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maxhodak / keras-molecules

Autoencoder network for learning a continuous representation of molecular structures.
MIT License
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Error downloading the chembl22 and Zinc #65

Open liuxianghui opened 7 years ago

liuxianghui commented 7 years ago

[xianghui@login-c01 keras-molecules]$ python download_dataset.py --dataset chembl22 Bus error (core dumped)#################################################################################################################################### | ETA: 0:00:00 1.44 MB/s

Please kindly suggest.

pechersky commented 7 years ago

If I understand correctly, you might have an issue with how programs write to your HDD/SSD. What Python and TF/Theano are you using?

On Fri, May 19, 2017 at 10:18 AM, liuxianghui notifications@github.com wrote:

[xianghui@login-c01 keras-molecules]$ python download_dataset.py --dataset chembl22 Bus error (core dumped)####################### ############################################################ ################################################# | ETA: 0:00:00 1.44 MB/s

Please kindly suggest.

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liuxianghui commented 7 years ago

All the packages shall meet requirement. Problem happened at last step. I tried to download the file and import into python step by step. It failed at last step df.to_hdf(outfile, 'table', format = 'table', data_columns = True). Is the problem with hdf5?

[xianghui@login-c01 keras-molecules]$ python Python 2.7.13 (default, Feb 1 2017, 12:21:40) [xianghui@login-c01 keras-molecules]$ pip install -r requirements.txt Requirement already satisfied [xianghui@login-c01 keras-molecules]$ pip list appdirs (1.4.0) backports.shutil-get-terminal-size (1.0.0) bcbio-gff (0.6.4) biopython (1.68) bitarray (0.8.1) checkm-genome (1.0.7) concoct (0.4.1) cycler (0.10.0) Cython (0.25.2) decorator (4.0.11) DendroPy (4.2.0) desman (0.1.dev0) EMIRGE (0.61.0) enum34 (1.1.6) funcsigs (1.0.2) functools32 (3.2.3.post2) h5py (2.6.0) ipdb (0.10.2) ipython (5.3.0) ipython-genutils (0.1.0) Keras (1.1.1) matplotlib (2.0.0) mock (2.0.0) nose (1.3.0) numexpr (2.6.2) numpy (1.12.0) packaging (16.8) pandas (0.19.2) pathlib2 (2.2.1) pbr (3.0.1) pexpect (4.2.1) pickleshare (0.7.4) pip (9.0.1) progressbar (2.3) prompt-toolkit (1.0.13) protobuf (3.0.0) ptyprocess (0.5.1) pybedtools (0.7.9) pybloom (1.1) Pygments (2.2.0) pyparsing (2.1.10) pysam (0.10.0) python-dateutil (2.6.0) pytz (2016.10) PyYAML (3.12) scandir (1.5) scikit-learn (0.18) scipy (0.18.1) ScreamingBackpack (0.2.333) setuptools (34.1.0) simplegeneric (0.8.1) six (1.10.0) subprocess32 (3.2.7) tables (3.4.2) tensorflow (0.11.0rc1) Theano (0.9.0) traitlets (4.3.2) wcwidth (0.1.7) wheel (0.29.0)