Updates to run notebook on cpu

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

Author: ericspod

2d_classification/monai_101.ipynb

@@ -242,11 +242,12 @@
    "outputs": [],
    "source": [
     "max_epochs = 5\n",
-    "model = densenet121(spatial_dims=2, in_channels=1, out_channels=6).to(\"cuda:0\")\n",
+    "device = torch.device(\"cuda:0\" if torch.cuda.device_count() > 0 else \"cpu\")\n",
+    "model = densenet121(spatial_dims=2, in_channels=1, out_channels=6).to(device)\n",
     "\n",
     "logging.basicConfig(stream=sys.stdout, level=logging.INFO)\n",
     "trainer = SupervisedTrainer(\n",
-    "    device=torch.device(\"cuda:0\"),\n",
+    "    device=device,\n",
     "    max_epochs=max_epochs,\n",
     "    train_data_loader=DataLoader(dataset, batch_size=512, shuffle=True, num_workers=4),\n",
     "    network=model,\n",
@@ -312,7 +313,7 @@
     "max_items_to_print = 10\n",
     "with eval_mode(model):\n",
     "    for item in DataLoader(testdata, batch_size=1, num_workers=0):\n",
-    "        prob = np.array(model(item[\"image\"].to(\"cuda:0\")).detach().to(\"cpu\"))[0]\n",
+    "        prob = np.array(model(item[\"image\"].to(device)).detach().to(\"cpu\"))[0]\n",
     "        pred = class_names[prob.argmax()]\n",
     "        gt = item[\"class_name\"][0]\n",
     "        print(f\"Class prediction is {pred}. Ground-truth: {gt}\")\n",

requirements.txt

@@ -4,4 +4,5 @@ autopep8
 jupytext<=1.16.3
 autoflake
 ipywidgets
+ipykernel
 tensorboard>=2.4.0

runner.sh

@@ -466,6 +466,15 @@ trap finish EXIT
 # After setup, don't want to exit immediately after error
 set +e
 
+# FIXME: https://github.com/Project-MONAI/MONAI/issues/4354
+protobuf_major_version=$(${PY_EXE} -m pip list | grep '^protobuf ' | tr -s ' ' | cut -d' ' -f2 | cut -d'.' -f1)
+if [ "$protobuf_major_version" -ge "4" ]
+then
+    export PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python
+else
+    unset PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION
+fi
+
 ########################################################################
 #                                                                      #
 #  loop over files                                                     #
@@ -559,15 +568,6 @@ for file in "${files[@]}"; do
 
         python -c 'import monai; monai.config.print_config()'
 
-        # FIXME: https://github.com/Project-MONAI/MONAI/issues/4354
-        protobuf_major_version=$(${PY_EXE} -m pip list | grep '^protobuf ' | tr -s ' ' | cut -d' ' -f2 | cut -d'.' -f1)
-        if [ "$protobuf_major_version" -ge "4" ]
-        then
-            export PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python
-        else
-            unset PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION
-        fi
-
         cmd=$(echo "papermill ${papermill_opt} --progress-bar --log-output -k ${kernelspec}")
         echo "$cmd"
         time out=$(echo "$notebook" | eval "$cmd")