I just start a project with Library MCS.
I work on a dataset of 8000 compounds in a mol2 file, and when I open with LibMCS, a dendogram appears on the top of the GUI and a message 'Calculating Library MCS' on the bottom. The prevision of computational time is around 90 hours !! Is that trivial ?
So far, the program run since 18 hours and 9% of the data are completed.
This can happen... in particular if compund set is very diverse or contains large structures. Perhaps you may with to tweak some parameters that affects the performance indirectly. These are gathered in Cluster->Options dialogue. Try to tune the minimum mcs size to let's say 7. Also, on the Clustering Options tab of the same dialog window increase the Required cluster count to few 10 or even few 100 if input has high intrinsic diversity and decrease the Maximum level count to 4.
Does this help?