hamedmx/bsf-py

Python wrapper for Blazing Signature Filter

bsf-py: Python wrapper for Blazing Signature Filter

The Blazing Signature Filter (BSF) is a highly efficient pairwise similarity algorithm which enables extensive data mining within a reasonable amount of time.

How to install

1. Install python. Python3+ and conda recommended. Please refer to https://conda.io/docs/download.html and https://www.continuum.io/downloads.
2. Clone this repository. Go to the desired folder and clone it as follows:

git clone --recursive https://github.com/PNNL-Comp-Mass-Spec/bsf-py

The 'bsf-core' is a submodule for this repository so that this command will recursively clone the 'bsf-core' too.

3. Install BSF package. You can select either -DBSF_XOR or -DBSF_AND as a build option.

python setup.py build_ext -DDEBUG -DBSF_AND install

• NOTE: This python package contains the C extention module for C++ library of BSF. We employ the OpenMP (Open Multi-Processing) 4.0 specification and C++11 standard for BSF. Therefore, if you don't have any C/C++ compiler which supports these, please install GCC 4.9 or newer.

Also, you can explicitly set a valid compiler path or name on the command line as below.

CC=g++-4.9 CXX=g++-4.9 python setup.py build_ext -DDEBUG -DBSF_AND install

After installing, it will automatically run the unit test.

4. Run the test via jupyter notebook

jupyter notebook

On browsers, you can access the tree GUI.

http://localhost:8888/

Docker version

Docker is a container platform which enables to deliver the software pipeline as a vitually isolated environment. In other words, without any concerns about the version of c++ compilers and python packages, you can easily build the same environment by running a docker image. You can find more information in here. Please refer to this documentation for getting started and this user guide for more details.

1. Install the latest docker in your machine. Please refer to https://docs.docker.com/engine/installation/.
2. Pull the BSF image.

docker pull coldfire79/bsf-py

3. Run the BSF image.

docker run -i -t --name bsf coldfire79/bsf-py /bin/bash

4. Run python and import BSF.

root@3d0db695399b:/tmp/bsfpy# python

You can see the python prompt. Then you can get started via following the next tutorial example.

import bsf

Also, you can simply run the unit test to check out the installation.

root@3d0db695399b:/tmp/bsfpy# python tutorial/test_bsf.py

Tutorial

Please refer to this tutorial.

License

BSD License.

Install GCC 4.9 or newers

MAC

Unfortunately, for the MAC users, the project to support the OpenMP 4.0 specification in the Clang C language family front-end for the LLVM compiler is still going on. They don't fully support yet. Please refer to this link. However, you can install GCC 4.9 with Homebrew. It's tested on Yosemite and macOS Sierra.

brew update
brew install gcc49

If you have the following trouble to install GCC 4.9 due to no permission, please try to change the ownership and make a link again as follows.

sudo chown -R $USER /usr/local/lib /usr/local/include /usr/local/bin /usr/local/Cellar /usr/local/share/
brew link [email protected]

Linux/Unix

Basically, the most latest linux kernels (Debian:jessie, Ubuntu, CentOS, ...) support the GCC 4.9 or later. But if you don't have one, please refer to the below. If you have better ideas, please feel free to share that with us.

Debian:jessie

sudo apt-get update
sudo apt-get install gcc-4.9 g++-4.9

Ubuntu

sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install gcc-4.9 g++-4.9
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9

CentOS

sudo yum install libmpc-devel mpfr-devel gmp-devel

cd ~/Downloads
curl ftp://ftp.mirrorservice.org/sites/sourceware.org/pub/gcc/releases/gcc-4.9.2/gcc-4.9.2.tar.bz2 -O
tar xvfj gcc-4.9.2.tar.bz2

cd gcc-4.9.2
./configure --disable-multilib --enable-languages=c,c++
make -j 4

make install

Windows

You can install GCC through cygwin now. Please refer to this link to install cygwin on windows.

Troubleshooting

1. Install BSF but cannot import bsf in python prompt.

with some error message as follows:

ImportError: /path/to/anaconda3/lib/python3.6/site-packages/bsf.cpython-36m-x86_64-linux-gnu.so: undefined symbol: GOMP_parallel

That's because you don't have correct gmp or gomp library for supporting OpenMP. In general, you should have these when you install gcc through the stable package installation, such as apt-get, yum, and brew. Otherwise, you need to install these dependencies. In this case, you can just try to install gcc through conda package system. It assumes that you have installed anaconda for your python.

Please refer to the following commands.

# remove the bsf package first.
pip uninstall bsf
conda install -y gcc

And you can see it will install the following new dependent packages.

    cloog: 0.18.0-0
    gcc:   4.8.5-7
    gmp:   6.1.0-0
    isl:   0.12.2-0
    mpc:   1.0.3-0
    mpfr:  3.1.5-0