How to Use a Retrained Model with pbrun deepvariant

Healthcare & Life Sciences Parabricks
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1

Hi, I followd this doc Retraining_DeepVariant and get a checkpoint ‘ckpt-6689’.
How can i use this checkpoints to ‘clara-parabricks:4.4.0-1 pbrun deepvariant’

2

Hi @csyourui, you can use this repo to convert the model file to a TRT engine

3

thanks for reply but it looks like a private repository

here is my test for convert model, seems work fine for me

PBDV_DIR="/mnt/ssd1/yourui/pbdv"
CHECKPOINT_DIR="ckpt-6689"
BATCH_SIZE=128
docker run --rm --gpus all \
    -v $PBDV_DIR:/pbdv \
    nvcr.io/nvidia/tensorflow:23.06-tf2-py3 \
    bash -c "
    python3 -m pip install tf2onnx && \
    python3 -m tf2onnx.convert --saved-model /pbdv/train/training_dir/checkpoints/$CHECKPOINT_DIR \
                                --output /pbdv/train/model/onnx_engine/model.onnx && \
    trtexec --onnx=/pbdv/train/model/onnx_engine/model.onnx \
            --saveEngine=/pbdv/train/model/onnx_engine/model.eng \
            --minShapes=input_1:${BATCH_SIZE}x100x221x7 \
            --optShapes=input_1:${BATCH_SIZE}x100x221x7 \
            --maxShapes=input_1:${BATCH_SIZE}x100x221x7 && \
    polygraphy inspect model /pbdv/train/model/onnx_engine/model.eng --model-type engine
    "