diff --git a/examples/Training a MEGNet Formation Energy Model with PyTorch Lightning.ipynb b/examples/Training a MEGNet Formation Energy Model with PyTorch Lightning.ipynb index ec3cc0f2..b0665eae 100644 --- a/examples/Training a MEGNet Formation Energy Model with PyTorch Lightning.ipynb +++ b/examples/Training a MEGNet Formation Energy Model with PyTorch Lightning.ipynb @@ -88,13 +88,17 @@ "name": "stderr", "output_type": "stream", "text": [ - "69239it [02:47, 413.66it/s] \n" + "69239it [02:55, 395.06it/s] \n" ] } ], "source": [ "# load the MP raw dataset\n", - "structures, mp_ids, eform_per_atom = load_dataset()" + "structures, mp_ids, eform_per_atom = load_dataset()\n", + "\n", + "# For demo purposes, we are only going to select 100 structures from the entire set of structures.\n", + "structures = structures[:100]\n", + "eform_per_atom = eform_per_atom[:100]" ] }, { @@ -115,7 +119,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████| 69239/69239 [01:27<00:00, 793.93it/s]\n" + "100%|███████████████████████████████████████████████████████████████████████████████████████| 100/100 [00:00<00:00, 765.89it/s]\n" ] } ], @@ -131,7 +135,7 @@ "# separate the dataset into training, validation and test data\n", "train_data, val_data, test_data = split_dataset(\n", " mp_dataset,\n", - " frac_list=[0.9, 0.05, 0.05],\n", + " frac_list=[0.8, 0.1, 0.1],\n", " shuffle=True,\n", " random_state=42,\n", ")" @@ -187,9 +191,7 @@ " niters_set2set=2,\n", " hidden_layer_sizes_output=(32, 16),\n", " is_classification=False,\n", - " layer_node_embedding=node_embed,\n", " activation_type=\"softplus2\",\n", - " graph_converter=converter,\n", " bond_expansion=bond_expansion,\n", " cutoff=4.0,\n", " gauss_width=0.5,\n", @@ -252,7 +254,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "23e00465d65141d49b278ad6f9abb612", + "model_id": "5b26b3a39f98418f9d1d61acc28d656a", "version_major": 2, "version_minor": 0 }, @@ -264,56 +266,1415 @@ "output_type": "display_data" }, { - "ename": "RuntimeError", - "evalue": "Predictions and targets are expected to have the same shape, but got torch.Size([1]) and torch.Size([]).", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mRuntimeError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m/var/folders/w6/yrmcztx969j0r2f2v6yy3gp00000gn/T/ipykernel_63656/3372854937.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0mtrainer\u001b[0m \u001b[0;34m=\u001b[0m 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ignore\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 66\u001b[0m \u001b[0;34m\"\"\"Update state with predictions and targets.\"\"\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 67\u001b[0;31m \u001b[0msum_abs_error\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mn_obs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_mean_absolute_error_update\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpreds\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtarget\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 68\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 69\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msum_abs_error\u001b[0m \u001b[0;34m+=\u001b[0m \u001b[0msum_abs_error\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/miniconda3/envs/mavrl/lib/python3.9/site-packages/torchmetrics/functional/regression/mae.py\u001b[0m in 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\u001b[0;34m=\u001b[0m \u001b[0mtarget\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mtarget\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_floating_point\u001b[0m \u001b[0;32melse\u001b[0m \u001b[0mtarget\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfloat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/miniconda3/envs/mavrl/lib/python3.9/site-packages/torchmetrics/utilities/checks.py\u001b[0m in \u001b[0;36m_check_same_shape\u001b[0;34m(preds, target)\u001b[0m\n\u001b[1;32m 39\u001b[0m \u001b[0;34m\"\"\"Check that predictions and target have the same shape, else raise error.\"\"\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 40\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mpreds\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshape\u001b[0m \u001b[0;34m!=\u001b[0m \u001b[0mtarget\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 41\u001b[0;31m raise RuntimeError(\n\u001b[0m\u001b[1;32m 42\u001b[0m \u001b[0;34mf\"Predictions and targets are expected to have the same shape, but got {preds.shape} and {target.shape}.\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 43\u001b[0m )\n", - "\u001b[0;31mRuntimeError\u001b[0m: Predictions and targets are expected to have the same shape, but got torch.Size([1]) and torch.Size([])." + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Validation: 0it [00:00, ?it/s]" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Validation: 0it 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"output_type": "display_data" + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Validation: 0it [00:00, ?it/s]" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Validation: 0it [00:00, ?it/s]" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "`Trainer.fit` stopped: `max_epochs=100` reached.\n" ] } ], "source": [ - "trainer = pl.Trainer(max_epochs=2, accelerator=\"cpu\")\n", + "trainer = pl.Trainer(max_epochs=100, accelerator=\"cpu\")\n", "trainer.fit(model=lit_module, train_dataloaders=train_loader, val_dataloaders=val_loader)" ] },