iphysresearch/gwmlsc1 repository overview

# 1. Pull the image
$ singularity pull gwmlsc1_mfcnn_update3.sif library://iphysresearch/gwmlsc1/mfcnn:1.2
# 2. Build a sandbox (container in a directory) (~22Gb)
$ singularity build --sandbox submission gwmlsc1_mfcnn_update3.sif
# 3. Run a Bourne shell within the container
$ singularity shell --nv \
       --bind /usr/local:/usr/local \
       --bind <input_file_dir>:/workspace/mfcnn/input_file \
       --bind <output_file_dir>:/workspace/mfcnn/output_file  submission/ 
# 4. Find the workplace
$Singularity> cd /workspace/mfcnn/
# 5. Run the scripts
$Singularity> /opt/conda/envs/gwmlsc1/bin/python run_gpus.py \
              /workspace/mfcnn/input_file/foreground.hdf \
              /workspace/mfcnn/output_file/foreground_output.hdf

$ singularity pull gwmlsc1_mfcnn.sif library://iphysresearch/gwmlsc1/mfcnn:1.1
$ singularity exec --nv \
       --bind /usr/local:/usr/local \
       gwmlsc1_mfcnn_update.sif \
       /opt/conda/envs/gwmlsc1/bin/python -c "import torch; print(torch.cuda.is_available())"
$ singularity run --nv \
       --bind /usr/local:/usr/local \
       --bind <input_file_dir>:/workspace/mfcnn/input_file \
       --bind <output_file_dir>:/workspace/mfcnn/output_file  \
       gwmlsc1_mfcnn.sif /workspace/mfcnn/input_file/foreground.hdf /workspace/mfcnn/output_file/outputfile.hdf

$ singularity pull mfcnn.sif docker://iphysresearch/gwmlsc1:1.0
$ singularity shell --nv mfcnn.sif
$ cd /mfcnn
$ /opt/conda/envs/gwmlsc1/bin/python run.py --help

$ sudo docker run iphysresearch/gwmlsc1:1.0 --help

$ sudo docker run \
       -v <input_file_dir>:/mfcnn/intput_file/ \
       -v <output_file_dir>:/mfcnn/output_file/  \
       iphysresearch/gwmlsc1:1.0 \ 
       /mfcnn/intput_file/foreground.hdf /mfcnn/output_file/output.hdf