Motif algorithms do not run in parallel
Hi, when I run the motif
and motif_significance
function on a graph, the algorithm didn't run in parallel. I have specified the --enable-openmp
flag during the configuration. This is the config.log.
My system:
Ubuntu 16.04.1 LTS (xenial)
Linux 4.4.0-31-generic
gcc 5.4.0
Code:
from graph_tool.all import motif_significance, load_graph_from_csv
bc = load_graph_from_csv('blogcatalog.edges', directed=False, csv_options={'quotechar': '"', 'delimiter': ' '})
m, z = motif_significance(bc, k=4, n_shuffles=10)
The graph has 10,312 nodes and 333,983 edges. The edgelist can be obtained here. I tried to run this small piece of code and monitor the process using Ubuntu's System Monitor to see the CPU usage and I expect the algorithm to utilize multiple threads. However, only one thread was used for computation.
I am not sure if I configured the graph-tool
installation correctly. Could you point out where did I get it wrong. Thank you very much for your time!