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DeepSEA test error #99

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arundurvasula opened this issue Jun 27, 2018 · 5 comments
Open

DeepSEA test error #99

arundurvasula opened this issue Jun 27, 2018 · 5 comments
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@arundurvasula
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Hi! I'm trying to run the DeepSEA predict example, but I am running into the following error:

(py36) [arun@login3 project-sriram]$ python
Python 3.6.5 | packaged by conda-forge | (default, Apr  6 2018, 13:39:56) 
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import kipoi
>>> model = kipoi.get_model('DeepSEA/predict')
Already up-to-date.
>>> pred = model.pipeline.predict_example()
  0%|                                                                                    | 0/1 [00:00<?, ?it/s]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/pipeline.py", line 84, in predict_example
    pred_list.append(self.model.predict_on_batch(batch['inputs']))
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/model.py", line 757, in predict_on_batch
    pred, _ = self.np_run_pred(x)
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/model.py", line 788, in np_run_pred
    pred = self.model(input)
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/torch/nn/modules/module.py", line 206, in __call__
    result = self.forward(*input, **kwargs)
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/torch/nn/modules/container.py", line 64, in forward
    input = module(input)
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/torch/nn/modules/module.py", line 206, in __call__
    result = self.forward(*input, **kwargs)
  File "model_files/deepsea_cpu.py", line 89, in forward
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/torch/autograd/variable.py", line 63, in __getattr__
    raise AttributeError(name)
AttributeError: shape

This is from running the example code here: http://kipoi.org/models/DeepSEA/predict/

I installed kipoi using pip, as well as the dependencies pybedtools, pyfaidx. I installed pytorch using conda.

Any ideas here?
@arundurvasula
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It could be a version issue. Here are the versions of packages I have installed:

(py36) [arun@login3 project-sriram]$ conda list
# packages in environment at /u/home/a/arun/anaconda3/envs/py36:
#
arrow                     0.12.1                    <pip>
asn1crypto                0.24.0                   py36_0    conda-forge
attrs                     18.1.0                    <pip>
bcftools                  1.7                           0    bioconda
bedtools                  2.27.1                        1    bioconda
binaryornot               0.4.4                     <pip>
bzip2                     1.0.6                         1    conda-forge
ca-certificates           2018.4.16                     0    conda-forge
certifi                   2018.4.16                py36_0    conda-forge
cffi                      1.11.5                   py36_0    conda-forge
chardet                   3.0.4                    py36_0    conda-forge
click                     6.7                       <pip>
colorlog                  3.1.4                     <pip>
cookiecutter              1.6.0                     <pip>
cudatoolkit               8.0                           3  
cudnn                     6.0.21                cuda8.0_0  
curl                      7.60.0                        0    conda-forge
enum34                    1.1.6                     <pip>
freetype                  2.8.1                         0    conda-forge
future                    0.16.0                    <pip>
git-lfs                   2.4.2                         0    conda-forge
h5py                      2.8.0                     <pip>
hdf5                      1.10.1                        2    conda-forge
htslib                    1.7                           0    bioconda
idna                      2.7                       <pip>
Jinja2                    2.10                      <pip>
jinja2-time               0.2.0                     <pip>
jpeg                      9b                            2    conda-forge
kipoi                     0.3.6                     <pip>
krb5                      1.14.6                        0    conda-forge
libffi                    3.2.1                         3    conda-forge
libgcc                    5.2.0                         0  
libgfortran               3.0.0                         1  
libpng                    1.6.34                        0    conda-forge
libssh2                   1.8.0                         2    conda-forge
libtiff                   4.0.9                         0    conda-forge
MarkupSafe                1.0                       <pip>
mkl                       2017.0.3                      0  
nccl                      1.3.4                 cuda8.0_1  
ncurses                   5.9                          10    conda-forge
numpy                     1.14.5                    <pip>
numpy                     1.13.1                   py36_0  
olefile                   0.45.1                   py36_0    conda-forge
openssl                   1.0.2o                        0    conda-forge
pandas                    0.23.1                    <pip>
pillow                    5.1.0                    py36_0    conda-forge
pip                       9.0.3                    py36_0    conda-forge
poyo                      0.4.1                     <pip>
pybedtools                0.7.10                    <pip>
pycparser                 2.18                     py36_0    conda-forge
pyfaidx                   0.5.4.1                   <pip>
pysam                     0.14.1                    <pip>
python                    3.6.5                         1    conda-forge
python-dateutil           2.7.3                     <pip>
pytorch                   0.1.12          py36cuda8.0cudnn6.0_1  
pytz                      2018.4                    <pip>
PyYAML                    4.1                       <pip>
readline                  7.0                           0    conda-forge
related                   0.6.3                     <pip>
requests                  2.19.1                    <pip>
setuptools                39.2.0                   py36_0    conda-forge
singledispatch            3.4.0.3                   <pip>
six                       1.11.0                    <pip>
six                       1.11.0                   py36_1    conda-forge
sqlite                    3.20.1                        2    conda-forge
tk                        8.6.7                         0    conda-forge
torchvision               0.1.8                    py36_0  
tqdm                      4.23.4                    <pip>
urllib3                   1.23                      <pip>
wheel                     0.31.0                   py36_0    conda-forge
whichcraft                0.4.1                     <pip>
xz                        5.2.3                         0    conda-forge
yaml                      0.1.7                         0    conda-forge
zlib                      1.2.11                        0    conda-forge

@Avsecz
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Avsecz commented Jun 27, 2018 •
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the pytorch version seems very old. I think we used >=0.3. Can you try create a new virtual environment using:

kipoi env create DeepSEA/predict
source activate kipoi-DeepSEA__predict

@arundurvasula
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Hmm weird. That command results in:

(py36) [arun@login3 project-sriram]$ kipoi env create DeepSEA/predict
INFO [kipoi.cli.env] Writing environment file: /tmp/kipoi/envfiles/2c223561
INFO [kipoi.cli.env] Loading model: DeepSEA/predict description
INFO [kipoi.remote] Update /u/home/a/arun/.kipoi/models/
Already up-to-date.
INFO [kipoi.cli.env] Inferred dataloader name: DeepSEA/predict from the model.
INFO [kipoi.cli.env] Environment name: kipoi-DeepSEA__predict
INFO [kipoi.cli.env] Output env file: /tmp/kipoi/envfiles/2c223561/kipoi-DeepSEA                                                __predict.yaml
INFO [kipoi.cli.env] Done writing the environment file!
INFO [kipoi.cli.env] Creating conda env from file: /tmp/kipoi/envfiles/2c223561/                                                kipoi-DeepSEA__predict.yaml
Using Anaconda API: https://api.anaconda.org
Fetching package metadata ...............
Solving package specifications: .


NoPackagesFoundError: Dependency missing in current linux-64 channels:
  - pytorch-cpu >=0.2.0 -> mkl >=2018


Traceback (most recent call last):
  File "/u/home/a/arun/anaconda3/envs/py36/bin/kipoi", line 11, in <module>
    sys.exit(main())
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/__m                                                ain__.py", line 74, in main
    command_fn(args.command, sys.argv[2:])
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/cli                                                /env.py", line 307, in cli_main
    command_fn(args.command, raw_args[1:])
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/cli                                                /env.py", line 231, in cli_create
    kipoi.conda.create_env_from_file(env_file)
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/con                                                da.py", line 78, in create_env_from_file
    return _call_conda(cmd_list, use_stdout=True)
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/con                                                da.py", line 162, in _call_conda
    return _call_command("conda", extra_args, use_stdout)
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/con                                                da.py", line 149, in _call_command
    raise subprocess.CalledProcessError(return_code, cmd_list)
subprocess.CalledProcessError: Command '['conda', 'env', 'create', '--file', '/t                                                mp/kipoi/envfiles/2c223561/kipoi-DeepSEA__predict.yaml']' returned non-zero exit                                                 status 1.

I will try and update pytorch myself and see if that helps.

@Avsecz
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Avsecz commented Jun 28, 2018

Let me know if updating the pytorch fixes the error

@krrome
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krrome commented Jun 28, 2018

If you keep having this problem, try updating / upgrading conda itself by conda update conda and then try to use kipoi env create DeepSEA/predict. also keep in mind that this command has to be run outside of environments. A similar issue with pytorch had been reported here: https://discuss.pytorch.org/t/issues-installing-pytorch-for-os-x-with-conda/11496/9
hope this helps

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@arundurvasula @Avsecz @krrome @haimasree