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Installation

Installation using Conda

The easiest way to install SMURFF is to use Conda:

conda install -c vanderaa smurff

From source on Linux or MacOs

Building using cmake

Before continuing installation please check that

  • cmake version is at least 3.6
  • eigen3 version 3.3.3 or later is installed.

This is required due to the fixed Find scripts for BLAS libraries that are present in latest version.

Next, cmake has multiple switches:

  • Build type switches:
    • CMAKE_BUILD_TYPE - Debug/Release
  • Algebra library switches (select only one):
    • When no switches are specified, CMake will try to find any LAPACK and BLAS library on your system.
    • ENABLE_OPENBLAS - ON/OFF (should include openblas library when linking. openblas also contains implementation of lapack called relapack)
    • ENABLE_MKL - ON/OFF: tries to find the MKL single dynamic library.

Run CMake:

# install dependencies:
sudo apt-get install libopenblas-dev autoconf gfortran

# checkout and install Smurff
git clone https://github.com/ExaScience/smurff.git
cd smurff/lib/smurff-cpp/
mkdir build
cd build
cmake ../cmake -DENABLE_OPENBLAS=ON -DCMAKE_BUILD_TYPE=Debug
make
make test

# test the command-line program:
wget http://homes.esat.kuleuven.be/~jsimm/chembl-IC50-346targets.mm
Debug/smurff --train chembl-IC50-346targets.mm

The last command running smurff will be very slow, since we have compiled smurff in Debug mode.

Install command line smurff and Python package

Install:

make install
cd python/Smurff
python setup.py install

Test scripts for python are in smurff/python/smurff/tests. When the python package has been installed correctly, you can run python -m unittest discover in this directory.

From source on Windows

Before continuing installation please check that
  • cmake version is at least 3.6
  • Visual Studio version is 2013 or better 2015 because code uses some c++11 features

Install boost

Download latest version of boost from http://www.boost.org/

Start Visual Studio command prompt and execute the following commands.

bootstrap.bat
b2 toolset=msvc-14.0 address-model=64 --build-type=complete stage

This will compile and install boost libraries into build directory.

If you have Visual Studio different from 2015 - select proper toolset.

Configure boost environment variables as in the example:

BOOST_INCLUDEDIR=E:\boost_1_65_0
BOOST_LIBRARYDIR=E:\boost_1_65_0\stage\lib

Install eigen3

Execute the following commands from command prompt:

git clone https://github.com/RLovelett/eigen.git
cd eigen
mkdir build
cd build
cmake ../ -G "Visual Studio 14 2015 Win64"

If you have Visual Studio different from 2015 - select proper generator.

Build INSTALL target in Visual Studio in Release configuration.

This will build all projects and install them in Program Files by default.

Configure eigen3 environment variables as in the example:

EIGEN3_INCLUDE_DIR=C:\Program Files\Eigen3\include\eigen3

Install MinGW-64

MinGW-64 is required to build OpenBLAS library. MinGW-64 is chosen because it is easy to install fortran compiler dependency. Fortran compiler is requried for building ReLAPACK part of OpenBLAS. Other option (not described here) is to install fortran compiler directly. There are few binary distributions described here: http://fortranhelp.blogspot.ru/2010/09/i-have-just-installed-gfortran-on.html

Download installer at http://www.msys2.org/

Configure msys2 exactly as described in the guide.

Install corresponding packages with pacman

pacman -S gcc
pacman -S gcc-fortran
pacman -S make
pacman -S autoconf
pacman -S automake

Add path to MinGW-64 binaries to PATH variable as in the example:

C:\msys64\usr\bin

Install OpenBLAS

Open MinGW-64 command prompt

Execute the following commands:

git clone https://github.com/xianyi/OpenBLAS.git
cd OpenBLAS
make
make PREFIX=/e/openblas_install_64 install

You can change installation prefix if you want.

Set environment variables as in the example:

BLAS_INCLUDES=E:\openblas_install_64\include
BLAS_LIBRARIES=E:\openblas_install_64\lib\libopenblas.dll.a

Add path to OpenBLAS binaries as in the example:

E:\openblas_install_64\bin

Install Smurff

Execute the following commands from command prompt:

git clone https://github.com/ExaScience/smurff.git
cd smurff\lib\smurff-cpp\cmake
mkdir build
cd build
cmake ../ -G "Visual Studio 14 2015 Win64" -DENABLE_OPENBLAS=ON -DENABLE_VERBOSE_COMPILER_LOG=ON

If you have Visual Studio different from 2015 - select proper generator.

Build INSTALL target in Visual Studio in Release configuration.

This will build all projects and install them in Program Files by default.