Straightforward, functional installation on Apple Silicon // moving to PySide6 // rc2 #2022

jeylau · 2022-10-22T09:24:24Z

Transition from pyside2 to pyside6–only the latter is supported on M1/M2 chips (https://wiki.qt.io/Qt_for_Python)
Utilize Apple's tensorflow plugin (https://developer.apple.com/metal/tensorflow-plugin/). Note that I had to remove tensorflow from the required dependencies in the setup.py; we otherwise run into an error due to the mismatch between tensorflow and tensorflow-macos. I would argue that's also advantageous, as this allows for lighter installation e.g. for users training remotely, or lets users pip install the version matching their GPU device.

I paste below the simple steps to follow to get a working installation with python 3.9 and tensorflow 2.10:

We'll get the miniconda M1 bash installer, as explained in https://docs.conda.io/projects/conda/en/latest/user-guide/install/macos.html. In the Terminal, run the following commands:

wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-MacOSX-arm64.sh -O ~/miniconda.sh
bash ~/miniconda.sh -b -p $HOME/miniconda
source ~/miniconda/bin/activate
conda init zsh

Then, clone DeepLabCut (git clone https://github.com/DeepLabCut/DeepLabCut.git), and run conda env create -f conda-environments/DEEPLABCUT_M1.yaml. Next, activate the environment (conda activate DEEPLABCUT_M1), and launch DLC with pythonw -m deeplabcut.

MMathisLab · 2022-10-29T12:22:47Z

bringing in setup.py changes from PR #1970

MMathisLab

I found the miniconda install annoying, as it broke all my anaconda env, so that is a warning to users...

MMathisLab · 2022-10-29T12:54:34Z

EDIT: resolved!

@jeylau please address:

Testing on macbook intel chip (2020), v12.5.1:

git checkout m1m2

pip install -e '.[gui,tf]'

python -m deeplabcut

GUI launches, load demo openfield project,

Loading DLC 2.3rc1...
Starting GUI...
/Users/mwmathis/opt/anaconda3/envs/DEEPLABCUT/lib/python3.10/site-packages/qtpy/__init__.py:267: RuntimeWarning: Selected binding "pyside2" could not be found, using "pyside6"
  warnings.warn('Selected binding "{}" could not be found, '

edit config to extract 2 frames, go to extract, and it hangs on yes/no, which I cannot select ...

have to hard crash out of it :(.

Traceback (most recent call last):
  File "/Users/mwmathis/Documents/DeepLabCut/deeplabcut/gui/tabs/label_frames.py", line 31, in label_frames
    dialog.setFileMode(dialog.DirectoryOnly)
AttributeError: 'PySide6.QtWidgets.QFileDialog' object has no attribute 'DirectoryOnly'. Did you mean: 'directoryUrl'?

jeylau · 2022-10-31T14:51:43Z

I found the miniconda install annoying, as it broke all my anaconda env, so that is a warning to users...

Yeah I agree...
Perhaps we could get anaconda arm64 from the bottom of that page, I'm not sure whether that would avoid breaking conda though.

MMathisLab · 2022-11-02T16:48:43Z

Install now works great for me! Note, it does require miniconda3, as normal anaconda does fail ;) I had to check :)

but, when I run the python testscript.py it is missing tf_slim:

Loading DLC 2.3rc1...
DLC loaded in light mode; you cannot use any GUI (labeling, relabeling and standalone GUI)
  File "/Users/mwmathis/Documents/DeepLabCut/deeplabcut/pose_estimation_tensorflow/core/train.py", line 24, in <module>
    import tf_slim as slim
ModuleNotFoundError: No module named 'tf_slim'

so I need to run:
pip install tf_slim

then it runs 👍

MMathisLab · 2022-11-02T16:51:10Z

but it seems to not download the model correctly:

❯ python testscript.py
Loading DLC 2.3rc1...
Imported DLC!
On Windows/OSX tensorpack is not tested by default.
CREATING PROJECT
Created "/Users/mwmathis/Documents/DeepLabCut/examples/TEST-Alex-2022-11-02/videos"
Created "/Users/mwmathis/Documents/DeepLabCut/examples/TEST-Alex-2022-11-02/labeled-data"
Created "/Users/mwmathis/Documents/DeepLabCut/examples/TEST-Alex-2022-11-02/training-datasets"
Created "/Users/mwmathis/Documents/DeepLabCut/examples/TEST-Alex-2022-11-02/dlc-models"
Copying the videos
/Users/mwmathis/Documents/DeepLabCut/examples/TEST-Alex-2022-11-02/videos/reachingvideo1.avi
Generated "/Users/mwmathis/Documents/DeepLabCut/examples/TEST-Alex-2022-11-02/config.yaml"

A new project with name TEST-Alex-2022-11-02 is created at /Users/mwmathis/Documents/DeepLabCut/examples and a configurable file (config.yaml) is stored there. Change the parameters in this file to adapt to your project's needs.
 Once you have changed the configuration file, use the function 'extract_frames' to select frames for labeling.
. [OPTIONAL] Use the function 'add_new_videos' to add new videos to your project (at any stage).
EXTRACTING FRAMES
Config file read successfully.
Extracting frames based on kmeans ...
Kmeans-quantization based extracting of frames from 0.0  seconds to 8.53  seconds.
Extracting and downsampling... 256  frames from the video.
256it [00:01, 176.07it/s]
Kmeans clustering ... (this might take a while)
Frames were successfully extracted, for the videos listed in the config.yaml file.

You can now label the frames using the function 'label_frames' (Note, you should label frames extracted from diverse videos (and many videos; we do not recommend training on single videos!)).
CREATING-SOME LABELS FOR THE FRAMES
Plot labels...
Creating images with labels by Alex.
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 5/5 [00:00<00:00,  5.70it/s]
If all the labels are ok, then use the function 'create_training_dataset' to create the training dataset!
CREATING TRAININGSET
The training dataset is successfully created. Use the function 'train_network' to start training. Happy training!
CHANGING training parameters to end quickly!
TRAIN
Selecting single-animal trainer
Config:
{'all_joints': [[0], [1], [2], [3]],
 'all_joints_names': ['bodypart1', 'bodypart2', 'bodypart3', 'objectA'],
 'alpha_r': 0.02,
 'apply_prob': 0.5,
 'batch_size': 1,
 'contrast': {'clahe': True,
              'claheratio': 0.1,
              'histeq': True,
              'histeqratio': 0.1},
 'convolution': {'edge': False,
                 'emboss': {'alpha': [0.0, 1.0], 'strength': [0.5, 1.5]},
                 'embossratio': 0.1,
                 'sharpen': False,
                 'sharpenratio': 0.3},
 'crop_pad': 0,
 'cropratio': 0.4,
 'dataset': 'training-datasets/iteration-0/UnaugmentedDataSet_TESTNov2/TEST_Alex80shuffle1.mat',
 'dataset_type': 'default',
 'decay_steps': 30000,
 'deterministic': False,
 'display_iters': 2,
 'fg_fraction': 0.25,
 'global_scale': 0.8,
 'init_weights': '/Users/mwmathis/Documents/DeepLabCut/deeplabcut/pose_estimation_tensorflow/models/pretrained/resnet_v1_50.ckpt',
 'intermediate_supervision': False,
 'intermediate_supervision_layer': 12,
 'location_refinement': True,
 'locref_huber_loss': True,
 'locref_loss_weight': 0.05,
 'locref_stdev': 7.2801,
 'log_dir': 'log',
 'lr_init': 0.0005,
 'max_input_size': 1500,
 'mean_pixel': [123.68, 116.779, 103.939],
 'metadataset': 'training-datasets/iteration-0/UnaugmentedDataSet_TESTNov2/Documentation_data-TEST_80shuffle1.pickle',
 'min_input_size': 64,
 'mirror': False,
 'multi_stage': False,
 'multi_step': [[0.001, 5]],
 'net_type': 'resnet_50',
 'num_joints': 4,
 'optimizer': 'sgd',
 'pairwise_huber_loss': False,
 'pairwise_predict': False,
 'partaffinityfield_predict': False,
 'pos_dist_thresh': 17,
 'project_path': '/Users/mwmathis/Documents/DeepLabCut/examples/TEST-Alex-2022-11-02',
 'regularize': False,
 'rotation': 25,
 'rotratio': 0.4,
 'save_iters': 5,
 'scale_jitter_lo': 0.5,
 'scale_jitter_up': 1.25,
 'scoremap_dir': 'test',
 'shuffle': True,
 'snapshot_prefix': '/Users/mwmathis/Documents/DeepLabCut/examples/TEST-Alex-2022-11-02/dlc-models/iteration-0/TESTNov2-trainset80shuffle1/train/snapshot',
 'stride': 8.0,
 'weigh_negatives': False,
 'weigh_only_present_joints': False,
 'weigh_part_predictions': False,
 'weight_decay': 0.0001}
Batch Size is 1
/Users/mwmathis/miniconda/envs/DEEPLABCUT_M1/lib/python3.9/site-packages/tensorflow/python/keras/engine/base_layer_v1.py:1694: UserWarning: `layer.apply` is deprecated and will be removed in a future version. Please use `layer.__call__` method instead.
  warnings.warn('`layer.apply` is deprecated and '
Metal device set to: Apple M1 Pro

systemMemory: 32.00 GB
maxCacheSize: 10.67 GB

2022-11-02 17:49:29.132517: I tensorflow/core/common_runtime/pluggable_device/pluggable_device_factory.cc:306] Could not identify NUMA node of platform GPU ID 0, defaulting to 0. Your kernel may not have been built with NUMA support.
2022-11-02 17:49:29.132647: I tensorflow/core/common_runtime/pluggable_device/pluggable_device_factory.cc:272] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 0 MB memory) -> physical PluggableDevice (device: 0, name: METAL, pci bus id: <undefined>)
Loading ImageNet-pretrained resnet_50
2022-11-02 17:49:29.302387: I tensorflow/core/common_runtime/pluggable_device/pluggable_device_factory.cc:306] Could not identify NUMA node of platform GPU ID 0, defaulting to 0. Your kernel may not have been built with NUMA support.
2022-11-02 17:49:29.302418: I tensorflow/core/common_runtime/pluggable_device/pluggable_device_factory.cc:272] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 0 MB memory) -> physical PluggableDevice (device: 0, name: METAL, pci bus id: <undefined>)
/Users/mwmathis/Documents/DeepLabCut/deeplabcut/pose_estimation_tensorflow/core/train.py:225: UserWarning: Switching to Adam, as SGD crashes on Apple Silicon.
  warnings.warn("Switching to Adam, as SGD crashes on Apple Silicon.")
2022-11-02 17:49:29.701147: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:354] MLIR V1 optimization pass is not enabled
2022-11-02 17:49:29.726137: W tensorflow/core/platform/profile_utils/cpu_utils.cc:128] Failed to get CPU frequency: 0 Hz
2022-11-02 17:49:29.731388: I tensorflow/core/grappler/optimizers/custom_graph_optimizer_registry.cc:114] Plugin optimizer for device_type GPU is enabled.
2022-11-02 17:49:30.449692: I tensorflow/core/grappler/optimizers/custom_graph_optimizer_registry.cc:114] Plugin optimizer for device_type GPU is enabled.
2022-11-02 17:49:31.673542: I tensorflow/core/grappler/optimizers/custom_graph_optimizer_registry.cc:114] Plugin optimizer for device_type GPU is enabled.
Traceback (most recent call last):
  File "/Users/mwmathis/Documents/DeepLabCut/examples/testscript.py", line 164, in <module>
    deeplabcut.train_network(path_config_file)
  File "/Users/mwmathis/Documents/DeepLabCut/deeplabcut/pose_estimation_tensorflow/training.py", line 221, in train_network
    raise e
  File "/Users/mwmathis/Documents/DeepLabCut/deeplabcut/pose_estimation_tensorflow/training.py", line 210, in train_network
    train(
  File "/Users/mwmathis/Documents/DeepLabCut/deeplabcut/pose_estimation_tensorflow/core/train.py", line 242, in train
    restorer.restore(sess, cfg["init_weights"])
  File "/Users/mwmathis/miniconda/envs/DEEPLABCUT_M1/lib/python3.9/site-packages/tensorflow/python/training/saver.py", line 1407, in restore
    raise ValueError("The passed save_path is not a valid checkpoint: " +
ValueError: The passed save_path is not a valid checkpoint: /Users/mwmathis/Documents/DeepLabCut/deeplabcut/pose_estimation_tensorflow/models/pretrained/resnet_v1_50.ckpt

jeylau · 2022-11-02T18:26:38Z

@MMathisLab, was this run on a M1 or M2 chip? (Although I'm not sure it makes a big difference)

MMathisLab · 2022-11-04T13:43:17Z

alright, ALL solved! easy install, great work @jeylau :)

* Fix typo * Fix failing tests (#2021) * Fix pandas regression * Update requirements.txt * Update installation.md (#2020) * Update installation.md * Update installTips.md * Update installation.md * Add benchmark API (#1777) * Add benchmark API Co-authored-by: Jessy <[email protected]> * black formatting, added ref for datasets in benchmark * Update installation.md (#2029) Just a typo Co-authored-by: Jessy Lauer <[email protected]> Co-authored-by: Steffen Schneider <[email protected]> Co-authored-by: AlexEMG <[email protected]> Co-authored-by: Ale Santuz <[email protected]>

…o PySide6 // rc2 (DeepLabCut#2022) * Drop pyside2 for pyside6 * Functional Apple Silicon conda environment file

jeylau added 3 commits October 22, 2022 00:40

Drop pyside2 for pyside6

43fa94a

Functional Apple Silicon conda environment file

56e59b1

Fix pyside6 bugs

749a96a

jeylau added the Installation label Oct 22, 2022

jeylau requested a review from MMathisLab October 22, 2022 09:24

jeylau self-assigned this Oct 22, 2022

jeylau mentioned this pull request Oct 26, 2022

DLC installation errors on Mac M2 #2011

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2 tasks

Update setup.py

84dbab1

MMathisLab approved these changes Oct 29, 2022

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typo fix

a769a4d

MMathisLab self-requested a review October 29, 2022 12:40

MMathisLab changed the title ~~Straightforward, functional installation on Apple Silicon~~ Straightforward, functional installation on Apple Silicon // moving to PySide6 Oct 29, 2022

jeylau added 6 commits October 31, 2022 13:07

No feedback when extracting frames

3c94de5

Update setup.py

01ff18f

Exit pyside qthread gracefully

83bf78c

Revert git install in setup.py

f8de24e

Fix setFileMode

cd9ed6a

Fix file dialog crash

bea96c0

jeylau added 2 commits October 31, 2022 16:21

Fix qtpy RuntimeWarning upon GUI launch

5f04465

Use Adam rather than SGD on Apple Silicon

6898b99

jeylau marked this pull request as draft November 2, 2022 16:17

Delete testM1.sh

d3309ec

MMathisLab marked this pull request as ready for review November 4, 2022 13:10

Update installation.md

c6e7843

MMathisLab added 5 commits November 4, 2022 14:33

keep tf_slim

6ce6c2b

Update setup.py

380395d

rename to tf as added install...

2aa83f7

Update installation.md

ce76446

Update installation.md

777dae4

MMathisLab approved these changes Nov 4, 2022

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MMathisLab and others added 5 commits November 4, 2022 14:47

Update DEEPLABCUT.yaml

9ec6c75

rc2

0587d0c

Update version.py

44b6b86

Update setup.py

805a264

MMathisLab mentioned this pull request Nov 4, 2022

Mwm/apple m1 [WIP] #1970

Closed

MMathisLab changed the title ~~Straightforward, functional installation on Apple Silicon // moving to PySide6~~ Straightforward, functional installation on Apple Silicon // moving to PySide6 // rc2 Nov 4, 2022

jeylau added 2 commits November 4, 2022 17:12

Fix project loading dialog

63a915e

Fix config IO in ConfigEditor

3aca7c9

MMathisLab approved these changes Nov 4, 2022

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AlexEMG approved these changes Nov 4, 2022

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minor versioning

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AlexEMG merged commit 993a640 into master Nov 4, 2022

jeylau deleted the m1m2 branch November 8, 2022 08:44

n-poulsen mentioned this pull request May 5, 2023

removed deprecated install tips for mac m1/m2 #2234

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Straightforward, functional installation on Apple Silicon // moving to PySide6 // rc2 #2022

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