Hi, I am trying to run the program on Ubuntu 16.04 with python 2.7. I have the rdkit package installed and the data downloaded. However, when I tried to run the main program I got the following error:

(venv) siyuan:nmp_qc$ python main.py 
Prepare files
Define model
python: /usr/include/boost/thread/pthread/mutex.hpp:111: boost::mutex::~mutex(): Assertion `!res' failed.
Aborted (core dumped)

The program crashed here: https://github.com/priba/nmp_qc/blob/177db7ea738a7a91f1262ce954f9c7a4a2b98849/main.py#L101-L103

What would possibly be the reason for that? Thanks in advance!

When I followed the installation that installed rdkit and all other requirements, and downloaded the data, run the "python main.py", I got the error below. Does there something error in the code?

Prepare files
Define model
Traceback (most recent call last):
  File "/home/ay27/repo/nmp_qc/main.py", line 320, in <module>
    main()
  File "/home/ay27/repo/nmp_qc/main.py", line 103, in main
    g_tuple, l = data_train[0]
  File "/home/ay27/repo/nmp_qc/datasets/qm9.py", line 47, in __getitem__
    h = self.vertex_transform(g)
  File "/home/ay27/repo/nmp_qc/datasets/utils.py", line 28, in qm9_nodes
    for n, d in g.nodes_iter(data=True):
AttributeError: 'Graph' object has no attribute 'nodes_iter'

In the original paper, the readout function is different between ggcn and the function used in the paper. But I noticed that you implement them as the same function. Have I missed something?

I have made some changes and try to fix #3 #4 . The improvement includes:

1. fix requirements
2. make compatible with pytorch 0.3.0

Finally, I got a descending loss and Error Ratio, but I'm not confident whether the fixes match the original logic. Someone may verify it.

Hello, thank you for your implemenation!

I've just tried to run default experiment with

python main.py --no-cuda --epochs 1

and run into the following problem

/opt/conda/lib/python3.6/importlib/_bootstrap.py:205: RuntimeWarning: compiletime version 3.5 of module 'tensorflow.python.framework.fast_tensor_util' does not match runtime version 3.6 return f(*args, **kwds)
Prepare files
Define model
        Statistics
        Create model
Optimizer
Logger
=> no best model found at './checkpoint/qm9/mpnn/model_best.pth'
Check cuda
Traceback (most recent call last):
  File "main.py", line 321, in <module>
    main()
  File "main.py", line 182, in main
    train(train_loader, model, criterion, optimizer, epoch, evaluation, logger)
  File "main.py", line 242, in train
    output = model(g, h, e)
  File "/opt/conda/lib/python3.6/site-packages/torch/nn/modules/module.py", line 319, in __call__
    result = self.forward(*input, **kwargs)
  File "/data/grishin/nmp_qc/models/MPNN.py", line 78, in forward
    m = self.m[0].forward(h[t], h_aux, e_aux)
  File "/data/grishin/nmp_qc/MessageFunction.py", line 43, in forward
    return self.m_function(h_v, h_w, e_vw, args)
  File "/data/grishin/nmp_qc/MessageFunction.py", line 175, in m_mpnn
    h_w_rows = h_w[..., None].expand(h_w.size(0), h_v.size(1), h_w.size(1)).contiguous()
RuntimeError: The expanded size of the tensor (25) must match the existing size (73) at non-singleton dimension 1

Am i doing something wrong? Thank you in advance.