CandidateVectorSearch 1.7.2
Searching for peptide candidates using sparse matrix + matrix/vector multiplication.
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Compilation on Ubuntu 22.04 (and other Linux-based systems)

This is a rough guide for compiling CandidateVectorSearch on Ubuntu, which should generally work on most Linux-based systems.

Installing dependencies

The following dependencies are required for compilation:

  • gcc / g++: sudo apt-get install -y gcc g++
  • dotnet [more info]:
    • dotnet-sdk-6.0: sudo apt-get install -y dotnet-sdk-6.0
    • dotnet-runtime-6.0: sudo apt-get install -y dotnet-runtime-6.0
  • Additional dependencies may be required, please check Dockerfile to see a full list!

Alternatively, a Docker image with all necessary build tools is also available via Dockerfile:

  • Build the Dockerfile: docker build . -f Dockerfile -t cvs
  • Run the container: docker run -it cvs

Building the matrix multiplication backend (C++)

To build the C++ library used for matrix multiplication the following steps are required:

  • Navigate to the VectorSearch directory: cd VectorSearch
  • Build the DLL: g++ -shared -I eigen-3.4.0 -fPIC -fopenmp -O3 -o VectorSearch.dll dllmainUnix.cpp

Building the prototype testing suite (C#)

To build the C# testing application the following steps need to be carried out:

  • Navigate to the DataLoader directory: cd DataLoader
  • Build the executable: dotnet publish DataLoader.csproj --runtime ubuntu.22.04-x64 --self-contained --configuration Release
  • [Alternatively: dotnet publish DataLoader.csproj --runtime linux-x64 --self-contained --configuration Release]

Running the executable

  • Copy VectorSearch.dll to the build directory of DataLoader.
  • Run the executable. For example with ./DataLoader EigenSIntB 10000.
  • Note that we only supply the compiled binaries for CPU-based search. If you want to run GPU-based searches please compile VectorSearchCUDA yourself!

Running the executable without building / compiling yourself

We provide compiled binaries in DataLoaderExecutable/ubuntu22.04_x64 and in the Releases tab. Please again note that we only supply the compiled binaries for CPU-based search. If you want to run GPU-based searches please compile VectorSearchCUDA yourself! Running the compiled binaries requires dotnet-runtime-6.0 and g++.