RuntimeError in molopt/pretrain.py

[MinkyuHa]

Dear Wengong Jin

I'd like to ask your help about molopt during running pretrain.py
I have successfully done all of example in molopt with data/train.txt , data/vocab.txt, data/train.logP-SA.

However RuntimeError has occurred with my own training dataset , vocab generated with python ../jtnn/mol_tree.py < my_dataset.txt and my own logP property file.

It seems to be wrong dimension during node aggregation.
What's your opinion about this issue ?

Best Regards, Minkyu Ha

( environment is same with you. python 2.7, cuda 8.0, pytorch 0.3.1)

Model #Params: 4271K
Traceback (most recent call last):
File "pretrain.py", line 69, in
loss, kl_div, wacc, tacc, sacc, dacc, pacc = model(batch, beta=0)
File "/home/minkyuha/anaconda2/lib/python2.7/site-packages/torch/nn/modules/module.py", line 357, in call
result = self.forward(*input, **kwargs)
File "/home/minkyuha/new-jtnn/icml18-jtnn/jtnn/jtprop_vae.py", line 76, in forward
tree_mess, tree_vec, mol_vec = self.encode(mol_batch)
File "/home/minkyuha/new-jtnn/icml18-jtnn/jtnn/jtprop_vae.py", line 57, in encode
tree_mess,tree_vec = self.jtnn(root_batch)
File "/home/minkyuha/anaconda2/lib/python2.7/site-packages/torch/nn/modules/module.py", line 357, in call
result = self.forward(*input, **kwargs)
File "/home/minkyuha/new-jtnn/icml18-jtnn/jtnn/jtnn_enc.py", line 62, in forward
cur_h_nei = torch.cat(cur_h_nei, dim=0).view(-1,MAX_NB,self.hidden_size)
RuntimeError: invalid argument 2: size '[-1 x 8 x 420]' is invalid for input with 144900 elements at /opt/conda/conda-bld/pytorch_1523240155148/work/torch/lib/TH/THStorage.c:37

[XiuHuan-Yap]

Hi @MinkyuHa , try increasing MAX_NB global parameter in jtnn_dec.py and jtnn_enc.py.

I increased it from 8 to 32. Note that this will increase GPU memory usage.

[minstar]

I've got the same issue when I tried to start training with my own dataset.
However, increasing global parameter MAX_NB doesn't fit in my case.
Have anyone solve this issue in another way?