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Francis Lata b7ce9a1530 UNet3D MLPerf (#3470) ... * add training set transforms * add DICE cross entropy loss * convert pred and label to Tensor when calculating DICE score * cleanups and allow train dataset batching * fix DICE CE loss calculation * jitted training step * clean up DICE CE loss calculation * initial support for sharding * Revert "initial support for sharding" This reverts commit e3670813b8. * minor updates * cleanup imports * add support for sharding * apply temp patch to try to avoid OOM * revert cstyle changes * add gradient acc * hotfix * add FP16 support * add ability to train on smaller image sizes * add support for saving and loading checkpoints + cleanup some various modes * fix issue with using smaller patch size + update W&B logging * disable LR_WARMUP_EPOCHS * updates * minor cleanups * cleanup * update order of transformations * more cleanups * realize loss * cleanup * more cleanup * some cleanups * add RAM usage * minor cleanups * add support for gradient accumulation * cleanup imports * minor updates to not use GA_STEPS * remove FP16 option since it's available now globally * update multi-GPU setup * add timing logs for training loop * go back to using existing dataloader and add ability to preprocess data to save time * clean up optimization and re-enable JIT and multi-GPU support for training and evaluation * free train and eval steps memory * cleanups and scale batch size based on the number of GPUs * fix GlobalCounters import * fix seed * fix W&B setup * update batch size default size * add back metric divergence check * put back JIT on UNet3d eval * move dataset preprocessing inside training code * add test for dice_loss * add config logging support to W&B and other cleanups * change how default float is getting retrieved * remove TinyJit import duplicate * update config logging to W&B and remove JIT on eval_step * no need for caching preprocessed data anymore * fix how evaluation is ran and how often * add support for LR scaling * fix issue with gaussian being moved to scipy.signal.windows * remove DICE loss unit test * fix issue where loss isn't compatible with multiGPU * add individual BEAM control for train and eval steps * fix ndimage scipy import * add BENCHMARK * cleanups on BENCHMARK + fix on rand_flip augmentation during training * cleanup train and eval BEAM envs * add checkpointing support after every eval * cleanup model_eval * disable grad during eval * use new preprocessing dataset mechanism * remove unused import * use training and inference_mode contexts * start eval after benchmarking * add data fetching time * cleanup decorators * more cleanups on training script * add message during benchmarking mode * realize when reassigning LR on scheduler and update default number of epochs * add JIT on eval step * remove JIT on eval_step * add train dataloader for unet3d * move checkpointing to be done after every epoch * revert removal of JIT on unet3d inference * save checkpoint if metric is not successful * Revert "add train dataloader for unet3d" This reverts commit c166d129df. * Revert "Revert "add train dataloader for unet3d"" This reverts commit 36366c65d2. * hotfix: seed was defaulting to a value of 0 * fix SEED value * remove the usage of context managers for setting BEAM and going from training to inference * support new stack API for calculating eval loss and metric * Revert "remove the usage of context managers for setting BEAM and going from training to inference" This reverts commit 2c0ba8d322. * check training and test preprocessed folders separately * clean up imports and log FUSE_CONV_BW * use train and val preprocessing constants * add kits19 dataset setup script * update to use the new test decorator for disabling grad * update kits19 dataset setup script * add docs on how to train the model * set default value for BASEDIR * add detailed instruction about BASEDIR usage --------- Co-authored-by: chenyu <chenyu@fastmail.com>		2024-09-10 04:37:28 -04:00
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setup_kits19_dataset.sh	UNet3D MLPerf (#3470)	2024-09-10 04:37:28 -04:00