Can’t find the in-place operation anywhere? Tried replacing many variables with variable_temp… It comes from loss.backward here:
for epoch in range(10):
  print(epoch)
  for i, l in trainloader:
    i_temp = i.to(device)                 # i added temps in this section 20:50 30.04.20
    l_temp = l.to(device)
    print(i_temp.size(), l_temp.size())
    optimizer.zero_grad()
    output = model(i_temp)
    loss = criterion(output, l_temp)
    print(output.size(), loss.size())
    loss.backward(retain_graph=True)
    optimizer.step()

Here is the full code for reference:
#!/usr/bin/env python3
import networkx as nx
import math
import csv
import random as rand
import sys
import matplotlib.pyplot as plt
from matplotlib import colors as mcolors

import torch_geometric
from torch_geometric.datasets import Planetoid

dataset = Planetoid(root='/local/scratch/al822/test', name='Cora')

G = torch_geometric.utils.to_networkx(dataset[0])

G = G.to_undirected()

#G.remove_nodes_from(range(2000,2709))

fig = plt.figure(1,figsize=(20,20))
nx.draw(G,node_size=60,font_size=8, with_labels=False, edge_color="white")
fig.set_facecolor("#00000F")
plt.show()
print(G.nodes())

G_list = nx.read_gpickle("g_list.gpickle")


print(G_list)
figtest = plt.figure(3,figsize=(30,30)) 
print(G_list[0].number_of_edges())
print(G_list[0].number_of_nodes())
nx.draw(G_list[0],node_size=10,font_size=8, with_labels=False)
plt.show()

pos=nx.spring_layout(G_list[0],k=3)

comms_1 = [{0}, {1, 2}, {3}, {4}, {5}, {6}, {208, 7}, {8, 281, 101, 269}, {9}, {10}, {11}, {12}, {13}, {158, 180, 14, 159}, {15}, {16}, {201, 297, 17, 24, 185}, {18, 139, 103}, {19}, {20}, {21}, {22, 39}, {23}, {25}, {99, 26, 123, 122}, {27}, {28}, {29}, {30}, {31}, {32, 242, 270, 279}, {33, 286}, {34}, {35}, {36}, {164, 37, 210, 211, 55, 60}, {38}, {40}, {41, 175}, {42, 87}, {152, 43}, {44}, {45}, {46}, {163, 47}, {48}, {49}, {50}, {51}, {52}, {53}, {54}, {56}, {57}, {58}, {105, 59}, {61}, {62}, {63}, {64}, {65, 239}, {66}, {282, 67}, {68}, {69}, {70}, {206, 71}, {72}, {73}, {74}, {75, 84, 284}, {88, 162, 76, 130}, {77}, {78}, {79}, {80, 257}, {81}, {82}, {83}, {85}, {86}, {89, 258}, {90, 155, 156}, {91}, {92}, {93}, {195, 94}, {95}, {96}, {97}, {98}, {100}, {289, 133, 102, 138, 236, 109, 153, 124, 126}, {104}, {106}, {107}, {108}, {110}, {111}, {112}, {113}, {114}, {115}, {116}, {259, 117}, {118, 255}, {119}, {120}, {121}, {125}, {127}, {128, 233}, {129}, {131}, {132}, {134}, {137, 135}, {136}, {140}, {141}, {142}, {143}, {144, 145, 213}, {146}, {147}, {148}, {149}, {150}, {151}, {154}, {157}, {160, 277}, {161}, {165}, {166, 271}, {168, 167}, {169}, {170}, {171}, {240, 172}, {173}, {174}, {197, 231, 232, 176, 179}, {177}, {178}, {181}, {182, 183}, {184}, {186}, {187}, {188}, {189}, {190}, {191}, {192}, {193}, {194}, {196}, {198}, {199}, {200}, {202}, {203}, {204}, {205}, {207}, {209}, {212}, {214}, {215}, {216}, {217, 243}, {218}, {219}, {220}, {221}, {222}, {223}, {224}, {225}, {226}, {227}, {228}, {229}, {230}, {234}, {235}, {237}, {238}, {241}, {244}, {245}, {246}, {247}, {248}, {249}, {250}, {251, 253}, {252}, {254}, {256}, {260}, {261}, {262}, {263}, {264}, {265}, {266}, {267}, {268}, {272}, {273}, {274}, {275}, {276}, {278}, {280}, {283}, {285}, {287}, {288}, {290}, {291}, {292}, {293}, {294}, {295}, {296}, {298}, {299}]


colors = dict(mcolors.BASE_COLORS, **mcolors.CSS4_COLORS)




fig2 = plt.figure(2,figsize=(20,20)) 
#for key, com in zip(colors.keys(), comms_1):
    #com = list(map(str,com))

    #nx.draw_networkx_nodes(G_list[0], pos,
                       #nodelist=com,
                       #node_color=key,
                       #node_size=50, 
                       #alpha=1)


#nx.draw_networkx_edges(G_list[0],pos, width=0.5,alpha=1,edge_color='k')
      #  nx.draw_networkx_edges(G,pos,edgelist=removed_edges, width=2, edge_color='k')

#plt.show()
#nx.draw_networkx_edges(G,pos,edgelist=exist_edges, width=2,alpha=1,edge_color='k')
    #    nx.draw_networkx_edges(G,pos,edgelist=removed_edges, width=2, edge_color='k')   #, style='dashed')

G_list[0].number_of_nodes()

G_list[0].nodes[4]


new_dataset = [None] * len(G_list)

#networkx removed all the features and other dataset keys, so have to reinsert them 
for i in list(range(0,len(G_list))):
  new_dataset[i] = torch_geometric.utils.from_networkx(G_list[i])
  new_dataset[i].x = dataset[0].x
  new_dataset[i].y = dataset[0].y
  new_dataset[i].train_mask = dataset[0].train_mask
  new_dataset[i].val_mask = dataset[0].val_mask
  new_dataset[i].test_mask = dataset[0].test_mask
  new_dataset[i].num_classes = dataset.num_classes

print(new_dataset)

new_dataset[0].num_node_features

dataset[0].train_mask[0:200]

new_dataset[0].test_mask

len(new_dataset)

new_dataset[0].train_mask.size()

import torch
import torch.nn.functional as F
from torch_geometric.nn import GCNConv
from torch import nn, optim

class GCNN(torch.nn.Module):
    def __init__(self):
        super(GCNN, self).__init__()
        self.conv1 = GCNConv(new_dataset[0].num_node_features, 957)
        self.conv2 = GCNConv(957, 480)
        self.conv3 = GCNConv(480, new_dataset[0].num_classes)

    def forward(self, data):
        x, edge_index = data.x, data.edge_index

        x = self.conv1(x, edge_index)
        x = F.relu(x)
        x = F.dropout(x, training=self.training)
        x = self.conv2(x, edge_index)
        x = F.relu(x)
        x = F.dropout(x, training=self.training)
        x = self.conv3(x, edge_index)
        

        return F.log_softmax(x, dim=1)

out_list = []

for i in list(range(0,len(G_list)-1,200)):                                                # -1 since last graph has no edges so GCNN cant work on it
  print(i)
  device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
  model = GCNN().to(device)
  data = new_dataset[i].to(device)
  optimizer = torch.optim.Adam(model.parameters(), lr=0.01, weight_decay=5e-4)


  model.train()
  for epoch in range(50):
      optimizer.zero_grad()
      out = model(data)
      print(out.size())
      loss_gcn = F.nll_loss(out[data.train_mask], data.y[data.train_mask])
      loss_gcn.backward(retain_graph=True)                 #change back to true
      optimizer.step()

  
  out_list.append(out)

print(out_list)
out_flat = torch.flatten(torch.cat(out_list, dim=0))
out_nodes = torch.split(out_flat, new_dataset[0].num_classes, dim=0)
labels = torch.cat([new_dataset[0].y]*(len(new_dataset)-1))
print(labels.size())
print(len(out_nodes))

labels_temp = labels.tolist()

train_data = []
for i in range(len(out_nodes)):
   train_data.append([out_nodes[i], labels_temp[i]])

len(train_data)


from itertools import compress                                                       ############ filtering so only "train mask = true" nodes are put into training dataloader
train_data_temp = list(compress(train_data, (torch.cat([new_dataset[0].train_mask]*(len(new_dataset)-1))).tolist()   ))        # maybe in place



trainloader = torch.utils.data.DataLoader(train_data_temp, shuffle=True, batch_size=100)
i1, l1 = next(iter(trainloader))
print(l1.shape)

class FC(torch.nn.Module):
    def __init__(self):
        super(FC, self).__init__()
        self.fc1 = nn.Linear(new_dataset[0].num_classes, new_dataset[0].num_classes)
        self.fc2 = nn.Linear(new_dataset[0].num_classes, new_dataset[0].num_classes)
        self.dropout = nn.Dropout(0.25)
        self.dropout2 = nn.Dropout(0.25)

    def forward(self, x):
        # add dropout layer
        x = self.dropout(x)
        # add 1st hidden layer, with relu activation function
        x = F.relu(self.fc1(x))
        # add dropout layer
        x = self.dropout2(x)
        # add 2nd hidden layer, with relu activation function
        x = self.fc2(x)
        return F.log_softmax(x, dim=1)

#self.fc1 = nn.Linear(len(new_dataset) * new_dataset[0].num_nodes * new_dataset[0].num_classes, 500)
#self.fc2 = nn.Linear(500, new_dataset[0].num_nodes * new_dataset[0].num_classes)



model = FC().to(device)
optimizer = torch.optim.Adam(model.parameters(), lr=0.01, weight_decay=5e-4)
criterion = nn.NLLLoss()

model.train()
for epoch in range(10):
  print(epoch)
  for i, l in trainloader:
    i_temp = i.to(device)                 # i added temps in this section 20:50 30.04.20
    l_temp = l.to(device)
    print(i_temp.size(), l_temp.size())
    optimizer.zero_grad()
    output = model(i_temp)
    loss = criterion(output, l_temp)
    print(output.size(), loss.size())
    loss.backward(retain_graph=True)
    optimizer.step()

test_data = []
for i in range(len(out_nodes)):
   test_data.append([out_nodes[i], labels_temp[i]])


from itertools import compress                                                       ############ filtering so only "test mask = true" nodes are put into testing dataloader
test_data = list(compress(test_data, (torch.cat([new_dataset[0].test_mask]*(len(new_dataset)-1))).tolist()   ))


testloader = torch.utils.data.DataLoader(test_data, shuffle=True, batch_size=100)


model.eval()
correct = 0

for i, l in testloader:
    i = i.to(device)
    l = l.to(device)
    pred = model(i).max(1)[1]
    correct = correct + pred.eq(l).sum().item()

print(str(correct / len(test_data)))



file = open("mgcnn_depth2.txt","w") 
 
file.write(str(correct / len(test_data))) 

file.close()



RuntimeError                              Traceback (most recent call last)
 in ()
15     loss = criterion(output, l_temp)
16     print(output.size(), loss.size())
—> 17     loss.backward(retain_graph=True)
18     optimizer.step()
19
1 frames
/usr/local/lib/python3.6/dist-packages/torch/autograd/init.py in backward(tensors, grad_tensors, retain_graph, create_graph, grad_variables)
98     Variable._execution_engine.run_backward(
99         tensors, grad_tensors, retain_graph, create_graph,
–> 100         allow_unreachable=True)  # allow_unreachable flag
101
102
RuntimeError: one of the variables needed for gradient computation has been modified by an inplace operation: [torch.cuda.FloatTensor [480, 7]] is at version 50; expected version 49 instead. Hint: enable anomaly detection to find the operation that failed to compute its gradient, with torch.autograd.set_detect_anomaly(True).