Installation of graph-tool from source

graph-tool_installation.md

INSTALLATION OF GRAPH-TOOL FROM SOURCE

System

• 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/)
• Hardware : Lenovo Thinkpad L440

Requirements as given under - http://graph-tool.skewed.de/download

1. 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
2. The Boost libraries, version 1.54 or above.
   • sudo apt-get install libboost-all-dev (http://packages.ubuntu.com/trusty/libboost-all-dev)
3. Python version 2.7 or 3 and above.
   • bash Anaconda-2.1.0-Linux-x86_64.sh
4. The expat library.
   • sudo apt-get install expat (http://packages.ubuntu.com/trusty/expat)
5. The SciPy python module.
   • Included in Anaconda's Python distribution (conda list | grep numpy)
6. The Numpy python module.
   • Included in Anaconda's Python distribution (conda list | grep scipy)
7. 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&section=all)
8. The sparsehash template library (optional, but recommended).
   • 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
9. 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&section=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)
10. The Graphviz packaged for graph drawing, with the python bindings enabled (optional, deprecated).
    • I am not installing this as it is optional.

Download graph-tool

• wget http://downloads.skewed.de/graph-tool/graph-tool-2.2.35.tar.bz2
• cd ./graph-tool-2.2.35.tar.bz2
• ./configure CPPFLAGS=-I/home/<user>/anaconda/pkgs/py2cairo-1.10.0-py27_2/include/ (http://lists.skewed.de/pipermail/graph-tool/2014-January/001145.html)
• make
• make install

DONE

Hi floriangeigl,
I tried the above, making sure I had the right g++,gcc.
Everything appears to be fine, but I get the following message when I import:

in ()
----> 1 import graph_tool

/home/tommy/anaconda2/lib/python2.7/site-packages/graph_tool/init.py in ()
103
104 from .dl_import import *
--> 105 dl_import("from . import libgraph_tool_core as libcore")
106 version = libcore.mod_info().version
107

/home/tommy/anaconda2/lib/python2.7/site-packages/graph_tool/dl_import.py in dl_import(import_expr)
55
56 try:
---> 57 exec(import_expr, local_dict, global_dict)
58 finally:
59 sys.setdlopenflags(orig_dlopen_flags) # reset it to normal case to

in ()

ImportError: /home/tommy/anaconda2/lib/python2.7/site-packages/graph_tool/../../../libgomp.so.1: version `GOMP_4.0' not found (required by /home/tommy/anaconda2/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so)

EDIT:
When I run from /usr/bin/python graph_tool works.

Hi @floriangeigl,
Thank you for the Anaconda packages! However I got into following issue during import:

import graph_tool
../../../../miniconda/envs/test-environment/lib/python2.7/site-packages/graph_tool/__init__.py:3122: in <module>
    openmp_set_schedule("static", 0)
../../../../miniconda/envs/test-environment/lib/python2.7/site-packages/graph_tool/__init__.py:3119: in openmp_set_schedule
    return libcore.openmp_set_schedule(schedule, chunk)
E   ArgumentError: Python argument types in
E       graph_tool.libgraph_tool_core.openmp_set_schedule(str, int)
E   did not match C++ signature:
E       openmp_set_schedule(std::string, int)

Any ideas?

Hi @floriangeigl,

I'm having the same problem than @olegsinyavskiy on Linux Mint 17, do you know what could be happening?

I've also tried uninstalling and installing the package againg, this time with the instructions of @v-pravin. Installation goes well, but when I call the module from python, it gives me the standard ImportError: No module named graph_tool.all. ¿Do you have any clue? Thanks!
(I could manage to install it in another PC, with Ubuntu 14.04 LTS, but I really need to install it in my office PC)

Hi,

I got the same error as @olegsinyavskiy (even when directly installing graph-tool from apt-get).

Thanks,

Hi guys (@nahuelalmeira, @olegsinyavskiy, @ttfoley) - I'm sorry I didn't notice you're writing me. I just never had a look at my github notifications.... Anyways I spend a lot of time trying to fix the anaconda pkg and some of my attempts seemed to work (at least to some extend - graph-drawing or multiprocessing mostly fucks up). The current available pkg from my anaconda channel seems to work at least for some guys (including multiproc.). However, I just found out that one can link system libs to anaconda lib. Thus, I would highly recommend to just install the graph-tool version available over apt and then link the install pkg via:

ln -s /usr/lib/python2.7/dist-packages/graph_tool /home/USER/anaconda/lib/python2.7/site-packages/graph_tool

Sry again for not responding earlier -

@ttfoley : Hi, I am encountering the same error, were you able to resolve yours? If yes, then how?

@v-pravin : Is there any significant difference while installing it in Centos 6.5 using the similar steps?

I'm also getting the same error as nahuelalmeira. What is the resolution for Windows users?

@jbrant according to graph-tool's developer, it doesn't work on windows. The solution this user found was to install Linux http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/Error-installing-graph-tool-on-windows-td4024889.html