yuanjun commented 5 years ago

Hi, I've tried to run your code on my Mac, after I input the command the terminal just looks like this. Would you take a look, and see if this is normal?

_YJMacAir:source yuanjun$ sudo python3 run_experiments.py --num_windows 32 --seq_window_lengths 8 12 --smi_window_lengths 4 8 --batch_size 256 --num_epoch 100 --max_seq_len 1000 --max_smi_len 100 --dataset_path 'data/kiba/‘ --problem_type 1 --log_dir 'logs'

hkmztrk commented 5 years ago

Hi @yuanjun, first of all, I couldn't run the code on Windows environment, since I couldn't find a proper Windows machine, so yeah, it'd be safer if you run it on a Linux-based os.

So what exactly is the problem on Mac? I'm adding you the screenshot of my run here on OpenSuse. You should see some Tensorflow related messages and then, messages from the code stating the process.

screenshot1

You can also just add the command to a sh file and use "bash go.sh" which I actually included in source folder just now.

yuanjun commented 5 years ago

Hi @hkmztrk thanks for your prompt reply, I've followed your suggestion and run bash file again. seems the code is running for a while, and on one stage there is another new error info showed as below.

Are pydot and Graphviz necessary for this code?

================================================ Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pydot.py", line 1861, in create stderr=subprocess.PIPE, stdout=subprocess.PIPE) File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/subprocess.py", line 709, in init restore_signals, start_new_session) File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/subprocess.py", line 1344, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'dot': 'dot'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/keras/utils/vis_utils.py", line 26, in _check_pydot pydot.Dot.create(pydot.Dot()) File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pydot.py", line 1867, in create raise OSError(*args) FileNotFoundError: [Errno 2] "dot" not found in path.

During handling of the above exception, another exception occurred:

) and ensure that its executables are in the $PATH.

hkmztrk commented 5 years ago

Hi @yuanjun, i think this problem is also referenced here

Could you try commenting out plot_model in line 142 of "run_experiments.py" or try the other suggestions in the link?

yuanjun commented 5 years ago

hi @hkmztrk, i've successfully finish the calculation, thanks for your help~! really appreciate

hkmztrk commented 5 years ago

Hello @yuanjun, glad it worked! I'll be doing modifications so that it'll be a lot easier to use your own data.

@Running-z, I'll try to do the mentioned update in the following weeks.

hkmztrk / DeepDTA

I’ve tested on my mac #2