minor code clean

RussellLi87 · Nov 2, 2020 · e72d43a · e72d43a
1 parent bd33f29
commit e72d43a
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Showing 9 changed files with 26 additions and 27 deletions.
diff --git a/data/SBMs.py b/data/SBMs.py
@@ -140,7 +140,7 @@ def positional_encoding(g, pos_enc_dim):
     #EigVal, EigVec = sp.linalg.eigs(L, k=pos_enc_dim+1, which='SR')
     EigVal, EigVec = sp.linalg.eigs(L, k=pos_enc_dim+1, which='SR', tol=1e-2) # for 40 PEs
     EigVec = EigVec[:, EigVal.argsort()] # increasing order
-    g.ndata['pos_enc'] = torch.from_numpy(EigVec[:,1:pos_enc_dim+1]).float() 
+    g.ndata['pos_enc'] = torch.from_numpy(np.real(EigVec[:,1:pos_enc_dim+1])).float()
 
     return g
 

diff --git a/docs/03_run_codes.md b/docs/03_run_codes.md
@@ -64,11 +64,10 @@ tensorboard --logdir='./' --port 6006
 
 
 #### 2.3 To see the training logs in Tensorboard on remote machine
-1. Go to the logs directory, i.e. `out/molecules_graph_regression/logs/`.
-2. Run the [script](../scripts/TensorBoard/script_tensorboard.sh) with `bash script_tensorboard.sh`.
-3. On your local machine, run the command `ssh -N -f -L localhost:6006:localhost:6006 user@xx.xx.xx.xx`.
-4. Open `http://localhost:6006` in your browser. Note that `user@xx.xx.xx.xx` corresponds to your user login and the IP of the remote machine.
-
+1. Move this [script](../scripts/TensorBoard/script_tensorboard.sh) to the root of the repository, i.e. benchmarking-gnns/.
+2. Run the script `bash script_tensorboard.sh`.
+3. On your local machine, run the command `ssh -N -f -L localhost:6006:localhost:6006 user@xx.xx.xx.xx`.
+4. Open `http://localhost:6006` in your browser. Note that `user@xx.xx.xx.xx` corresponds to your user login and the IP of the remote machine.
 
 
 <br>

diff --git a/main_COLLAB_edge_classification.ipynb b/main_COLLAB_edge_classification.ipynb
@@ -134,9 +134,9 @@
     "    return device\n",
     "\n",
     "\n",
-    "use_gpu = True\n",
-    "gpu_id = -1\n",
-    "device = None\n"
+    "# select GPU or CPU\n",
+    "#use_gpu = True; gpu_id = 0; device = None # default GPU\n",
+    "use_gpu = False; gpu_id = -1; device = None # CPU\n"
    ]
   },
   {

diff --git a/main_CSL_graph_classification.ipynb b/main_CSL_graph_classification.ipynb
@@ -134,9 +134,9 @@
     "    return device\n",
     "\n",
     "\n",
-    "use_gpu = True\n",
-    "gpu_id = -1\n",
-    "device = None\n"
+    "# select GPU or CPU\n",
+    "#use_gpu = True; gpu_id = 0; device = None # default GPU\n",
+    "use_gpu = False; gpu_id = -1; device = None # CPU\n"
    ]
   },
   {

diff --git a/main_SBMs_node_classification.ipynb b/main_SBMs_node_classification.ipynb
@@ -135,9 +135,9 @@
     "    return device\n",
     "\n",
     "\n",
-    "use_gpu = True\n",
-    "gpu_id = -1\n",
-    "device = None"
+    "# select GPU or CPU\n",
+    "#use_gpu = True; gpu_id = 0; device = None # default GPU\n",
+    "use_gpu = False; gpu_id = -1; device = None # CPU"
    ]
   },
   {

diff --git a/main_TSP_edge_classification.ipynb b/main_TSP_edge_classification.ipynb
@@ -135,9 +135,9 @@
     "    return device\n",
     "\n",
     "\n",
-    "use_gpu = True\n",
-    "gpu_id = -1\n",
-    "device = None\n"
+    "# select GPU or CPU\n",
+    "#use_gpu = True; gpu_id = 0; device = None # default GPU\n",
+    "use_gpu = False; gpu_id = -1; device = None # CPU\n"
    ]
   },
   {

diff --git a/main_TUs_graph_classification.ipynb b/main_TUs_graph_classification.ipynb
@@ -136,9 +136,9 @@
     "    return device\n",
     "\n",
     "\n",
-    "use_gpu = True\n",
-    "gpu_id = -1\n",
-    "device = None\n"
+    "# select GPU or CPU\n",
+    "#use_gpu = True; gpu_id = 0; device = None # default GPU\n",
+    "use_gpu = False; gpu_id = -1; device = None # CPU\n"
    ]
   },
   {

diff --git a/main_molecules_graph_regression.ipynb b/main_molecules_graph_regression.ipynb
@@ -133,9 +133,9 @@
     "    return device\n",
     "\n",
     "\n",
-    "use_gpu = True\n",
-    "gpu_id = -1\n",
-    "device = None"
+    "# select GPU or CPU\n",
+    "#use_gpu = True; gpu_id = 0; device = None # default GPU\n",
+    "use_gpu = False; gpu_id = -1; device = None # CPU"
    ]
   },
   {

diff --git a/main_superpixels_graph_classification.ipynb b/main_superpixels_graph_classification.ipynb
@@ -134,9 +134,9 @@
     "    return device\n",
     "\n",
     "\n",
-    "use_gpu = True\n",
-    "gpu_id = -1\n",
-    "device = None\n"
+    "# select GPU or CPU\n",
+    "#use_gpu = True; gpu_id = 0; device = None # default GPU\n",
+    "use_gpu = False; gpu_id = -1; device = None # CPU\n"
    ]
   },
   {