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Tensorflow support for DIGITS #1714

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merged 5 commits into from
Jul 17, 2017
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ethantang95
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@gheinrich @TimZaman @lukeyeager for review please

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@TimZaman TimZaman left a comment

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I think we need to be pragmatic with this review. I've already been through most of this several times. I think we need to be pragmatic here. I'm going to:
(1) again, go through all the docs as a user one final time.
(2) start install from 0 and see if everything works for me

"""
return self.SUPPORTS_PYTHON_LAYERS_FILE

def supports_timeline_traces(self):
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Ah yeah, timeline traces. Those were pretty fancy. Did you ever test this? You don't need to.

super(TestTensorflowCreatedWithGradientDataExtensionNoValSet, cls).setUpClass(val_image_count=0)


# class TestTensorflowCreatedWithImageProcessingExtensionMeanImage(BaseTestCreatedWithImageProcessingExtension,
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What's the story here? these didnt work?

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I never noticed this was commented out. I'll retest it

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Looks to be working fine

@TimZaman
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TimZaman commented Jul 9, 2017

I just verified the CI job here just ran only 14 tests for tensorflow, while it ran 437 for torch and 388 for caffe. I thought you fixed this? This needs fixing asap!
We can run the specific tensorflow tests now locally using:

export DIGITS_TEST_FRAMEWORK=tensorflow
./digits-test -v

Running them now again on my @desktop, looks good, thankfully. But CI really needs to be working though! I ran 247 tensorflow tests successfully. Phew!

@TimZaman
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TimZaman commented Jul 9, 2017

You also forgot to change to update the versions from 5.x to 6.0! I already noted this in a previous review.. See for example DIGITS/digits/version.py.

@@ -21,13 +21,16 @@ class ImageClassificationDatasetForm(ImageDatasetForm):
choices=[
('lmdb', 'LMDB'),
('hdf5', 'HDF5'),
('tfrecords', 'TFRecords'),
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Hey, come on, it seems you've adopted nothing from our previous reviews. This should be removed, so that we do have the back-end implementation for it, but people don't use it as it's currently not working as it should.

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You said previously to keep it in case some others want to extend it and get it working?

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I am not in favor of merging a feature which isn't working.

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@TimZaman TimZaman Jul 11, 2017

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The generator (of tfrecords) actually works fine. But I don't want to support it (for training). So block out the item so people can't click on it anymore.

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TimZaman commented Jul 9, 2017

MNIST HDF5 intestion works. MNIST LMDB ingestion works. Tensorflow MNIST-HDF5 training works. Tensorflow MNIST-LMDB training works.

@gheinrich
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Hi Ethan, not a huge deal but you have assumed authorship of all my changes. You can easily fixed this with a git commit --amend --author="...". If you do this, it's not quite necessary to name the author in the commit message as it's implicitly captured by Git.

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TimZaman commented Jul 10, 2017 via email

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Hi Ethan, can you rebase the tensorflow branch? A lot of changes are already on master, which makes it difficult to figure out what you changed there v.s. what you got from master.

@@ -29,7 +29,7 @@ def load_url_list():
if 'DIGITS_MODEL_STORE_URL' in os.environ:
url_list = os.environ['DIGITS_MODEL_STORE_URL']
else:
url_list = ""
url_list = "http://developer.download.nvidia.com/compute/machine-learning/modelstore/5.0"
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I thought you were planning to add the GAN model there. In which case you might want to move to a 6.0 version?

@@ -34,7 +34,7 @@ def test_tf_import(python_exe):

if not tf_enabled:
print('Tensorflow support disabled.')
# print('Failed importing Tensorflow with python executable "%s"\n%s' % (tf_python_exe, err))
# print('Failed importing Tensorflow with python executable "%s"\n%s' % (tf_python_exe, err))
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you could remove this altogether

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for now, I need it to debug the travis-CI problem. Will remove in the merge to master

@@ -156,12 +157,14 @@ def from_files(job, form):
"""
# labels
if form.textfile_use_local_files.data:
job.labels_file = form.textfile_local_labels_file.data.strip()
labels_file_from = form.textfile_local_labels_file.data.strip()
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This change is already on master. You might want to rebase the tensorflow branch into master first - then add your patches. This will keep commit history cleaner.

@@ -100,6 +100,14 @@ def __setstate__(self, state):
if not hasattr(self, 'compression') or self.compression is None:
self.compression = 'none'

if not hasattr(self, 'entries_error'):
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this change is also on master

namespace='/jobs',
room=self.job_id,
)
self.distribution[match.group(1)] = {
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this change is also on master

normalize=normalize,
allow_heatmap=bool(top != 'data'),
channel_order='BGR')
vis = utils.image.get_layer_vis_square(data * 255,
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this change is also on master.

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Hi @ethantang95 I see you've merged your branch and tensorflow. For easier-to-read reviews, rebasing is preferred, so that we can see exactly which patches you're adding to the target branch.

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@TimZaman yes I can double check GANs.

@ethantang95 ethantang95 force-pushed the pr-request-2 branch 6 times, most recently from fbcb7c6 to 45a51d9 Compare July 11, 2017 00:11
@lukeyeager
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Finally got the git history all cleaned up. It's backed up here. Reviewing now ...

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Pfew, this is a lot of code to review! Here's a start. I'll keep working through it tomorrow. NOTE: so far, I'm only looking at coding style and decisions. Haven't actually tested that anything runs.

README.md Outdated
@@ -4,6 +4,8 @@

DIGITS (the **D**eep Learning **G**PU **T**raining **S**ystem) is a webapp for training deep learning models.

The currently supported frameworks are: Caffe 1, Torch, and Tensorflow

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Remove the newline so this section is just one paragraph. Call it just "Caffe", not "Caffe 1". Add a period at the end.

README.md Outdated
@@ -44,4 +47,3 @@ Then, take a look at some of the other documentation at [docs/](docs/) and [exam
* Please let us know by [filing a new issue](https://github.com/NVIDIA/DIGITS/issues/new)
* Bonus points if you want to contribute by opening a [pull request](https://help.github.com/articles/using-pull-requests/)!
* You will need to send a signed copy of the [Contributor License Agreement](CLA) to [email protected] before your change can be accepted.

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Unnecessary

digits-lint Outdated
else
python2 -m flake8 .
python2 -m flake8 --exclude ./examples,./digits/standard-networks/tensorflow,./digits/jobs .
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Our examples and standard networks should typically be lint-free. Is there a good reason to exclude these? I'm OK with the digits/jobs exclusion.

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@ethantang95 ethantang95 Jul 11, 2017

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The reason I excluded those is because of linting complaining about not being to find reference to UserModel or Tower or model_property in those files

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Can we import them at the top of the file, then?

from . import option_list

VARNAME_ENV_TFPY = 'TENSORFLOW_PYTHON'
DEFAULT_PYTHON_EXE = 'python2' # @TODO(tzaman) - use the python executable that was used to launch digits?
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# DYLD_LIBRARY_PATH and LD_LIBRARY_PATH is sometimes stripped, and the cuda libraries might need it
if "DYLD_LIBRARY_PATH" not in os.environ:
if "CUDA_HOME" in os.environ:
os.environ["DYLD_LIBRARY_PATH"] = str(os.environ["CUDA_HOME"] + '/lib')
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Why are we fixing people's bad environment for them here? Shouldn't this be a standard TF configuration issue?

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it's a bit more complicated than that but this can be removed yeah

# if form.method.data == 'custom':
# for filename in field.data.strip().split(os.path.pathsep):
# if filename and not os.path.exists(filename):
# raise validators.ValidationError('File "%s" does not exist' % filename)
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Uh, why would we remove this check?

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Ethan, try to see if you can do a framework check here.

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nothing references this method even

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Just verified, you seem to be right. If it's invoked it's through flask?

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yeah looks like it

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@ethantang95 ethantang95 Jul 12, 2017

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So the problem is with tensorflow files where it has the .data-00000-of-00001 problem. Add a fix or leave it?

@unittest.skipIf(
not CaffeFramework().can_accumulate_gradients(),
'This version of Caffe cannot accumulate gradients')
class TestBatchAccumulationCaffe(BaseViewsTestWithDataset, test_utils.CaffeMixin):
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Why are we getting rid of this test?

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@ethantang95 lets see if this can be re added

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it passes. Add it back?

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More tests is better, so yeah.

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done

@@ -431,7 +435,7 @@ def infer_many(self, data, model_epoch=None):
"""
return None

def get_snapshot(self, epoch=-1):
def get_snapshot(self, epoch=-1, download=False):
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Why are we adding the download keyword here? It's not being used...

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the flag was added here even though it's not used in order to keep a consistent interface between Tensorflow and other frameworks.

break

# verify snapshot exists
pretrained_model = old_job.train_task().get_snapshot(epoch, download=True)
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Why this change? It's better to throw a BadRequest than the ValueError that gets thrown if the epoch is missing unless there's a reason not to.

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This is unclear even to me..

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According to git history, @gheinrich was the one that added the line. @gheinrich can you comment on this please?

break

# verify snapshot exists
pretrained_model = old_job.train_task().get_snapshot(epoch, download=True)
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As above

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This download flag comes from the fact that Tensorflow appends the .data-00000-of-00001 suffix to the files it creates. So if you do something like tf.save('toto') it is going to create a file named toto.data-00000-of-00001. If you want to download the snapshot you need to get the file toto.data-00000-of-00001. The complication comes from the fact that if you want to reload the snapshot in Tensorflow you can't do tf.load('toto.data-00000-of-00001') you need to do tf.load('toto')...

I could have implemented this change differently and referred to the actual filename in get_snapshot() and I would just have had to strip the data-00000-of-00001 when reloading the snapshot in TF. That would have isolated the change to the TF implementation. I guess I didn't think it through thoroughly at the time. Didn't really expect to ever release this though :-)

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Oh I see. Ok. Let's just leave it, then. Thanks for the explanation!

@lukeyeager
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I'd take another look at how Tensorflow is being tested on Travis:

  • Caffe: Ran 388 tests in 445.581s
  • Torch: Ran 457 tests in 512.154s
  • Tensorflow: Ran 14 tests in 1.752s

@ethantang95
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I am aware of that problem and it is being fixed. However the tensorflow tests do pass perfectly locally without a problem. I just think it's a problem with the scripts that is causing that

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There's really no way to properly review a PR this huge. I wish we would have been able to do this with more, smaller PRs. Oh well. Here's some feedback.

if not snapshot_filename:
raise ValueError('Invalid epoch')
if download:
snapshot_filename = snapshot_filename + ".data-00000-of-00001"
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Just for my own edification, what is this about?

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I think it's because of the weird way tensorflow name snapshots... @gheinrich can you comment on this?

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yes, annoyingly TensorFlow doesn't save snapshots using exactly the specified file name but happens this .data-00000-of-00001 (possibly to make sharding possible if needed).

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Why would we ever want download=False? This little change seems to have spidered out into a surprisingly large number of files.

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guess it is due to tensorflow's .data-00000-of-00001 problem. That is the time the variable is used.

@override
def task_arguments(self, resources, env):

args = [config_value('tensorflow')['executable'],
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Why not sys.executable as with other tasks?

@staticmethod
def preprocess_output_tensorflow(line):
"""
Takes line of output and parses it according to caffe's output format
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"caffe" -> "tensorflow"

@@ -0,0 +1,38 @@
from model import Tower
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Why are we checking in two standard networks for AlexNet? Looks like only alexnet.py is used:
https://github.com/lukeyeager/DIGITS/blob/backup/ethan/tf-pr-20170710/digits/frameworks/tensorflow_framework.py#L63
Could we scrap the non-slim versions of these standard networks and just check-in the ones which use the slim API?

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I think Tim wants to have both version to show that if someone want to do slim, they can... @TimZaman can you confirm?

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They are two different approaches. One could even make a model with keras. It's up to the user. I don't mind much. What do you think @lukeyeager ? We can remove the slim versions?

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I like the conciseness of the slim versions. Are they functionally equivalent?

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yeah equivalent. one could even use keras. Tensorflow vanilla is really not concise, which is why keras is so popular :D

@@ -0,0 +1,20 @@
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Do these TF static files come directly from the TF repo? If so, we need copyright info on them. I believe this is the appropriate incantation:

Copyright (c) 2017, NVIDIA CORPORATION.  All rights reserved.
Copyright 2017 The TensorFlow Authors.  All rights reserved.

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Also, if there's a non-minimized version of this file, that would be preferable (even though the total LOC for this PR would skyrocket even higher!).

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@ethantang95 can you add those copyright lines? Just leave the minification. I did include the copyright files in digits/static/tb/... afaik.

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done

@@ -42,4 +42,3 @@ LOG_FILE="$LOCAL_DIR/torch-install.log"
# mark cache
WEEK=$(date +%Y-%W)
echo "$WEEK" >"${INSTALL_DIR}/cache-version.txt"

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Unnecessary

@@ -28,3 +28,5 @@ cd "$ROOT_DIR/packaging/deb/dist/"
cd ./*xenial/
debsign -k 97A4B458 ./*source.changes
dput -U "ppa:nvidia-digits/${PPA_NAME}/ubuntu/xenial" ./*source.changes

echo "ppa-upload.sh finished"
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Unnecessary

@@ -15,3 +15,5 @@ username = luke.yeager
password = ${PYPI_PASSWORD}
EOF
twine upload -r pypi dist/*

echo "pypi-upload.sh finished"
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Unnecessary

setup.cfg Outdated

[pep8]
max-line-length = 120
exclude = venv

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Unnecessary

setup.cfg Outdated
@@ -1,7 +1,8 @@
[flake8]
max-line-length = 120
exclude = venv
exclude = venv,standard-networks
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Can we check the standard networks, too?

@NVIDIA NVIDIA deleted a comment from TimZaman Jul 13, 2017
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@ethantang95 I merged #1723. Try rebasing this branch on origin/master and see if TravisCI works now.

result.txt Outdated
@@ -0,0 +1,470 @@
Level 1:tensorflow:Registering FakeQuantWithMinMaxArgs (<function _FakeQuantWithMinMaxArgsGradient at 0x7f177ce7e140>) in gradient.
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Don't add this file.

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Whoops, forgot to delete that after running the tests

@ethantang95 ethantang95 changed the base branch from tensorflow to master July 13, 2017 22:43
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TODOs:

  • Remove some unnecessary whitespace changes
  • Replace unslim standard networks with slim ones (and make sure they still work)
  • Get rid of the ridiculously verbose tensorflow logging messages in the tests (maybe start here?)

Then I'll approve, then you can squash all your changes (but not Tim's or Greg's), then we can merge.

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Suppressing the level 1 logs output by tensorflow is impossible as per tensorflow/tensorflow#8340

Also we want to have the debug logs which I think @TimZaman uses it to parse and get the learning status

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@ethantang95 one thing you might want to check: if you can find some info on .data-00000-of-00001 and whether TF will create more shards per snapshot if the model is huge. In which case the logic in the code might have to be revisited.

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So I looked around and asked a few others that uses tensorflow, none of them have seen it actually shard yet even with 16gb files... so I guess it's safe to say that it would be really hard to get sharding to actually happen and I guess we can deal with it when someone actually hit that case.

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TimZaman commented Jul 14, 2017 via email

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TimZaman commented Jul 17, 2017 via email

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Want to merge? Note this isnt to master yet.

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Looks like TravisCI is failing for reasons not related to this PR: pypa/setuptools#1086

TimZaman and others added 4 commits July 17, 2017 12:54
Added some initial tf tools

Implemented UI

Fixes for tensorflow 0.10

Removed tf-slim as its not part of the 0.10 master

Added the lmdb reader with a tf.cond that needs replacement

Implemented train and val seperation with a templating

Fixed issue with dequeueing both runners by pulling both graphs

Implemented training and validation rythm

Added support for both png and jpg and added 16 bit support

Implemented mean subtraction - but needs rework to load as constant

Added an optimized implementation of mean subtraction

Further optimized the mean loading by using a shared constant

Wrapped the data loader in a factory to easily support more data types

Implemented cropping

Implemented floating point support. Implemented seperate LMDB database. Implemented regression support. Added some brief nosetests. Need to invoke accuracy only on classification though.

Implemented variable restoration. Needs thorough testing

Implemented inferencing, not entirely polished

Moved some code into functions, started on modularization a bit

Implemented digits custom helper functions

Implemented custom printing ops

Implemented autoencoder

total rewrite of summaries

Implemented output to console from scalar summaries

Fixes for summary outputs: only simple scalar values are parsed to console

Implemented binary segmentation and necessary fixes

Some updates on binary seg

Implemented all possible optimizers and started work on learning rate shaper

Started work on the lr policies

Fixes for learning_rates, implemented optimizers, tested variable summary output to UI

Implemented and tested all learning rates and optimizers

Introduces new model definition and improvements in loss handling and graph layout

Major refactoring of main code. Implemented new model description. Implemented and tested inferencing. Implemented and tested weight/snapshot loading.

All-round minor updates and fixes

Fixes in summary cumulator and implemented an RNN model

Fixes for mean subtraction in tf and tf-ui, implemented data order selection in image-view extension

Implemented support for mean file of format: png, jpg, binaryproto - the latter being the fault that DIGITS will provide.

Added support for runtime statistics and some allround fixes

Added static tensorboard style network visualization for tensorflow. Added output of traces (no vis yet). Added a loader while waiting for network vis. Minor syntax cleanups.

Implemented alexnet standard network

Pulled in updates for travis build and added tensorflow install

Added two more files for Mr Travis

Implemented tensorflow configuration

Added tf config to doc

Fixes for ubuntu deployment of tf.

Moved tf tools

Fixes for tf ubuntu

Fixes for tf ubuntu

Some fixes and updates for TF in Travis

Fix in network viz test

Implemented default sinlge-gpu support and some nosetests

Fixes for inference

Added siamese network, bugfixes, minor features, some utility tf functions

Added siamese network and example png

Better error-ui format for network viz

Added an alternative simpler siamese network that doesnt need a seperate db, minor error update

Preliminary version of hdf5 implemented

Implemented fine-tuning by renaming variables

Implemented visualisation of variables and the activations of the Ops they belong to.

Fix in inf vis naming

Fixes in visualualisation shapes and naming

Implemented softmax upon classification

Implemented all nosetests for tf classification, and many allround bugfixes

Implemented generic nosetests - some need work

Fix for travis to find python exe

Implemented a better file format deducer, and implemented a bare minimal TFRecord-reader

Added top_n accuracy shortcut

Implemented on-line data augmentation for TF, 5 types. Some minor bugfixes. Need to do something with image whitening though during validation and inf..

Added tensorflow data augmentation test

Minor fixes and improvements from linter

Implemented minimal and bare multigpu and fixes to get it running for greg

Preliminary version of tfrecord writer for classification

Some changes to optimize dataloading for tfr

More fixes for tfrecrods

Fix generic data loading

Minor breaking changes but updates in namescoping

Implemented new model structure. Improvements to multi-gpu handling. Updates to namespaces. Implemented accounting for regularization. Many allround updates

Implemented proper visualisation for gpu devices

Minor updates and converted alexnet and vgg16 to new format

Fix in tfrecord shape

WIP on timeline traces

Finalized support for tensorflow timeline traces

Fixed alexnet for tf

Fix merge errors

Minify tf-graph-basic.build.js
bAbI data plug-in

Add utils

Add inference form to bAbI dataset

Allow inference without answer

Allow unknown words in BaBI data plug-in

Fix bAbI plugin Lint errors

Tensorflow integration updates

Use TFRecords for TF inference

TF: Don't rescale inputs

Fix some TF classification tests

Remove unnecessary print

Fix TF imports when uninstalled

Fix mean image scale

Fix generic model tests

Fix Torch single image inference

Fix inference

TMP TF Lint

Revert changes in digits-lint script

Lint: ignore tensorflow standard examples

More Lint fixes

Add gradient hook

Add memn2n model

Update memn2n with gradient hooks

GAN example

Make batch size variable

Training/inference paths

Small update to TF 0.12

Snapshot names, float inference, restore all vars

Do not restore global_step or optimizer variables

Add TB link

Update GAN network

Dynamically select inference form

TF inference: convert images to float

Update GAN z-gen network

Small Update model view layout

Add GAN plug-ins

Update GAN plug-in to create CelebA dataset

Add ability to show input in ImageOutput extension

Add all data to raw data view extension

Add model for CelebA dataset

Update GAN data plug-in

Update all losses in one session

Remove conversion to .png in GAN data plug-in

TF Slim Lenet example

Divide input by 255

Update GAN data plug-in

Fix TF model snapshot

Reduce scheduler delays to speed up inference

Update GAN plugins

Fix TF tests

Add API to LmdbReader (used by gan_features.py)

Save animated gif

Add GAN walk-through

Update GAN walkthrough with embeddings video

Fix GAN view for list encoding

Add animation task to GAN plugins

Add view task to see image attributes

Add comments to GAN models

Update README

Fix GAN features script

GAN app

Fix DIGITS inference

Adjust GAN window size automatically

Add attributes to GAN app

Move gandisplay.py

Remove wxpython 3.0 selection

Fix call to model

Adding disclaimer
some small tidying

changes WRT to pull request

lint fixes

re-enabled disabled tests

changes WRT pull request comments

Travis bug fixes

Testing a patch

fixed travis bugs

lint
changes wrt to PR comments

Updated version number

updated version number to 6.0

changed version number to proper format

updated manifest to fix bug 200328271

fixed typo in build tensorflow doc for bug 200328296

changes WRT PR comments

changes WRT PR comments

accidentally added test result file

removed dependency to the tensorflow environment variable

changed from 'python' to using sys.executable

changing version back to 5.1-dev for travis

whitespace fixes

white space changes

replaced the tensorflow networks with slim models

Removed tests referencing lenet slim
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Thanks @TimZaman for the (massive) initial work, @gheinrich for building an interesting workflow on top of Tim's work, and @ethantang95 for pulling it all together and bringing us to the finish line!

@lukeyeager lukeyeager merged commit 016d7c0 into NVIDIA:master Jul 17, 2017
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TimZaman commented Jul 17, 2017 via email

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