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image segmentation for SVD graphene SEM images

License: MIT License

Python 26.80% Shell 8.70% Jupyter Notebook 64.50%

unet graphene image-segmentation cvd machine-learning tensorflow2 keras

unet-sem's Introduction

unet-sem

image segmentation for CVD graphene SEM images
Based on: https://github.com/zhixuhao/unet

Usage

main.py [-h] [--crop] [--shuffle_data] [--augment_after AUGMENT_AFTER]
           [--augment] [--max_crop] [--crop_size CROP_SIZE]
           [--input_size INPUT_SIZE] [--ngpu NGPU] [--nepochs NEPOCHS]
           [--batch_size BATCH_SIZE] [--split SPLIT] [--lr LR]
           [--input_dir INPUT_DIR]

optional arguments:
  -h, --help            show this help message and exit
  --crop                Constructs batch using random crops.
  --shuffle_data        Shuffles data paths to switch what is in test/train.
  --augment_after AUGMENT_AFTER
                        Start augmenting data ater specified epoch,
                        inclusively.
  --augment             Constructs batch using augmentations.
  --max_crop            Crops using the maximum square size for each image.
                        Crop size is ignored.
  --crop_size CROP_SIZE
                        Size of cropped sample.
  --input_size INPUT_SIZE
                        Model input size. Cropped images will be rescaled to
                        this size.
  --ngpu NGPU           Number of GPUs.
  --nepochs NEPOCHS     Number of epochs.
  --batch_size BATCH_SIZE
                        Number of samples per batch.
  --split SPLIT         If float, fraction of data to use for validation. If
                        integer, number of folds. If zero, train on all data
                        (used for final model.
  --lr LR               Learning rate.
  --input_dir INPUT_DIR
                        Directory to pull images from

Image Data

Images used to train the neural network are available in the data directory:

All directories that end in _Bad contain low fidelity masks and their corresponding images
All directories that end in _Good contain high fidelity masks and their corresponding images
The Old_data directory also contains high fidelity masks and their corresponding images

Use the fileproc.py script to combine all the images into a single directory and rename them correctly

Domain Size Analysis

domain_size_analysis.ipynb is the jupyter notebook that contains the code to our method of domain size analysis. It has the following sections:

Import packages: imports all relevant packages
Define all analysis functions: All the required classes and functions for domain size analysis are defined here
Analysis of randomly generated data: A data generator is created to test the technqiue on artificially generated data
Follow process for one simulated image: Run through the analysis process step by step for only one image (might be broken)
Analysis of true data: Analysis of true data. User must select a directory that contains all the segmented masks
Experimental section: Code blocks used to trace out code in case of problems

unet-sem's People

Contributors

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alexshevelkin

unet-sem's Issues

bug in file save_output

epoch: 0 (35/36), ['loss', 'acc']: [0.6927258, 0.70576286]
Traceback (most recent call last):
  File "/home/dadams2/.conda/envs/unet/lib/python3.5/site-packages/PIL/BmpImagePlugin.py", line 231, in _save
    rawmode, bits, colors = SAVE[im.mode]
KeyError: 'F'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "main.py", line 33, in <module>
    run.train()
  File "/local/6081513/unet-sem/master_adb1e74_07-24-2019-14:00:15/unet-sem-6081513/model.py", line 133, in train
    save_output(out_imgs[0,...],out_masks[0,...],prediction[0,...],index=i,epoch=epoch)
  File "/local/6081513/unet-sem/master_adb1e74_07-24-2019-14:00:15/unet-sem-6081513/utils.py", line 12, in save_output
    print_img.save(os.path.join(directory,'%d_epoch'%epoch,'%d_input_image.bmp'%index))
  File "/home/dadams2/.conda/envs/unet/lib/python3.5/site-packages/PIL/Image.py", line 1950, in save
    save_handler(self, fp, filename)
  File "/home/dadams2/.conda/envs/unet/lib/python3.5/site-packages/PIL/BmpImagePlugin.py", line 233, in _save
    raise IOError("cannot write mode %s as BMP" % im.mode)
OSError: cannot write mode F as BMP

crash on ngpu > 1

Traceback (most recent call last):
  File "main.py", line 31, in <module>
    run = TrainUNET(**kwargs)
  File "/home/dadams2/unet-sem/model.py", line 94, in __init__
    if self.ngpu > 1:
TypeError: unorderable types: list() > int()

out of memory

Here's the trace using 4 K80 GPUs:

(unet) [dadams2@gpu008 unet-sem]$ python main.py 
Using TensorFlow backend.
{'ngpu': 1, 'crop_size': (256, 256), 'lr': 0.0001, 'nepochs': 5, 'crop': True, 'input_size': (256, 256), 'split': 0.1, 'batch_size': 32, 'max_crop': False, 'augment': True}
/home/dadams2/unet-sem/model.py:58: UserWarning: Update your `Model` call to the Keras 2 API: `Model(outputs=Tensor("co..., inputs=Tensor("in...)`
  model = Model(input = inputs, output = conv10)
2019-07-21 13:05:37.177869: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA
2019-07-21 13:05:37.413692: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1405] Found device 0 with properties: 
name: Tesla K80 major: 3 minor: 7 memoryClockRate(GHz): 0.8235
pciBusID: 0000:83:00.0
totalMemory: 11.17GiB freeMemory: 11.10GiB
2019-07-21 13:05:37.585531: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1405] Found device 1 with properties: 
name: Tesla K80 major: 3 minor: 7 memoryClockRate(GHz): 0.8235
pciBusID: 0000:84:00.0
totalMemory: 11.17GiB freeMemory: 11.10GiB
2019-07-21 13:05:37.585922: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1484] Adding visible gpu devices: 0, 1
2019-07-21 13:05:39.949113: I tensorflow/core/common_runtime/gpu/gpu_device.cc:965] Device interconnect StreamExecutor with strength 1 edge matrix:
2019-07-21 13:05:39.949181: I tensorflow/core/common_runtime/gpu/gpu_device.cc:971]      0 1 
2019-07-21 13:05:39.949195: I tensorflow/core/common_runtime/gpu/gpu_device.cc:984] 0:   N Y 
2019-07-21 13:05:39.949204: I tensorflow/core/common_runtime/gpu/gpu_device.cc:984] 1:   Y N 
2019-07-21 13:05:39.950090: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1097] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 10759 MB memory) -> physical GPU (device: 0, name: Tesla K80, pci bus id: 0000:83:00.0, compute capability: 3.7)
2019-07-21 13:05:40.128999: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1097] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:1 with 10759 MB memory) -> physical GPU (device: 1, name: Tesla K80, pci bus id: 0000:84:00.0, compute capability: 3.7)
2019-07-21 13:05:52.569072: W tensorflow/core/common_runtime/bfc_allocator.cc:219] Allocator (GPU_0_bfc) ran out of memory trying to allocate 4.00GiB. The caller indicates that this is not a failure, but may mean that there could be performance gains if more memory were available.
2019-07-21 13:05:53.564076: W tensorflow/core/common_runtime/bfc_allocator.cc:219] Allocator (GPU_0_bfc) ran out of memory trying to allocate 3.38GiB. The caller indicates that this is not a failure, but may mean that there could be performance gains if more memory were available.
2019-07-21 13:06:03.565416: W tensorflow/core/common_runtime/bfc_allocator.cc:275] Allocator (GPU_0_bfc) ran out of memory trying to allocate 512.00MiB.  Current allocation summary follows.
2019-07-21 13:06:03.565501: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (256): 	Total Chunks: 136, Chunks in use: 135. 34.0KiB allocated for chunks. 33.8KiB in use in bin. 7.1KiB client-requested in use in bin.
2019-07-21 13:06:03.565605: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (512): 	Total Chunks: 26, Chunks in use: 26. 13.0KiB allocated for chunks. 13.0KiB in use in bin. 13.0KiB client-requested in use in bin.
2019-07-21 13:06:03.565648: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (1024): 	Total Chunks: 27, Chunks in use: 27. 27.2KiB allocated for chunks. 27.2KiB in use in bin. 27.0KiB client-requested in use in bin.
2019-07-21 13:06:03.565674: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (2048): 	Total Chunks: 32, Chunks in use: 32. 65.5KiB allocated for chunks. 65.5KiB in use in bin. 65.5KiB client-requested in use in bin.
2019-07-21 13:06:03.565712: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (4096): 	Total Chunks: 17, Chunks in use: 17. 71.0KiB allocated for chunks. 71.0KiB in use in bin. 71.0KiB client-requested in use in bin.
2019-07-21 13:06:03.565736: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (8192): 	Total Chunks: 0, Chunks in use: 0. 0B allocated for chunks. 0B in use in bin. 0B client-requested in use in bin.
2019-07-21 13:06:03.565773: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (16384): 	Total Chunks: 0, Chunks in use: 0. 0B allocated for chunks. 0B in use in bin. 0B client-requested in use in bin.
2019-07-21 13:06:03.565810: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (32768): 	Total Chunks: 0, Chunks in use: 0. 0B allocated for chunks. 0B in use in bin. 0B client-requested in use in bin.
2019-07-21 13:06:03.565847: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (65536): 	Total Chunks: 0, Chunks in use: 0. 0B allocated for chunks. 0B in use in bin. 0B client-requested in use in bin.
2019-07-21 13:06:03.565871: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (131072): 	Total Chunks: 18, Chunks in use: 18. 2.44MiB allocated for chunks. 2.44MiB in use in bin. 2.44MiB client-requested in use in bin.
2019-07-21 13:06:03.565902: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (262144): 	Total Chunks: 12, Chunks in use: 12. 3.38MiB allocated for chunks. 3.38MiB in use in bin. 3.38MiB client-requested in use in bin.
2019-07-21 13:06:03.565933: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (524288): 	Total Chunks: 17, Chunks in use: 17. 9.19MiB allocated for chunks. 9.19MiB in use in bin. 9.19MiB client-requested in use in bin.
2019-07-21 13:06:03.565965: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (1048576): 	Total Chunks: 12, Chunks in use: 12. 13.50MiB allocated for chunks. 13.50MiB in use in bin. 13.50MiB client-requested in use in bin.
2019-07-21 13:06:03.565997: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (2097152): 	Total Chunks: 18, Chunks in use: 17. 39.00MiB allocated for chunks. 36.75MiB in use in bin. 36.75MiB client-requested in use in bin.
2019-07-21 13:06:03.566345: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (4194304): 	Total Chunks: 13, Chunks in use: 12. 58.50MiB allocated for chunks. 54.00MiB in use in bin. 54.00MiB client-requested in use in bin.
2019-07-21 13:06:03.566382: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (8388608): 	Total Chunks: 20, Chunks in use: 19. 172.00MiB allocated for chunks. 163.00MiB in use in bin. 163.00MiB client-requested in use in bin.
2019-07-21 13:06:03.566409: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (16777216): 	Total Chunks: 13, Chunks in use: 13. 232.00MiB allocated for chunks. 232.00MiB in use in bin. 232.00MiB client-requested in use in bin.
2019-07-21 13:06:03.566444: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (33554432): 	Total Chunks: 13, Chunks in use: 11. 462.00MiB allocated for chunks. 394.00MiB in use in bin. 376.00MiB client-requested in use in bin.
2019-07-21 13:06:03.566477: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (67108864): 	Total Chunks: 10, Chunks in use: 9. 673.12MiB allocated for chunks. 609.12MiB in use in bin. 576.00MiB client-requested in use in bin.
2019-07-21 13:06:03.566502: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (134217728): 	Total Chunks: 10, Chunks in use: 8. 1.38GiB allocated for chunks. 1.06GiB in use in bin. 1.00GiB client-requested in use in bin.
2019-07-21 13:06:03.566538: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (268435456): 	Total Chunks: 17, Chunks in use: 16. 7.50GiB allocated for chunks. 7.25GiB in use in bin. 7.25GiB client-requested in use in bin.
2019-07-21 13:06:03.566572: I tensorflow/core/common_runtime/bfc_allocator.cc:646] Bin for 512.00MiB was 256.00MiB, Chunk State: 
2019-07-21 13:06:03.566608: I tensorflow/core/common_runtime/bfc_allocator.cc:652]   Size: 256.00MiB | Requested Size: 256.00MiB | in_use: 0, prev:   Size: 128.00MiB | Requested Size: 128.00MiB | in_use: 1, next:   Size: 256.00MiB | Requested Size: 256.00MiB | in_use: 1
2019-07-21 13:06:03.566638: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2307d80000 of size 1280
2019-07-21 13:06:03.566671: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2307d80500 of size 256
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2019-07-21 13:06:03.573680: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Free  at 0x23dbdb5400 of size 67108864
2019-07-21 13:06:03.573696: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23dfdb5400 of size 67108864
2019-07-21 13:06:03.573712: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23e3db5400 of size 134217728
2019-07-21 13:06:03.573729: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23ebdb5400 of size 134217728
2019-07-21 13:06:03.573745: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23f3db5400 of size 67108864
2019-07-21 13:06:03.573762: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23f7db5400 of size 67108864
2019-07-21 13:06:03.573778: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Free  at 0x23fbdb5400 of size 134217728
2019-07-21 13:06:03.573800: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2403db5400 of size 134217728
2019-07-21 13:06:03.573817: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x240bdb5400 of size 268435456
2019-07-21 13:06:03.573840: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x241bdb5400 of size 268435456
2019-07-21 13:06:03.573856: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x242bdb5400 of size 134217728
2019-07-21 13:06:03.573872: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2433db5400 of size 134217728
2019-07-21 13:06:03.573889: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Free  at 0x243bdb5400 of size 268435456
2019-07-21 13:06:03.573909: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x244bdb5400 of size 268435456
2019-07-21 13:06:03.573926: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x245bdb5400 of size 536870912
2019-07-21 13:06:03.573942: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x247bdb5400 of size 536870912
2019-07-21 13:06:03.573964: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x249bdb5400 of size 268435456
2019-07-21 13:06:03.573985: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x24abdb5400 of size 268435456
2019-07-21 13:06:03.574002: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x24bbdb5400 of size 536870912
2019-07-21 13:06:03.574028: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x24dbdb5400 of size 536870912
2019-07-21 13:06:03.574053: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x24fbdb5400 of size 1073741824
2019-07-21 13:06:03.574070: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x253bdb5400 of size 1073741824
2019-07-21 13:06:03.574087: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x257bdb5400 of size 536870912
2019-07-21 13:06:03.574409: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Free  at 0x259bdb5400 of size 208746496
2019-07-21 13:06:03.574444: I tensorflow/core/common_runtime/bfc_allocator.cc:671]      Summary of in-use Chunks by size: 
2019-07-21 13:06:03.574466: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 135 Chunks of size 256 totalling 33.8KiB
2019-07-21 13:06:03.574486: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 26 Chunks of size 512 totalling 13.0KiB
2019-07-21 13:06:03.574506: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 26 Chunks of size 1024 totalling 26.0KiB
2019-07-21 13:06:03.574529: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 1 Chunks of size 1280 totalling 1.2KiB
2019-07-21 13:06:03.574552: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 26 Chunks of size 2048 totalling 52.0KiB
2019-07-21 13:06:03.574576: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 6 Chunks of size 2304 totalling 13.5KiB
2019-07-21 13:06:03.574594: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 11 Chunks of size 4096 totalling 44.0KiB
2019-07-21 13:06:03.574612: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 6 Chunks of size 4608 totalling 27.0KiB
2019-07-21 13:06:03.574631: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 6 Chunks of size 131072 totalling 768.0KiB
2019-07-21 13:06:03.574655: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 12 Chunks of size 147456 totalling 1.69MiB
2019-07-21 13:06:03.574673: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 12 Chunks of size 294912 totalling 3.38MiB
2019-07-21 13:06:03.574696: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 6 Chunks of size 524288 totalling 3.00MiB
2019-07-21 13:06:03.574713: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 11 Chunks of size 589824 totalling 6.19MiB
2019-07-21 13:06:03.574736: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 12 Chunks of size 1179648 totalling 13.50MiB
2019-07-21 13:06:03.574754: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 6 Chunks of size 2097152 totalling 12.00MiB
2019-07-21 13:06:03.574773: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 11 Chunks of size 2359296 totalling 24.75MiB
2019-07-21 13:06:03.574792: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 12 Chunks of size 4718592 totalling 54.00MiB
2019-07-21 13:06:03.574811: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 8 Chunks of size 8388608 totalling 64.00MiB
2019-07-21 13:06:03.574836: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 11 Chunks of size 9437184 totalling 99.00MiB
2019-07-21 13:06:03.574854: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 1 Chunks of size 16777216 totalling 16.00MiB
2019-07-21 13:06:03.574874: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 12 Chunks of size 18874368 totalling 216.00MiB
2019-07-21 13:06:03.574897: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 4 Chunks of size 33554432 totalling 128.00MiB
2019-07-21 13:06:03.574916: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 6 Chunks of size 37748736 totalling 216.00MiB
2019-07-21 13:06:03.574939: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 1 Chunks of size 52428800 totalling 50.00MiB
2019-07-21 13:06:03.574962: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 8 Chunks of size 67108864 totalling 512.00MiB
2019-07-21 13:06:03.574981: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 1 Chunks of size 101842944 totalling 97.12MiB
2019-07-21 13:06:03.575006: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 7 Chunks of size 134217728 totalling 896.00MiB
2019-07-21 13:06:03.575032: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 1 Chunks of size 200149248 totalling 190.88MiB
2019-07-21 13:06:03.575051: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 7 Chunks of size 268435456 totalling 1.75GiB
2019-07-21 13:06:03.575070: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 7 Chunks of size 536870912 totalling 3.50GiB
2019-07-21 13:06:03.575089: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 2 Chunks of size 1073741824 totalling 2.00GiB
2019-07-21 13:06:03.575112: I tensorflow/core/common_runtime/bfc_allocator.cc:678] Sum Total of in-use chunks: 9.79GiB
2019-07-21 13:06:03.575134: I tensorflow/core/common_runtime/bfc_allocator.cc:680] Stats: 
Limit:                 11281927373
InUse:                 10515600128
MaxInUse:              10649965312
NumAllocs:                     560
MaxAllocSize:           2709569536

2019-07-21 13:06:03.575219: W tensorflow/core/common_runtime/bfc_allocator.cc:279] **********************************************__***************************************************_
2019-07-21 13:06:03.575268: W tensorflow/core/framework/op_kernel.cc:1275] OP_REQUIRES failed at conv_ops.cc:693 : Resource exhausted: OOM when allocating tensor with shape[32,64,256,256] and type float on /job:localhost/replica:0/task:0/device:GPU:0 by allocator GPU_0_bfc
Traceback (most recent call last):
  File "main.py", line 32, in <module>
    run.train()
  File "/home/dadams2/unet-sem/model.py", line 113, in train
    loss = self.model.train_on_batch(aug_imgs,aug_masks)
  File "/home/dadams2/.conda/envs/unet/lib/python3.5/site-packages/keras/engine/training.py", line 1215, in train_on_batch
    outputs = self.train_function(ins)
  File "/home/dadams2/.conda/envs/unet/lib/python3.5/site-packages/keras/backend/tensorflow_backend.py", line 2666, in __call__
    return self._call(inputs)
  File "/home/dadams2/.conda/envs/unet/lib/python3.5/site-packages/keras/backend/tensorflow_backend.py", line 2636, in _call
    fetched = self._callable_fn(*array_vals)
  File "/home/dadams2/.conda/envs/unet/lib/python3.5/site-packages/tensorflow/python/client/session.py", line 1382, in __call__
    run_metadata_ptr)
  File "/home/dadams2/.conda/envs/unet/lib/python3.5/site-packages/tensorflow/python/framework/errors_impl.py", line 519, in __exit__
    c_api.TF_GetCode(self.status.status))
tensorflow.python.framework.errors_impl.ResourceExhaustedError: OOM when allocating tensor with shape[32,64,256,256] and type float on /job:localhost/replica:0/task:0/device:GPU:0 by allocator GPU_0_bfc
	 [[Node: conv2d_22/convolution = Conv2D[T=DT_FLOAT, _class=["loc:@training/Adam/gradients/conv2d_22/convolution_grad/Conv2DBackpropInput"], data_format="NCHW", dilations=[1, 1, 1, 1], padding="SAME", strides=[1, 1, 1, 1], use_cudnn_on_gpu=true, _device="/job:localhost/replica:0/task:0/device:GPU:0"](conv2d_21/Relu, conv2d_22/kernel/read)]]
Hint: If you want to see a list of allocated tensors when OOM happens, add report_tensor_allocations_upon_oom to RunOptions for current allocation info.

	 [[Node: metrics/acc/Mean_1/_429 = _Recv[client_terminated=false, recv_device="/job:localhost/replica:0/task:0/device:CPU:0", send_device="/job:localhost/replica:0/task:0/device:GPU:0", send_device_incarnation=1, tensor_name="edge_3038_metrics/acc/Mean_1", tensor_type=DT_FLOAT, _device="/job:localhost/replica:0/task:0/device:CPU:0"]()]]
Hint: If you want to see a list of allocated tensors when OOM happens, add report_tensor_allocations_upon_oom to RunOptions for current allocation info.

(unet) [dadams2@gpu008 unet-sem]$ exit
srun: error: gpu008: task 0: Exited with exit code 1
[dadams2@login005 unet-sem]$ interact -p GPU --gres=gpu:p100:2

A command prompt will appear when your session begins
"Ctrl+d" or "exit" will end your session

srun: job 6067144 queued and waiting for resources
^Csrun: Job allocation 6067144 has been revoked
srun: Force Terminated job 6067144
[dadams2@login005 unet-sem]$ git status
# On branch master
# Changes not staged for commit:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#	modified:   utils.py
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#	__pycache__/
#	data/
no changes added to commit (use "git add" and/or "git commit -a")
[dadams2@login005 unet-sem]$ git add utils.py 
[dadams2@login005 unet-sem]$ git commit -m "fixes #1"
[master c6c1740] fixes #1
 Committer: Darren Adams <[email protected]>
Your name and email address were configured automatically based
on your username and hostname. Please check that they are accurate.
You can suppress this message by setting them explicitly:

    git config --global user.name "Your Name"
    git config --global user.email [email protected]

After doing this, you may fix the identity used for this commit with:

    git commit --amend --reset-author

 1 file changed, 2 insertions(+), 2 deletions(-)
[dadams2@login005 unet-sem]$ git config --global user.name "Darren Adams"
[dadams2@login005 unet-sem]$ git config --global user.email [email protected]
[dadams2@login005 unet-sem]$ git commit --amend --reset-author
[master 5cf3d60] fixes #1
 1 file changed, 2 insertions(+), 2 deletions(-)
[dadams2@login005 unet-sem]$ git push
warning: push.default is unset; its implicit value is changing in
Git 2.0 from 'matching' to 'simple'. To squelch this message
and maintain the current behavior after the default changes, use:

  git config --global push.default matching

To squelch this message and adopt the new behavior now, use:

  git config --global push.default simple

See 'git help config' and search for 'push.default' for further information.
(the 'simple' mode was introduced in Git 1.7.11. Use the similar mode
'current' instead of 'simple' if you sometimes use older versions of Git)

Counting objects: 5, done.
Delta compression using up to 28 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 294 bytes | 0 bytes/s, done.
Total 3 (delta 2), reused 0 (delta 0)
remote: Resolving deltas: 100% (2/2), completed with 2 local objects.
To [email protected]:nanoMFG/unet-sem.git
   abe3dee..5cf3d60  master -> master
[dadams2@login005 unet-sem]$ interact -p GPU --gres=gpu:k80:4

A command prompt will appear when your session begins
"Ctrl+d" or "exit" will end your session

[dadams2@gpu012 unet-sem]$ module load anaconda3
[dadams2@gpu012 unet-sem]$ source activate unet
(unet) [dadams2@gpu012 unet-sem]$ python main.py 
Using TensorFlow backend.
{'input_size': (256, 256), 'batch_size': 32, 'split': 0.1, 'max_crop': False, 'crop': True, 'lr': 0.0001, 'ngpu': 1, 'crop_size': (256, 256), 'augment': True, 'nepochs': 5}
/home/dadams2/unet-sem/model.py:58: UserWarning: Update your `Model` call to the Keras 2 API: `Model(outputs=Tensor("co..., inputs=Tensor("in...)`
  model = Model(input = inputs, output = conv10)
2019-07-21 13:11:29.826699: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA
2019-07-21 13:11:30.139306: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1405] Found device 0 with properties: 
name: Tesla K80 major: 3 minor: 7 memoryClockRate(GHz): 0.8235
pciBusID: 0000:83:00.0
totalMemory: 11.17GiB freeMemory: 11.10GiB
2019-07-21 13:11:30.336060: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1405] Found device 1 with properties: 
name: Tesla K80 major: 3 minor: 7 memoryClockRate(GHz): 0.8235
pciBusID: 0000:84:00.0
totalMemory: 11.17GiB freeMemory: 11.10GiB
2019-07-21 13:11:30.529036: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1405] Found device 2 with properties: 
name: Tesla K80 major: 3 minor: 7 memoryClockRate(GHz): 0.8235
pciBusID: 0000:8a:00.0
totalMemory: 11.17GiB freeMemory: 11.10GiB
2019-07-21 13:11:30.726517: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1405] Found device 3 with properties: 
name: Tesla K80 major: 3 minor: 7 memoryClockRate(GHz): 0.8235
pciBusID: 0000:8b:00.0
totalMemory: 11.17GiB freeMemory: 11.10GiB
2019-07-21 13:11:30.728333: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1484] Adding visible gpu devices: 0, 1, 2, 3
2019-07-21 13:11:32.877048: I tensorflow/core/common_runtime/gpu/gpu_device.cc:965] Device interconnect StreamExecutor with strength 1 edge matrix:
2019-07-21 13:11:32.877111: I tensorflow/core/common_runtime/gpu/gpu_device.cc:971]      0 1 2 3 
2019-07-21 13:11:32.877125: I tensorflow/core/common_runtime/gpu/gpu_device.cc:984] 0:   N Y Y Y 
2019-07-21 13:11:32.877135: I tensorflow/core/common_runtime/gpu/gpu_device.cc:984] 1:   Y N Y Y 
2019-07-21 13:11:32.877144: I tensorflow/core/common_runtime/gpu/gpu_device.cc:984] 2:   Y Y N Y 
2019-07-21 13:11:32.877152: I tensorflow/core/common_runtime/gpu/gpu_device.cc:984] 3:   Y Y Y N 
2019-07-21 13:11:32.878632: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1097] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 10759 MB memory) -> physical GPU (device: 0, name: Tesla K80, pci bus id: 0000:83:00.0, compute capability: 3.7)
2019-07-21 13:11:33.037580: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1097] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:1 with 10759 MB memory) -> physical GPU (device: 1, name: Tesla K80, pci bus id: 0000:84:00.0, compute capability: 3.7)
2019-07-21 13:11:33.233135: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1097] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:2 with 10759 MB memory) -> physical GPU (device: 2, name: Tesla K80, pci bus id: 0000:8a:00.0, compute capability: 3.7)
2019-07-21 13:11:33.428766: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1097] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:3 with 10759 MB memory) -> physical GPU (device: 3, name: Tesla K80, pci bus id: 0000:8b:00.0, compute capability: 3.7)
2019-07-21 13:11:45.683327: W tensorflow/core/common_runtime/bfc_allocator.cc:219] Allocator (GPU_0_bfc) ran out of memory trying to allocate 4.00GiB. The caller indicates that this is not a failure, but may mean that there could be performance gains if more memory were available.
2019-07-21 13:11:46.713263: W tensorflow/core/common_runtime/bfc_allocator.cc:219] Allocator (GPU_0_bfc) ran out of memory trying to allocate 3.38GiB. The caller indicates that this is not a failure, but may mean that there could be performance gains if more memory were available.
2019-07-21 13:11:56.714689: W tensorflow/core/common_runtime/bfc_allocator.cc:275] Allocator (GPU_0_bfc) ran out of memory trying to allocate 512.00MiB.  Current allocation summary follows.
2019-07-21 13:11:56.714748: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (256): 	Total Chunks: 135, Chunks in use: 135. 33.8KiB allocated for chunks. 33.8KiB in use in bin. 7.1KiB client-requested in use in bin.
2019-07-21 13:11:56.714773: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (512): 	Total Chunks: 26, Chunks in use: 26. 13.0KiB allocated for chunks. 13.0KiB in use in bin. 13.0KiB client-requested in use in bin.
2019-07-21 13:11:56.714791: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (1024): 	Total Chunks: 27, Chunks in use: 27. 27.2KiB allocated for chunks. 27.2KiB in use in bin. 27.0KiB client-requested in use in bin.
2019-07-21 13:11:56.714808: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (2048): 	Total Chunks: 32, Chunks in use: 32. 65.5KiB allocated for chunks. 65.5KiB in use in bin. 65.5KiB client-requested in use in bin.
2019-07-21 13:11:56.714831: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (4096): 	Total Chunks: 17, Chunks in use: 17. 71.0KiB allocated for chunks. 71.0KiB in use in bin. 71.0KiB client-requested in use in bin.
2019-07-21 13:11:56.714849: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (8192): 	Total Chunks: 0, Chunks in use: 0. 0B allocated for chunks. 0B in use in bin. 0B client-requested in use in bin.
2019-07-21 13:11:56.714865: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (16384): 	Total Chunks: 0, Chunks in use: 0. 0B allocated for chunks. 0B in use in bin. 0B client-requested in use in bin.
2019-07-21 13:11:56.714881: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (32768): 	Total Chunks: 0, Chunks in use: 0. 0B allocated for chunks. 0B in use in bin. 0B client-requested in use in bin.
2019-07-21 13:11:56.714895: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (65536): 	Total Chunks: 0, Chunks in use: 0. 0B allocated for chunks. 0B in use in bin. 0B client-requested in use in bin.
2019-07-21 13:11:56.715015: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (131072): 	Total Chunks: 18, Chunks in use: 18. 2.44MiB allocated for chunks. 2.44MiB in use in bin. 2.44MiB client-requested in use in bin.
2019-07-21 13:11:56.715047: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (262144): 	Total Chunks: 12, Chunks in use: 12. 3.38MiB allocated for chunks. 3.38MiB in use in bin. 3.38MiB client-requested in use in bin.
2019-07-21 13:11:56.715068: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (524288): 	Total Chunks: 17, Chunks in use: 17. 9.19MiB allocated for chunks. 9.19MiB in use in bin. 9.19MiB client-requested in use in bin.
2019-07-21 13:11:56.715104: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (1048576): 	Total Chunks: 12, Chunks in use: 12. 13.50MiB allocated for chunks. 13.50MiB in use in bin. 13.50MiB client-requested in use in bin.
2019-07-21 13:11:56.715124: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (2097152): 	Total Chunks: 18, Chunks in use: 17. 39.00MiB allocated for chunks. 36.75MiB in use in bin. 36.75MiB client-requested in use in bin.
2019-07-21 13:11:56.715161: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (4194304): 	Total Chunks: 13, Chunks in use: 12. 58.50MiB allocated for chunks. 54.00MiB in use in bin. 54.00MiB client-requested in use in bin.
2019-07-21 13:11:56.715196: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (8388608): 	Total Chunks: 20, Chunks in use: 19. 172.00MiB allocated for chunks. 163.00MiB in use in bin. 163.00MiB client-requested in use in bin.
2019-07-21 13:11:56.715227: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (16777216): 	Total Chunks: 13, Chunks in use: 13. 232.00MiB allocated for chunks. 232.00MiB in use in bin. 232.00MiB client-requested in use in bin.
2019-07-21 13:11:56.715245: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (33554432): 	Total Chunks: 13, Chunks in use: 11. 462.00MiB allocated for chunks. 394.00MiB in use in bin. 376.00MiB client-requested in use in bin.
2019-07-21 13:11:56.715265: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (67108864): 	Total Chunks: 10, Chunks in use: 9. 673.12MiB allocated for chunks. 609.12MiB in use in bin. 576.00MiB client-requested in use in bin.
2019-07-21 13:11:56.715293: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (134217728): 	Total Chunks: 10, Chunks in use: 8. 1.38GiB allocated for chunks. 1.06GiB in use in bin. 1.00GiB client-requested in use in bin.
2019-07-21 13:11:56.715653: I tensorflow/core/common_runtime/bfc_allocator.cc:630] Bin (268435456): 	Total Chunks: 17, Chunks in use: 16. 7.50GiB allocated for chunks. 7.25GiB in use in bin. 7.25GiB client-requested in use in bin.
2019-07-21 13:11:56.715692: I tensorflow/core/common_runtime/bfc_allocator.cc:646] Bin for 512.00MiB was 256.00MiB, Chunk State: 
2019-07-21 13:11:56.715725: I tensorflow/core/common_runtime/bfc_allocator.cc:652]   Size: 256.00MiB | Requested Size: 256.00MiB | in_use: 0, prev:   Size: 128.00MiB | Requested Size: 128.00MiB | in_use: 1, next:   Size: 256.00MiB | Requested Size: 256.00MiB | in_use: 1
2019-07-21 13:11:56.715760: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x230fb00000 of size 1280
2019-07-21 13:11:56.715775: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x230fb00500 of size 256
2019-07-21 13:11:56.715786: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x230fb00600 of size 256
2019-07-21 13:11:56.715815: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x230fb00700 of size 256
2019-07-21 13:11:56.715833: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x230fb00800 of size 256
2019-07-21 13:11:56.715850: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x230fb00900 of size 256
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2019-07-21 13:11:56.715876: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x230fb00b00 of size 256
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2019-07-21 13:11:56.715974: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x230fb01000 of size 256
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2019-07-21 13:11:56.716004: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x230fb01200 of size 256
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2019-07-21 13:11:56.716036: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x230fb01400 of size 256
2019-07-21 13:11:56.716049: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x230fb01500 of size 256
2019-07-21 13:11:56.716070: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x230fb01600 of size 2304
2019-07-21 13:11:56.716091: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x230fb01f00 of size 294912
2019-07-21 13:11:56.716105: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x230fb49f00 of size 4718592
2019-07-21 13:11:56.716118: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x230ffc9f00 of size 18874368
2019-07-21 13:11:56.716131: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23111c9f00 of size 37748736
2019-07-21 13:11:56.716156: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23135c9f00 of size 4096
2019-07-21 13:11:56.716170: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23135caf00 of size 8388608
2019-07-21 13:11:56.716182: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2313dcaf00 of size 18874368
2019-07-21 13:11:56.716203: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2314fcaf00 of size 9437184
2019-07-21 13:11:56.716218: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23158caf00 of size 2048
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2019-07-21 13:11:56.716305: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23162ab700 of size 524288
2019-07-21 13:11:56.716331: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x231632b700 of size 1179648
2019-07-21 13:11:56.716357: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x231644b700 of size 589824
2019-07-21 13:11:56.716380: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23164db700 of size 512
2019-07-21 13:11:56.716395: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23164db900 of size 131072
2019-07-21 13:11:56.716412: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23164fb900 of size 294912
2019-07-21 13:11:56.716433: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2316543900 of size 1024
2019-07-21 13:11:56.716456: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2316543d00 of size 147456
2019-07-21 13:11:56.716470: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2316567d00 of size 256
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2019-07-21 13:11:56.716504: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2316569000 of size 256
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2019-07-21 13:11:56.716552: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2316569300 of size 2304
2019-07-21 13:11:56.716565: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2316569c00 of size 294912
2019-07-21 13:11:56.716586: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23165b1c00 of size 294912
2019-07-21 13:11:56.716601: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23165f9c00 of size 4718592
2019-07-21 13:11:56.716623: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2316a79c00 of size 18874368
2019-07-21 13:11:56.716636: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2317c79c00 of size 18874368
2019-07-21 13:11:56.716658: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2318e79c00 of size 37748736
2019-07-21 13:11:56.716674: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x231b279c00 of size 37748736
2019-07-21 13:11:56.716689: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x231d679c00 of size 4096
2019-07-21 13:11:56.716712: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x231d67ac00 of size 4096
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2019-07-21 13:11:56.716749: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x231d67cc00 of size 4096
2019-07-21 13:11:56.716762: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x231d67dc00 of size 8388608
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2019-07-21 13:11:56.716834: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2320a7dc00 of size 9437184
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2019-07-21 13:11:56.720885: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236e31c800 of size 512
2019-07-21 13:11:56.720900: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236e31ca00 of size 2304
2019-07-21 13:11:56.720914: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236e31d300 of size 2304
2019-07-21 13:11:56.720932: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236e31dc00 of size 589824
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2019-07-21 13:11:56.720962: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236e43dc00 of size 512
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2019-07-21 13:11:56.720994: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236e43e000 of size 1179648
2019-07-21 13:11:56.721016: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236e55e000 of size 1179648
2019-07-21 13:11:56.721030: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236e67e000 of size 1024
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2019-07-21 13:11:56.721065: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236e67e800 of size 2359296
2019-07-21 13:11:56.721080: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236e8be800 of size 2359296
2019-07-21 13:11:56.721092: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236eafe800 of size 1024
2019-07-21 13:11:56.721105: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236eafec00 of size 1024
2019-07-21 13:11:56.721125: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236eaff000 of size 4718592
2019-07-21 13:11:56.721144: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236ef7f000 of size 4718592
2019-07-21 13:11:56.721157: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236f3ff000 of size 2048
2019-07-21 13:11:56.721172: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236f3ff800 of size 2048
2019-07-21 13:11:56.721188: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236f400000 of size 9437184
2019-07-21 13:11:56.721202: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x236fd00000 of size 9437184
2019-07-21 13:11:56.721217: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2370600000 of size 2048
2019-07-21 13:11:56.721230: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2370600800 of size 2048
2019-07-21 13:11:56.721243: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2370601000 of size 256
2019-07-21 13:11:56.721266: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2370601100 of size 256
2019-07-21 13:11:56.721280: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2370601200 of size 18874368
2019-07-21 13:11:56.721293: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2371801200 of size 18874368
2019-07-21 13:11:56.721310: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2372a01200 of size 4096
2019-07-21 13:11:56.721332: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2372a02200 of size 4096
2019-07-21 13:11:56.721347: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2372a03200 of size 37748736
2019-07-21 13:11:56.721364: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2374e03200 of size 37748736
2019-07-21 13:11:56.721384: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2377203200 of size 4096
2019-07-21 13:11:56.721401: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2377204200 of size 4096
2019-07-21 13:11:56.721414: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2377205200 of size 8388608
2019-07-21 13:11:56.721430: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2377a05200 of size 8388608
2019-07-21 13:11:56.721445: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2378205200 of size 2048
2019-07-21 13:11:56.721461: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2378205a00 of size 2048
2019-07-21 13:11:56.721474: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2378206200 of size 18874368
2019-07-21 13:11:56.721495: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2379406200 of size 18874368
2019-07-21 13:11:56.721514: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237a606200 of size 2048
2019-07-21 13:11:56.721528: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237a606a00 of size 2048
2019-07-21 13:11:56.721550: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237a607200 of size 9437184
2019-07-21 13:11:56.721568: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237af07200 of size 9437184
2019-07-21 13:11:56.721582: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237b807200 of size 2048
2019-07-21 13:11:56.721603: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237b807a00 of size 2048
2019-07-21 13:11:56.721621: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237b808200 of size 147456
2019-07-21 13:11:56.721641: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237b82c200 of size 147456
2019-07-21 13:11:56.721659: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237b850200 of size 2097152
2019-07-21 13:11:56.721672: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237ba50200 of size 2097152
2019-07-21 13:11:56.721693: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237bc50200 of size 1024
2019-07-21 13:11:56.721710: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237bc50600 of size 1024
2019-07-21 13:11:56.721723: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237bc50a00 of size 4718592
2019-07-21 13:11:56.721741: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237c0d0a00 of size 4718592
2019-07-21 13:11:56.721759: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237c550a00 of size 1024
2019-07-21 13:11:56.721772: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237c550e00 of size 1024
2019-07-21 13:11:56.721789: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237c551200 of size 256
2019-07-21 13:11:56.721810: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237c551300 of size 256
2019-07-21 13:11:56.721824: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237c551400 of size 147456
2019-07-21 13:11:56.721841: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x237c575400 of size 536870912
2019-07-21 13:11:56.721863: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x239c575400 of size 268435456
2019-07-21 13:11:56.721877: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23ac575400 of size 268435456
2019-07-21 13:11:56.721890: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Free  at 0x23bc575400 of size 2359296
2019-07-21 13:11:56.721911: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23bc7b5400 of size 134217728
2019-07-21 13:11:56.721924: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Free  at 0x23c47b5400 of size 4718592
2019-07-21 13:11:56.721938: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23c4c35400 of size 67108864
2019-07-21 13:11:56.721955: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Free  at 0x23c8c35400 of size 9437184
2019-07-21 13:11:56.721971: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23c9535400 of size 67108864
2019-07-21 13:11:56.721989: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23cd535400 of size 67108864
2019-07-21 13:11:56.722002: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23d1535400 of size 67108864
2019-07-21 13:11:56.722020: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23d5535400 of size 16777216
2019-07-21 13:11:56.722038: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23d6535400 of size 52428800
2019-07-21 13:11:56.722051: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23d9735400 of size 33554432
2019-07-21 13:11:56.722068: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Free  at 0x23db735400 of size 37748736
2019-07-21 13:11:56.722081: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23ddb35400 of size 33554432
2019-07-21 13:11:56.722095: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Free  at 0x23dfb35400 of size 33554432
2019-07-21 13:11:56.722109: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23e1b35400 of size 33554432
2019-07-21 13:11:56.722129: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Free  at 0x23e3b35400 of size 67108864
2019-07-21 13:11:56.722143: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23e7b35400 of size 67108864
2019-07-21 13:11:56.722158: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23ebb35400 of size 134217728
2019-07-21 13:11:56.722181: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23f3b35400 of size 134217728
2019-07-21 13:11:56.722200: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23fbb35400 of size 67108864
2019-07-21 13:11:56.722213: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x23ffb35400 of size 67108864
2019-07-21 13:11:56.722230: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Free  at 0x2403b35400 of size 134217728
2019-07-21 13:11:56.722246: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x240bb35400 of size 134217728
2019-07-21 13:11:56.722260: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2413b35400 of size 268435456
2019-07-21 13:11:56.722277: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2423b35400 of size 268435456
2019-07-21 13:11:56.722295: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2433b35400 of size 134217728
2019-07-21 13:11:56.722312: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x243bb35400 of size 134217728
2019-07-21 13:11:56.722332: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Free  at 0x2443b35400 of size 268435456
2019-07-21 13:11:56.722352: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2453b35400 of size 268435456
2019-07-21 13:11:56.722369: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2463b35400 of size 536870912
2019-07-21 13:11:56.722382: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2483b35400 of size 536870912
2019-07-21 13:11:56.722397: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x24a3b35400 of size 268435456
2019-07-21 13:11:56.722419: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x24b3b35400 of size 268435456
2019-07-21 13:11:56.722436: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x24c3b35400 of size 536870912
2019-07-21 13:11:56.722450: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x24e3b35400 of size 536870912
2019-07-21 13:11:56.722465: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2503b35400 of size 1073741824
2019-07-21 13:11:56.722485: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2543b35400 of size 1073741824
2019-07-21 13:11:56.722503: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Chunk at 0x2583b35400 of size 536870912
2019-07-21 13:11:56.722516: I tensorflow/core/common_runtime/bfc_allocator.cc:665] Free  at 0x25a3b35400 of size 208746496
2019-07-21 13:11:56.722536: I tensorflow/core/common_runtime/bfc_allocator.cc:671]      Summary of in-use Chunks by size: 
2019-07-21 13:11:56.722554: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 135 Chunks of size 256 totalling 33.8KiB
2019-07-21 13:11:56.722569: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 26 Chunks of size 512 totalling 13.0KiB
2019-07-21 13:11:56.722588: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 26 Chunks of size 1024 totalling 26.0KiB
2019-07-21 13:11:56.722603: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 1 Chunks of size 1280 totalling 1.2KiB
2019-07-21 13:11:56.722617: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 26 Chunks of size 2048 totalling 52.0KiB
2019-07-21 13:11:56.722631: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 6 Chunks of size 2304 totalling 13.5KiB
2019-07-21 13:11:56.722655: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 11 Chunks of size 4096 totalling 44.0KiB
2019-07-21 13:11:56.722675: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 6 Chunks of size 4608 totalling 27.0KiB
2019-07-21 13:11:56.722691: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 6 Chunks of size 131072 totalling 768.0KiB
2019-07-21 13:11:56.722715: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 12 Chunks of size 147456 totalling 1.69MiB
2019-07-21 13:11:56.722734: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 12 Chunks of size 294912 totalling 3.38MiB
2019-07-21 13:11:56.722752: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 6 Chunks of size 524288 totalling 3.00MiB
2019-07-21 13:11:56.722767: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 11 Chunks of size 589824 totalling 6.19MiB
2019-07-21 13:11:56.722781: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 12 Chunks of size 1179648 totalling 13.50MiB
2019-07-21 13:11:56.722796: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 6 Chunks of size 2097152 totalling 12.00MiB
2019-07-21 13:11:56.722818: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 11 Chunks of size 2359296 totalling 24.75MiB
2019-07-21 13:11:56.722837: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 12 Chunks of size 4718592 totalling 54.00MiB
2019-07-21 13:11:56.722853: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 8 Chunks of size 8388608 totalling 64.00MiB
2019-07-21 13:11:56.722876: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 11 Chunks of size 9437184 totalling 99.00MiB
2019-07-21 13:11:56.722892: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 1 Chunks of size 16777216 totalling 16.00MiB
2019-07-21 13:11:56.722907: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 12 Chunks of size 18874368 totalling 216.00MiB
2019-07-21 13:11:56.722925: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 4 Chunks of size 33554432 totalling 128.00MiB
2019-07-21 13:11:56.722941: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 6 Chunks of size 37748736 totalling 216.00MiB
2019-07-21 13:11:56.722955: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 1 Chunks of size 52428800 totalling 50.00MiB
2019-07-21 13:11:56.722970: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 8 Chunks of size 67108864 totalling 512.00MiB
2019-07-21 13:11:56.722989: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 1 Chunks of size 101842944 totalling 97.12MiB
2019-07-21 13:11:56.723005: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 7 Chunks of size 134217728 totalling 896.00MiB
2019-07-21 13:11:56.723020: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 1 Chunks of size 200149504 totalling 190.88MiB
2019-07-21 13:11:56.723035: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 7 Chunks of size 268435456 totalling 1.75GiB
2019-07-21 13:11:56.723059: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 7 Chunks of size 536870912 totalling 3.50GiB
2019-07-21 13:11:56.723074: I tensorflow/core/common_runtime/bfc_allocator.cc:674] 2 Chunks of size 1073741824 totalling 2.00GiB
2019-07-21 13:11:56.723090: I tensorflow/core/common_runtime/bfc_allocator.cc:678] Sum Total of in-use chunks: 9.79GiB
2019-07-21 13:11:56.723110: I tensorflow/core/common_runtime/bfc_allocator.cc:680] Stats: 
Limit:                 11281927373
InUse:                 10515600384
MaxInUse:              10649965568
NumAllocs:                     560
MaxAllocSize:           2709569536

2019-07-21 13:11:56.723181: W tensorflow/core/common_runtime/bfc_allocator.cc:279] **********************************************__***************************************************_
2019-07-21 13:11:56.723221: W tensorflow/core/framework/op_kernel.cc:1275] OP_REQUIRES failed at conv_ops.cc:693 : Resource exhausted: OOM when allocating tensor with shape[32,64,256,256] and type float on /job:localhost/replica:0/task:0/device:GPU:0 by allocator GPU_0_bfc
Traceback (most recent call last):
  File "main.py", line 32, in <module>
    run.train()
  File "/home/dadams2/unet-sem/model.py", line 113, in train
    loss = self.model.train_on_batch(aug_imgs,aug_masks)
  File "/home/dadams2/.conda/envs/unet/lib/python3.5/site-packages/keras/engine/training.py", line 1215, in train_on_batch
    outputs = self.train_function(ins)
  File "/home/dadams2/.conda/envs/unet/lib/python3.5/site-packages/keras/backend/tensorflow_backend.py", line 2666, in __call__
    return self._call(inputs)
  File "/home/dadams2/.conda/envs/unet/lib/python3.5/site-packages/keras/backend/tensorflow_backend.py", line 2636, in _call
    fetched = self._callable_fn(*array_vals)
  File "/home/dadams2/.conda/envs/unet/lib/python3.5/site-packages/tensorflow/python/client/session.py", line 1382, in __call__
    run_metadata_ptr)
  File "/home/dadams2/.conda/envs/unet/lib/python3.5/site-packages/tensorflow/python/framework/errors_impl.py", line 519, in __exit__
    c_api.TF_GetCode(self.status.status))
tensorflow.python.framework.errors_impl.ResourceExhaustedError: OOM when allocating tensor with shape[32,64,256,256] and type float on /job:localhost/replica:0/task:0/device:GPU:0 by allocator GPU_0_bfc
	 [[Node: conv2d_22/convolution = Conv2D[T=DT_FLOAT, _class=["loc:@training/Adam/gradients/conv2d_22/convolution_grad/Conv2DBackpropInput"], data_format="NCHW", dilations=[1, 1, 1, 1], padding="SAME", strides=[1, 1, 1, 1], use_cudnn_on_gpu=true, _device="/job:localhost/replica:0/task:0/device:GPU:0"](conv2d_21/Relu, conv2d_22/kernel/read)]]
Hint: If you want to see a list of allocated tensors when OOM happens, add report_tensor_allocations_upon_oom to RunOptions for current allocation info.

	 [[Node: metrics/acc/Mean_1/_429 = _Recv[client_terminated=false, recv_device="/job:localhost/replica:0/task:0/device:CPU:0", send_device="/job:localhost/replica:0/task:0/device:GPU:0", send_device_incarnation=1, tensor_name="edge_3038_metrics/acc/Mean_1", tensor_type=DT_FLOAT, _device="/job:localhost/replica:0/task:0/device:CPU:0"]()]]
Hint: If you want to see a list of allocated tensors when OOM happens, add report_tensor_allocations_upon_oom to RunOptions for current allocation info.

bug in booleen mask assignment

 model = Model(input = inputs, output = conv10)
Traceback (most recent call last):
  File "main.py", line 32, in <module>
    run.train()
  File "/home/dadams2/unet-sem/model.py", line 112, in train
    max_crop = self.max_crop)
  File "/home/dadams2/unet-sem/utils.py", line 65, in generate_batch
    out_mask[mask > 0.5] = 1
IndexError: boolean index did not match indexed array along dimension 0; dimension is 256 but corresponding boolean dimension is 1279

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