Hello,
I have successfully installed graph-tool on Ubuntu 1310 using apt-get. So it works with the default python of the system. However, I would like to use it with the python included in the Anaconda distribution.
Can anybody please help how to do that? Does it need to be compiled from source in that case?
Thanks very much, Eszter
Hello,
You might consider setting up virtual environment where your anaconda version resides, there is an option to use system packages within this environment. On a similar setup, I had to uninstall the system's matplotlib to avoid libraries beeing mixed up while using graph-tool.
Guillaume
On 29/11/2013 16:58, Csernai, Eszter wrote:
Hello,
I have successfully installed graph-tool on Ubuntu 1310 using apt-get. So it works with the default python of the system.
However, I would like to use it with the python included in the Anaconda distribution.
Can anybody please help how to do that? Does it need to be compiled from source in that case?
Thanks very much,
Eszter
graph-tool mailing list graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool
On 11/29/2013 04:58 PM, Csernai, Eszter wrote:
Hello,
I have successfully installed graph-tool on Ubuntu 1310 using apt-get. So it works with the default python of the system.
However, I would like to use it with the python included in the Anaconda distribution.
Can anybody please help how to do that? Does it need to be compiled from source in that case?
If the anaconda python version is not the same as the system default, you will need to compile graph-tool from source. In that case just pointing the configure script to the desired python interpreter should work. Note also that you probably may also need to compile Boost python against the same python version.
Cheers, Tiago
Thank you! I am trying to compile graph-tool from source, but I don't have much experience in building software from source. The machine is the mentioned Ubuntu 13.10 running in Virtualbox. The Anaconda python version is 2.7.6 (I specified this in the PYTHON environment variable and the configure script seems to understand it). It seems all dependencies are satisfied, and the virtual machine is allocated quite a lot of memory (8GB). I get this error:
make[4]: Entering directory `/.../graph-tool-2.2.27/src/graph/centrality' CXX graph_betweenness.lo CXX graph_closeness.lo CXX graph_eigentrust.lo CXX graph_eigenvector.lo CXX graph_hits.lo CXX graph_katz.lo CXX graph_pagerank.lo virtual memory exhausted: Cannot allocate memory make[4]: *** [graph_pagerank.lo] Error 1
Any ideas how to solve this?
Thank you, Eszter
-----Original Message----- From: graph-tool [mailto:graph-tool-bounces@skewed.de] On Behalf Of Tiago de Paula Peixoto Sent: Saturday, November 30, 2013 9:50 PM To: Main discussion list for the graph-tool project Subject: Re: [graph-tool] Installing graph-tool to use with Anaconda
On 11/29/2013 04:58 PM, Csernai, Eszter wrote:
Hello,
I have successfully installed graph-tool on Ubuntu 1310 using apt-get. So it works with the default python of the system.
However, I would like to use it with the python included in the Anaconda distribution.
Can anybody please help how to do that? Does it need to be compiled from source in that case?
If the anaconda python version is not the same as the system default, you will need to compile graph-tool from source. In that case just pointing the configure script to the desired python interpreter should work. Note also that you probably may also need to compile Boost python against the same python version.
Cheers, Tiago
-- Tiago de Paula Peixoto tiago@skewed.de
On 12/03/2013 04:22 PM, Csernai, Eszter wrote:
Thank you! I am trying to compile graph-tool from source, but I don't have much experience in building software from source. The machine is the mentioned Ubuntu 13.10 running in Virtualbox. The Anaconda python version is 2.7.6 (I specified this in the PYTHON environment variable and the configure script seems to understand it). It seems all dependencies are satisfied, and the virtual machine is allocated quite a lot of memory (8GB). I get this error:
make[4]: Entering directory `/.../graph-tool-2.2.27/src/graph/centrality' CXX graph_betweenness.lo CXX graph_closeness.lo CXX graph_eigentrust.lo CXX graph_eigenvector.lo CXX graph_hits.lo CXX graph_katz.lo CXX graph_pagerank.lo virtual memory exhausted: Cannot allocate memory make[4]: *** [graph_pagerank.lo] Error 1
Any ideas how to solve this?
8GB ram should be more than enough to compile it. What GCC version are you using? Are you compiling it in parallel (with the -j option)?
Cheers, Tiago
I got some help from a sysadmin colleague -- turned out the problem was that the virtual machine was 32 bit, so it could not use all the allocated memory. I am sure it will work on a 64 bit one.
Thank you for the quick responses, Eszter
________________________________________ From: graph-tool [graph-tool-bounces@skewed.de] on behalf of Tiago de Paula Peixoto [tiago@skewed.de] Sent: Wednesday, December 04, 2013 10:58 AM To: Main discussion list for the graph-tool project Subject: Re: [graph-tool] Installing graph-tool to use with Anaconda
On 12/03/2013 04:22 PM, Csernai, Eszter wrote:
Thank you! I am trying to compile graph-tool from source, but I don't have much experience in building software from source. The machine is the mentioned Ubuntu 13.10 running in Virtualbox. The Anaconda python version is 2.7.6 (I specified this in the PYTHON environment variable and the configure script seems to understand it). It seems all dependencies are satisfied, and the virtual machine is allocated quite a lot of memory (8GB). I get this error:
make[4]: Entering directory `/.../graph-tool-2.2.27/src/graph/centrality' CXX graph_betweenness.lo CXX graph_closeness.lo CXX graph_eigentrust.lo CXX graph_eigenvector.lo CXX graph_hits.lo CXX graph_katz.lo CXX graph_pagerank.lo virtual memory exhausted: Cannot allocate memory make[4]: *** [graph_pagerank.lo] Error 1
Any ideas how to solve this?
8GB ram should be more than enough to compile it. What GCC version are you using? Are you compiling it in parallel (with the -j option)?
Cheers, Tiago
-- Tiago de Paula Peixoto tiago@skewed.de
-
Csernai, Eszter -
Guillaume Gay -
Tiago de Paula Peixoto