For the training submissions, I tried submitting a docker image created based on the example code "DREAM_DM_starter_code" provided. Specifically, I ran the 3 CLI instructions after pulling the code from GitHub:
docker build -t docker.synapse.org/syn123456/dm-trivial-model .
docker login -u -p docker.synapse.org
docker push docker.synapse.org/syn123456/dm-trivial-model
However, I am getting errors like:
STDOUT: +------------------------------------------------------+
STDOUT: | NVIDIA-SMI 352.99 Driver Version: 352.99 |
STDOUT: |-------------------------------+----------------------+----------------------+
STDOUT: | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
STDOUT: | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
STDOUT: |===============================+======================+======================|
STDOUT: | 0 Tesla K80 Off | 0000:87:00.0 Off | Off |
STDOUT: | N/A 31C P8 25W / 149W | 56MiB / 12287MiB | 0% Default |
STDOUT: +-------------------------------+----------------------+----------------------+
STDOUT: | 1 Tesla K80 Off | 0000:88:00.0 Off | Off |
STDOUT: | N/A 25C P8 29W / 149W | 56MiB / 12287MiB | 0% Default |
STDOUT: +-------------------------------+----------------------+----------------------+
STDOUT:
STDOUT: +-----------------------------------------------------------------------------+
STDOUT: | Processes: GPU Memory |
STDOUT: | GPU PID Type Process name Usage |
STDOUT: |=============================================================================|
STDOUT: | No running processes found |
STDOUT: +-----------------------------------------------------------------------------+
STDERR: Python 2.7.6
STDOUT: ---
STDOUT: Metadata-Version: 2.0
STDOUT: Name: tensorflow
STDOUT: Version: 0.9.0
STDOUT: Summary: TensorFlow helps the tensors flow
STDOUT: Home-page: http://tensorflow.org/
STDOUT: Author: Google Inc.
STDOUT: Author-email: opensource@google.com
STDOUT: Installer: pip
STDOUT: License: Apache 2.0
STDOUT: Location: /usr/local/lib/python2.7/dist-packages
STDOUT: Requires: numpy, six, wheel, protobuf
STDOUT: Classifiers:
STDOUT: Development Status :: 4 - Beta
STDOUT: Intended Audience :: Developers
STDOUT: Intended Audience :: Education
STDOUT: Intended Audience :: Science/Research
STDOUT: License :: OSI Approved :: Apache Software License
STDOUT: Programming Language :: Python :: 2.7
STDOUT: Topic :: Scientific/Engineering :: Mathematics
STDOUT: Topic :: Software Development :: Libraries :: Python Modules
STDOUT: Topic :: Software Development :: Libraries
STDOUT: Entry-points:
STDOUT: [console_scripts]
STDOUT: tensorboard = tensorflow.tensorboard.tensorboard:main
STDERR: /usr/local/lib/python2.7/dist-packages/sklearn/cross_validation.py:44: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
STDERR: "This module will be removed in 0.20.", DeprecationWarning)
STDERR: I tensorflow/stream_executor/dso_loader.cc:108] successfully opened CUDA library libcublas.so locally
STDERR: I tensorflow/stream_executor/dso_loader.cc:108] successfully opened CUDA library libcudnn.so locally
STDERR: I tensorflow/stream_executor/dso_loader.cc:108] successfully opened CUDA library libcufft.so locally
STDERR: I tensorflow/stream_executor/dso_loader.cc:108] successfully opened CUDA library libcuda.so locally
STDERR: I tensorflow/stream_executor/dso_loader.cc:108] successfully opened CUDA library libcurand.so locally
STDOUT: hdf5 not supported (please install/reinstall h5py)
STDOUT: Parsing the csv's.
STDERR: Traceback (most recent call last):
STDERR: File "DREAM_DM_starter_tf.py", line 700, in
STDERR: main(sys.argv)
STDERR: File "DREAM_DM_starter_tf.py", line 689, in main
STDERR: X_tr, X_te, Y_tr, Y_te = create_data_splits(path_csv_crosswalk, path_csv_metadata)
STDERR: File "DREAM_DM_starter_tf.py", line 89, in create_data_splits
STDERR: dict_tuple_to_cancer[(row[0].strip(), 'L')] = int(row[3])
STDERR: ValueError: invalid literal for int() with base 10: '.'
And more recently, the training submission cannot even be run:
Your Submission to the Digital Mammography challenge, syn7364784 (ID 7477301), was invalid. The message is:
The repository for image docker.synapse.org/syn7364762/dm-trivial-model@sha256:31dfd899c4de8e893dbf1073767f5f79a5195bcb115e3ab6892fd9af5c4f7500 does not exist or is not accessible by the submission processing infrastructure.
Please direct any questions to the challenge forum, https://www.synapse.org/#!Synapse:syn4224222/discussion .
Sincerely,
Challenge Administration
Am I doing something wrong or missing a step somewhere? Any help will be appreciated!
Created by Joshua Yun Keat Choo choo8 Yes. That's right. Yup, I realized that was the mistake I made. I have successfully made progress on the training model. However, I have one question. What do the values '.' in the fields of cancer L and cancer R mean? Does it mean that the data set is incomplete? Is this because you have not shared your repo with dmchallengeit?? Dear Thomas,
I previously changed the files slightly, mainly to train the images using VGG instead of GoogleNet. However, I just tried submitting another image with all files unchanged and got an error saying that my submission was invalid. Any suggestions?
Dear Joshua Yun Keat Choo (choo8):
Your Submission to the Digital Mammography challenge, syn7364784 (ID 7493923), was invalid. The message is:
The repository for image docker.synapse.org/syn7364762/dm-trivial-model@sha256:14206b01c67ef5b96ae9130e7242363f5e830e2686c950ca6b6be62d380bcf60 does not exist or is not accessible by the submission processing infrastructure.
Please direct any questions to the challenge forum, https://www.synapse.org/#!Synapse:syn4224222/discussion .
Sincerely,
Challenge Administration Dear Joshua,
Did you submit the example exactly as is or did you change something about it?
Best,
Thomas