problem when running dvf on HPC

[leihuaxin]

I used conda to install dvf following the github steps. But when I submitted my script to HPC, there is a problem:

DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'. Using Theano backend. miniconda3/envs/dvf/lib/python3.6/site-packages/theano/configdefaults.py:560: UserWarning: DeprecationWarning: there is no c++ compiler.This is deprecated and with Theano 0.11 a c++ compiler will be mandatory warnings.warn("DeprecationWarning: there is no c++ compiler." WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string. Traceback (most recent call last): File "tools/DeepVirFinder/dvf.py", line 132, in modDict[contigLengthk] = load_model(os.path.join(modDir, modName)) File "miniconda3/envs/dvf/lib/python3.6/site-packages/keras/engine/saving.py", line 419, in load_model model = _deserialize_model(f, custom_objects, compile) File "miniconda3/envs/dvf/lib/python3.6/site-packages/keras/engine/saving.py", line 224, in _deserialize_model model_config = json.loads(model_config.decode('utf-8')) AttributeError: 'str' object has no attribute 'decode'

But when I run the same script on the local computer, no such problem. It's really strange. Anyone know how to address this problem? Thanks!

[nduan1]

@leihuaxin I got the same problem.

[dionisiosk]

@leihuaxin as mentioned in this issue, try downgrading h5py to 2.10.0