- OS : Ubuntu 14.04.1 LTS Desktop 64-bit (http://www.ubuntu.com/download/alternative-downloads#external)
- Python Distribution : Anaconda Python (https://store.continuum.io/cshop/anaconda/)
If you have gcc > 5.0 installed on your server you can use my anaconda package which I compiled with openmp and boost 1.60:
just use conda install graph-tool -c floriangeigl -c msarahan -c conda-forge -c bioconda -c ostrokach -c vgauthier -c salford_systems to install it.
How to install gcc-5 on Ubuntu 14.04: http://askubuntu.com/questions/618474/how-to-install-the-latest-gcurrently-5-1-in-ubuntucurrently-14-04
Requirements as given under - http://graph-tool.skewed.de/download
- GCC, version 4.8 or above (version 4.9 is recommended). For MacOS X, the clang compiler is required.
sudo apt-get install gcc-4.8
- The Boost libraries, version 1.54 or above.
- using apt (may not be up-to-date)
sudo apt-get install libboost-all-dev(http://packages.ubuntu.com/trusty/libboost-all-dev)
- OR for boost:coroutines install newest boost from http://www.boost.org/users/download/
- run ./bootstrap.sh
- install to opt
./b2 install --prefix=/opt/boost
- using apt (may not be up-to-date)
- Python version 2.7 or 3 and above.
bash Anaconda-2.1.0-Linux-x86_64.sh
- The expat library.
sudo apt-get install expat(http://packages.ubuntu.com/trusty/expat)
- The SciPy python module.
- Included in Anaconda's Python distribution (
conda list | grep numpy)
- Included in Anaconda's Python distribution (
- The Numpy python module.
- Included in Anaconda's Python distribution (
conda list | grep scipy)
- Included in Anaconda's Python distribution (
- The CGAL C++ geometry library, version 3.5 or above.
sudo apt-get install libcgal*(http://packages.ubuntu.com/search?keywords=cgal&searchon=names&suite=trusty§ion=all)
- The sparsehash template library (optional, but recommended).
- using apt
sudo apt-get install sparsehash
- OR
- https://git.skewed.de/count0/graph-tool/issues/105
wget https://sparsehash.googlecode.com/files/sparsehash_2.0.2-1_amd64.deb(https://code.google.com/p/sparsehash/)sudo dpkg -i ./sparsehash_2.0.2-1_amd64.deb
- using apt
- The cairomm, pycairo and matplotlib libraries, used for graph drawing (optional).
sudo apt-get install libcairomm-*(http://packages.ubuntu.com/search?keywords=cairomm&searchon=names&suite=trusty§ion=all)conda install py2cairo(http://repo.continuum.io/pkgs/free/linux-64/index.html)- Matplotlib - Included in Anaconda's Python distribution (
conda list | grep matplotlib)
- The Graphviz packaged for graph drawing, with the python bindings enabled (optional, deprecated).
- I am not installing this as it is optional.
wget http://downloads.skewed.de/graph-tool/graph-tool-2.2.35.tar.bz2cd ./graph-tool-2.2.35.tar.bz2./configure CPPFLAGS=-I$(find /PATH_TO_ANACONDA/pkgs -regextype posix-extended -regex ".*py[0-9]+cairo.*/include" -type d | head -1) --enable-openmp- add if you compiled boost on your own
--with-boost=/opt/boost LDFLAGS="-L/opt/boost/lib" CPPFLAGS="-I/opt/boost/lib"
- add if you compiled boost on your own
makemake install
DONE
I have gcc 5.4 installed and installed your anaconda package with
conda install graph-tool -c floriangeigl -c msarahan -c conda-forge -c bioconda -c ostrokach -c vgauthier -c salford_systems -n graph-toolI can
import graph_toolwithout problems, butfrom_graph_tool import inferencewill giveWhat's happening here? (installed packages as follows:)