howardchanth
commented
10 months ago Hi there,
I also encountered the same error when trying to batch heterogeneous graphs. It seems that this is because our designed HG has some compatibility issues with dgl library (any version). Since the batch size or batching does not have a large impact on time complexity, I evaded the problem by setting the batch size = 1 and manually loading them into a list. You could give it a shot as a temporary solution. Will update the code if I find the solutions. Thanks
(pytorch) zhangyuedi@csr-SYS-4028GR-TR:~/His$ /home/zhangyuedi/anaconda3/envs/pytorch/bin/python /home/zhangyuedi/His/WSI-HGNN-main/main.py Loaded configs from /home/zhangyuedi/His/WSI-HGNN-main/configs/BRCA/HEAT4_kimia_classification_v2.yml Start training Homogeneous GNN 0%| | 0/500 [00:00<?, ?it/s] Traceback (most recent call last): File "/home/zhangyuedi/His/WSI-HGNN-main/main.py", line 65, in
main()
File "/home/zhangyuedi/His/WSI-HGNN-main/main.py", line 50, in main
trainer.train()
File "/home/zhangyuedi/His/WSI-HGNN-main/trainer/train_gnn.py", line 96, in train
for graphs, label in self.dataloader:
File "/home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/torch/utils/data/dataloader.py", line 633, in next
data = self._next_data()
File "/home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/torch/utils/data/dataloader.py", line 677, in _next_data
data = self._dataset_fetcher.fetch(index) # may raise StopIteration
File "/home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/torch/utils/data/_utils/fetch.py", line 54, in fetch
return self.collate_fn(data)
File "/home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/dgl/dataloading/dataloader.py", line 1376, in collate
return [self.collate(samples) for samples in transposed]
File "/home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/dgl/dataloading/dataloader.py", line 1376, in
return [self.collate(samples) for samples in transposed]
File "/home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/dgl/dataloading/dataloader.py", line 1330, in collate
batched_graphs = batch_graphs(items)
File "/home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/dgl/batch.py", line 173, in batch
gidx = disjoint_union(
File "/home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/dgl/heterograph_index.py", line 1432, in disjoint_union
return _CAPI_DGLHeteroDisjointUnion_v2(metagraph, graphs)
File "dgl/_ffi/_cython/./function.pxi", line 295, in dgl._ffi._cy3.core.FunctionBase.call
File "dgl/_ffi/_cython/./function.pxi", line 227, in dgl._ffi._cy3.core.FuncCall
File "dgl/_ffi/_cython/./function.pxi", line 217, in dgl._ffi._cy3.core.FuncCall3
dgl._ffi.base.DGLError: [17:24:52] /opt/dgl/src/graph/unit_graph.cc:1195: Check failed: mat.num_rows == mat.num_cols (36 vs. 19) :
Stack trace:
[bt] (0) /home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/dgl/libdgl.so(+0x86d61a) [0x7fb1c666d61a]
[bt] (1) /home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/dgl/libdgl.so(dgl::UnitGraph::CreateFromCOO(long, dgl::aten::COOMatrix const&, unsigned char)+0x2a8) [0x7fb1c666ff28]
[bt] (2) /home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/dgl/libdgl.so(dgl::DisjointUnionHeteroGraph2(std::shared_ptr, std::vector<std::shared_ptr, std::allocator<std::shared_ptr > > const&)+0x408) [0x7fb1c6660f68]
[bt] (3) /home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/dgl/libdgl.so(+0x78926e) [0x7fb1c658926e]
[bt] (4) /home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/dgl/libdgl.so(+0x789414) [0x7fb1c6589414]
[bt] (5) /home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/dgl/libdgl.so(DGLFuncCall+0x48) [0x7fb1c650e3f8]
[bt] (6) /home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/dgl/_ffi/_cy3/core.cpython-310-x86_64-linux-gnu.so(+0x15413) [0x7fb1c4a15413]
[bt] (7) /home/zhangyuedi/anaconda3/envs/pytorch/lib/python3.10/site-packages/dgl/_ffi/_cy3/core.cpython-310-x86_64-linux-gnu.so(+0x15c2b) [0x7fb1c4a15c2b]
[bt] (8) /home/zhangyuedi/anaconda3/envs/pytorch/bin/python(_PyObject_MakeTpCall+0x26b) [0x557a527709db]