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DeepMASS2 Distributed System

1. Environment Dependencies(Central Server、Subserver、User Interface)

  1. Clone the repository and navigate into it:

    git clone https://github.com/hcji/DeepMASS2_GUI.git
cd DeepMASS2_GUI

  2. Create and activate the Conda environment:

    conda env create -f environment.yml
conda activate deepmass

  3. Install additional dependencies:

    pip install cryptography

  4. Model and database files (only required when running client.py on subservers)

Download the following files and place them in the model/ directory: dependent data

Ms2Vec_allGNPSnegative.hdf5
Ms2Vec_allGNPSnegative.hdf5.syn1neg.npy
Ms2Vec_allGNPSnegative.hdf5.wv.vectors.npy
Ms2Vec_allGNPSpositive.hdf5
Ms2Vec_allGNPSpositive.hdf5.syn1neg.npy
Ms2Vec_allGNPSpositive.hdf5.wv.vectors.npy

Reference Database (Optional)

  • If you do not have a custom database, place all the following files in the data/ directory: dependent data

    DeepMassStructureDB-v1.1.csv
references_index_negative_spec2vec.bin
references_index_positive_spec2vec.bin
references_spectrums_negative.pickle
references_spectrums_positive.pickle

  • If you use a custom database:

    • Keep DeepMassStructureDB-v1.1.csv unchanged in the data/ directory.
    • Replace the .pickle and .bin files with your own data (you may keep the original filenames).
    • Or update the paths in client.py to point to your custom files.

Important

Refer to vectorize_reference_by_ms2vec.py to regenerate each .bin file from its corresponding .pickle file.

Note: Step 4 is only required when running client.py.

2. Deployment Architecture

Role Script Startup Example
Central Server server.py python server.py <SERVER_IP> <REG_PORT> <FILE_PORT>
Subserver client.py python client.py <SERVER_IP> <REG_PORT> <FILE_PORT> <CLIENT_IP> <CLIENT_FILE_PORT>
User Interface DistributedDeepMASS2.py In the GUI prompt, enter <SERVER_IP>:<FILE_PORT> and run
  • CENTRAL_SERVER_IP: IP address of the central server (e.g., 192.168.1.10)
  • SUBSERVER_IP: IP address of each subserver (e.g., 192.168.1.3, 192.168.1.4, …)
  • REG_PORT: Port for subserver registration (e.g., 5001)
  • FILE_PORT: Port for user file uploads on the central server (e.g., 5002)
  • CLIENT_FILE_PORT: Port on each subserver for listening to file requests (e.g., 6001, 6002, …)

3. Usage Steps

1. Check Local IP

  • Linux:

    ip addr show   # or `hostname -I`

  • Windows:

    ipconfig

Look for the inet / IPv4 Address entry to find your LAN IP.

2. Start the Central Server

Run on the central server (e.g., at IP 192.168.1.10):

cd DeepMASS2_GUI/server
python server.py 192.168.1.10 5001 5002
  • Listening for registrations: 5001
  • Listening for user file uploads: 5002

3. Start Subservers (Multiple Instances Supported)

Run on the subserver (e.g., at IP 192.168.1.3):

cd DeepMASS2_GUI
python client.py 192.168.1.10 5001 5002 192.168.1.3 6001
  • 192.168.1.10: Central server IP
  • 5001: Registration port
  • 5002: User file upload port
  • 192.168.1.3: This subserver’s IP
  • 6001: File service listening port on this subserver

Subservers will automatically register with the central server upon startup.

4. Start the User Interface

cd DeepMASS2_GUI
python DistributedDeepMASS2.py
  1. Click IP Address, then enter the central server’s IP and file-port in the format <SERVER_IP>:<FILE_PORT> (for example, 192.168.1.10:5002).
  2. Click Open to upload your mass spectrometry file.
  3. Click Run DeepMASS to encrypt and upload your file to the central server, which then distributes it to all subservers.
  4. To save results, click Save to export them as CSV files.