camelyon-cnns-batchConcurrencyLimit-3.red.yml

batches:
- inputs:
    arch: '1'
    epochs: '8'
    fast_hdf5: '1'
    hdf5:
      class: Directory
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          dirPath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/merged_tiles/single_mode_mask_5000
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
        mount: true
    mask_threshold: '0.1'
    queue_size: '1'
  outputs:
    acc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/1/acc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    checkpoint:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/1/checkpoint
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    log:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/1/log.json
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    loss_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/1/loss.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_data:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/1/model_checkpoint.ckpt.data
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_index:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/1/model_checkpoint.ckpt.index
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_final:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/1/model_final.hdf5
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    roc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/1/roc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
- inputs:
    arch: '1'
    epochs: '8'
    fast_hdf5: '1'
    hdf5:
      class: Directory
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          dirPath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/merged_tiles/single_mode_mask_5000
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
        mount: true
    mask_threshold: '0.1'
    queue_size: '1'
  outputs:
    acc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/2/acc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    checkpoint:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/2/checkpoint
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    log:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/2/log.json
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    loss_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/2/loss.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_data:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/2/model_checkpoint.ckpt.data
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_index:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/2/model_checkpoint.ckpt.index
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_final:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/2/model_final.hdf5
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    roc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/2/roc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
- inputs:
    arch: '1'
    epochs: '8'
    fast_hdf5: '1'
    hdf5:
      class: Directory
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          dirPath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/merged_tiles/single_mode_mask_5000
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
        mount: true
    mask_threshold: '0.1'
    queue_size: '1'
  outputs:
    acc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/3/acc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    checkpoint:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/3/checkpoint
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    log:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/3/log.json
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    loss_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/3/loss.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_data:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/3/model_checkpoint.ckpt.data
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_index:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/3/model_checkpoint.ckpt.index
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_final:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/3/model_final.hdf5
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    roc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/3/roc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
- inputs:
    arch: '1'
    epochs: '8'
    fast_hdf5: '1'
    hdf5:
      class: Directory
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          dirPath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/merged_tiles/single_mode_mask_5000
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
        mount: true
    mask_threshold: '0.1'
    queue_size: '1'
  outputs:
    acc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/4/acc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    checkpoint:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/4/checkpoint
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    log:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/4/log.json
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    loss_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/4/loss.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_data:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/4/model_checkpoint.ckpt.data
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_index:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/4/model_checkpoint.ckpt.index
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_final:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/4/model_final.hdf5
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    roc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/4/roc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
- inputs:
    arch: '1'
    epochs: '8'
    fast_hdf5: '1'
    hdf5:
      class: Directory
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          dirPath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/merged_tiles/single_mode_mask_5000
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
        mount: true
    mask_threshold: '0.1'
    queue_size: '1'
  outputs:
    acc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/5/acc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    checkpoint:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/5/checkpoint
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    log:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/5/log.json
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    loss_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/5/loss.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_data:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/5/model_checkpoint.ckpt.data
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_index:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/5/model_checkpoint.ckpt.index
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_final:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/5/model_final.hdf5
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    roc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/5/roc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
- inputs:
    arch: '1'
    epochs: '8'
    fast_hdf5: '1'
    hdf5:
      class: Directory
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          dirPath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/merged_tiles/single_mode_mask_5000
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
        mount: true
    mask_threshold: '0.1'
    queue_size: '1'
  outputs:
    acc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/6/acc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    checkpoint:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/6/checkpoint
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    log:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/6/log.json
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    loss_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/6/loss.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_data:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/6/model_checkpoint.ckpt.data
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_index:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/6/model_checkpoint.ckpt.index
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_final:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/6/model_final.hdf5
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    roc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/6/roc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
- inputs:
    arch: '1'
    epochs: '8'
    fast_hdf5: '1'
    hdf5:
      class: Directory
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          dirPath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/merged_tiles/single_mode_mask_5000
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
        mount: true
    mask_threshold: '0.1'
    queue_size: '1'
  outputs:
    acc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/7/acc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    checkpoint:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/7/checkpoint
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    log:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/7/log.json
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    loss_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/7/loss.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_data:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/7/model_checkpoint.ckpt.data
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_index:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/7/model_checkpoint.ckpt.index
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_final:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/7/model_final.hdf5
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    roc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/7/roc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
- inputs:
    arch: '1'
    epochs: '8'
    fast_hdf5: '1'
    hdf5:
      class: Directory
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          dirPath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/merged_tiles/single_mode_mask_5000
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
        mount: true
    mask_threshold: '0.1'
    queue_size: '1'
  outputs:
    acc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/8/acc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    checkpoint:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/8/checkpoint
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    log:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/8/log.json
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    loss_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/8/loss.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_data:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/8/model_checkpoint.ckpt.data
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_index:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/8/model_checkpoint.ckpt.index
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_final:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/8/model_final.hdf5
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    roc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/8/roc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
- inputs:
    arch: '1'
    epochs: '8'
    fast_hdf5: '1'
    hdf5:
      class: Directory
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          dirPath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/merged_tiles/single_mode_mask_5000
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
        mount: true
    mask_threshold: '0.1'
    queue_size: '1'
  outputs:
    acc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/9/acc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    checkpoint:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/9/checkpoint
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    log:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/9/log.json
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    loss_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/9/loss.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_data:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/9/model_checkpoint.ckpt.data
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_checkpoint_index:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/9/model_checkpoint.ckpt.index
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    model_final:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/9/model_final.hdf5
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
    roc_plot:
      class: File
      connector:
        access:
          auth: {password: '{{cbmi_password}}', username: '{{cbmi_username}}'}
          filePath: /data/ldap/histopathologic/processed/camelyon/CAMELYON16_2019_02_06/camelyon_cnns_training_experiments/cc_sshfs_arch1_lim3_5000/9/roc.png
          host: avocado01.f4.htw-berlin.de
        command: red-connector-ssh
cli:
  baseCommand: [camelyon-cnns]
  class: CommandLineTool
  cwlVersion: v1.0
  doc: CAMELYON CNNs trains Convolutional Neural Networks on the CAMELYON image database.
  inputs:
    arch:
      doc: Architecture to use. 0=VGG16 (not working yet), 1=InceptionV3, 2=InceptionResNetV2.
      inputBinding: {prefix: --arch}
      type: string?
    batch_size_neg:
      doc: Batch size for negative examples.
      inputBinding: {prefix: --batch-size-neg}
      type: string?
    batch_size_pos:
      doc: Batch size for positive examples.
      inputBinding: {prefix: --batch-size-pos}
      type: string?
    batches_train:
      doc: Batches per train epoch.
      inputBinding: {prefix: --batches-train}
      type: string?
    batches_val:
      doc: Batches per validation epoch.
      inputBinding: {prefix: --batches-val}
      type: string?
    color_norm:
      doc: Colornormalization yes/no (1/0).
      inputBinding: {prefix: --color-norm}
      type: string?
    epochs:
      doc: Epochs to train.
      inputBinding: {prefix: --epochs}
      type: string?
    fast_hdf5:
      doc: Switch HDF5 Format to IO optimized version yes/no (1/0).
      inputBinding: {prefix: --fast-hdf5}
      type: string?
    hdf5:
      doc: File path to hdf5 file. Can also be a directory path, if the directory
        contains a file called merged.hdf5.
      inputBinding: {position: 0}
      type: Directory
    l_rate:
      doc: Number of batches to preload while training.
      inputBinding: {prefix: --l-rate}
      type: string?
    mask_threshold:
      doc: Threshold of tissue in a cropped 224x224 tile to be valid. Or threshold
        of tumor tissue in a 224x224 slide to be valid.
      inputBinding: {prefix: --mask-threshold}
      type: string?
    queue_size:
      doc: Number of batches to preload while training.
      inputBinding: {prefix: --queue-size}
      type: string?
    workers:
      doc: Number of parallel batch--generator workers. Setting this option enables
        multiprocessing.
      inputBinding: {prefix: --workers}
      type: string?
  outputs:
    acc_plot:
      doc: Validation and training accuracy per epoch.
      outputBinding: {glob: acc.png}
      type: File
    checkpoint:
      outputBinding: {glob: checkpoint}
      type: File
    log:
      doc: Log file containing performance measurements.
      outputBinding: {glob: log.json}
      type: File
    loss_plot:
      doc: Validation and training loss per epoch.
      outputBinding: {glob: loss.png}
      type: File
    model_checkpoint_data:
      outputBinding: {glob: model_checkpoint.ckpt.data*}
      type: File
    model_checkpoint_index:
      outputBinding: {glob: model_checkpoint.ckpt.index}
      type: File
    model_final:
      doc: Final Model.
      outputBinding: {glob: model_final.hdf5}
      type: File
    roc_plot:
      doc: ROC.
      outputBinding: {glob: roc.png}
      type: File
container:
  engine: nvidia-docker
  settings:
    gpus: {count: 1}
    image: {url: 'docker.io/deepprojects/camelyon-cnns:0.1.1'}
    ram: 32768
execution:
  engine: ccagency
  settings:
    access:
      auth: {password: '{{agency_password}}', username: '{{agency_username}}'}
      url: https://agency.f4.htw-berlin.de/cc
    batchConcurrencyLimit: 3
    retryIfFailed: false
redVersion: '7'