnn.is_available()'
    torch.has_cudnn,

test/nn/test_fx.py::test_dropout
  /hpc2n/eb/software/PyTorch/2.1.2-foss-2023a-CUDA-12.1.1/lib/python3.11/site-packages/torch/overrides.py:117: UserWarning: 'has_mps' is deprecated, please use 'torch.backends.mps.is_built()'
    torch.has_mps,

test/nn/test_fx.py::test_dropout
  /hpc2n/eb/software/PyTorch/2.1.2-foss-2023a-CUDA-12.1.1/lib/python3.11/site-packages/torch/overrides.py:118: UserWarning: 'has_mkldnn' is deprecated, please use 'torch.backends.mkldnn.is_available()'
    torch.has_mkldnn,

test/nn/conv/test_message_passing.py::test_traceable_my_conv_with_self_loops[4]
test/nn/conv/test_message_passing.py::test_traceable_my_conv_with_self_loops[8]
test/nn/conv/test_message_passing.py::test_traceable_my_conv_with_self_loops[2]
test/nn/conv/test_message_passing.py::test_traceable_my_conv_with_self_loops[0]
  /scratch/eb-ake-tmp/eb-cfax5r0s/tmpll4yzsnu/lib/python3.11/site-packages/torch_geometric/edge_index.py:337: TracerWarning: torch.Tensor results are registered as constants in the trace. You can safely ignore this warning if you use this function to create tensors out of constant variables that would be the same every time you call this function. In any other case, this might cause the trace to be incorrect.
    out = super().__new__(cls, data)

test/nn/dense/test_linear.py::test_hetero_linear[cpu]
test/nn/dense/test_linear.py::test_hetero_linear[cuda:0]
  /hpc2n/eb/software/PyTorch/2.1.2-foss-2023a-CUDA-12.1.1/lib/python3.11/site-packages/torch/jit/_check.py:178: UserWarning: The TorchScript type system doesn't support instance-level annotations on empty non-base types in `__init__`. Instead, either 1) use a type annotation in the class body, or 2) wrap the type in `torch.jit.Attribute`.
    warnings.warn(

test/nn/models/test_dimenet.py: 10 warnings
  /scratch/eb-ake-tmp/eb-cfax5r0s/tmpll4yzsnu/lib/python3.11/site-packages/torch_geometric/nn/models/dimenet_utils.py:69: DeprecationWarning: `np.math` is a deprecated alias for the standard library `math` module (Deprecated Numpy 1.25). Replace usages of `np.math` with `math`
    return ((2 * k + 1) * np.math.factorial(k - abs(m)) /

test/nn/models/test_dimenet.py: 10 warnings
  /scratch/eb-ake-tmp/eb-cfax5r0s/tmpll4yzsnu/lib/python3.11/site-packages/torch_geometric/nn/models/dimenet_utils.py:70: DeprecationWarning: `np.math` is a deprecated alias for the standard library `math` module (Deprecated Numpy 1.25). Replace usages of `np.math` with `math`
    (4 * np.pi * np.math.factorial(k + abs(m))))**0.5

test/transforms/test_laplacian_lambda_max.py::test_laplacian_lambda_max
test/transforms/test_laplacian_lambda_max.py::test_laplacian_lambda_max
test/transforms/test_laplacian_lambda_max.py::test_laplacian_lambda_max
test/transforms/test_laplacian_lambda_max.py::test_laplacian_lambda_max
  /scratch/eb-ake-tmp/eb-cfax5r0s/tmpll4yzsnu/lib/python3.11/site-packages/torch_geometric/transforms/laplacian_lambda_max.py:65: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    data.lambda_max = float(lambda_max.real)

test/utils/test_map.py::test_map_index[100000000-cuda:0]
test/utils/test_map.py::test_map_index_na[100000000-cuda:0]
test/utils/test_subgraph.py::test_subgraph_large_index[cuda:0]
test/utils/test_subgraph.py::test_bipartite_subgraph_large_index[cuda:0]
test/utils/test_subgraph.py::test_bipartite_subgraph_large_index[cuda:0]
  /scratch/eb-ake-tmp/eb-cfax5r0s/tmpll4yzsnu/lib/python3.11/site-packages/torch_geometric/utils/map.py:95: UserWarning: Using CPU-based processing within 'map_index' which may cause slowdowns and device synchronization. Consider installing 'cudf' to accelerate computation
    warnings.warn("Using CPU-based processing within 'map_index' "

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
========================================================== short test summary info ===========================================================
FAILED test/loader/test_mixin.py::test_multithreading_neighbor_loader - ValueError: 'worker_threads' should be smaller than the total available number of threads 1 (got 2)
================================== 1 failed, 5187 passed, 835 skipped, 13066 warnings in 116.90s (0:01:56) ===================================
 (at easybuild/tools/run.py:682 in parse_cmd_output)
== 2024-04-10 14:30:10,075 build_log.py:267 INFO 	... (took 2 mins 12 secs)
== 2024-04-10 14:30:10,075 build_log.py:267 INFO ... (took 57 mins 54 secs)
== 2024-04-10 14:30:10,076 config.py:699 DEBUG software install path as specified by 'installpath' and 'subdir_software': /home/a/ake/easybuild-amd64_ubuntu2204_zen3/software
== 2024-04-10 14:30:10,076 filetools.py:2013 INFO Removing lock /home/a/ake/easybuild-amd64_ubuntu2204_zen3/software/.locks/_home_a_ake_easybuild-amd64_ubuntu2204_zen3_software_PyTorch-Geometric_2.5.0-foss-2023a-PyTorch-2.1.2-CUDA-12.1.1.lock...
== 2024-04-10 14:30:10,081 filetools.py:383 INFO Path /home/a/ake/easybuild-amd64_ubuntu2204_zen3/software/.locks/_home_a_ake_easybuild-amd64_ubuntu2204_zen3_software_PyTorch-Geometric_2.5.0-foss-2023a-PyTorch-2.1.2-CUDA-12.1.1.lock successfully removed.
== 2024-04-10 14:30:10,081 filetools.py:2017 INFO Lock removed: /home/a/ake/easybuild-amd64_ubuntu2204_zen3/software/.locks/_home_a_ake_easybuild-amd64_ubuntu2204_zen3_software_PyTorch-Geometric_2.5.0-foss-2023a-PyTorch-2.1.2-CUDA-12.1.1.lock
== 2024-04-10 14:30:10,081 easyblock.py:4291 WARNING build failed (first 300 chars): cmd "export PYTHONPATH=/scratch/eb-ake-tmp/eb-cfax5r0s/tmpll4yzsnu/lib/python3.11/site-packages:$PYTHONPATH &&  pytest --ignore=test/test_edge_index.py --ignore=test/nn/models/test_graph_unet.py --ignore=test/nn/pool/test_asap.py --ignore=test/transforms/test_add_metapaths.py --ignore=test/transform
== 2024-04-10 14:30:10,081 easyblock.py:328 INFO Closing log for application name PyTorch-Geometric version 2.5.0