Problems Using Dnaclust With Multithreaded Options On A Metagenomic Sample

Question

[arnauvich]

Hi,

I'm trying to use Dnaclust software to bin a metagenomic sample. The program works well but the multithread options seems to fail. Maybe is a compilation error, because, when I compile I get the following error:

dnaclust.cpp:1312:12: warning: variable ‘num_threads_to_use’ set but not used [-Wunused-but-set-variable]
dnaclust.cpp:1418:11: warning: variable ‘num_threads_to_use’ set but not used [-Wunused-but-set-variable]
dnaclust.cpp: In function ‘int main(int, char**)’:
dnaclust.cpp:1862:11: warning: variable ‘num_threads_to_use’ set but not used [-Wunused-but-set-variable]
dnaclust.cpp:2000:14: warning: variable ‘num_threads_to_use’ set but not used [-Wunused-but-set-v

I will appreciate any idea or suggestions. Thank you very much!

Cheers.

[Istvan Albert]

warnings are not errors, do you get a compile or runtime error?

[arnauvich]

No, any error, the compilation is OK, but the multi-thread option doesn't work

[Istvan Albert]

Often this is enabled in the makefile - check inside

[Martin A Hansen]

Dnaclust looked very promising when published, alas it appears orphaned. You can use Uclust or CD-HIT instead, the latest CD-HIT have impressive performance.

[arnauvich]

Thanks. Actually I'm comparing these algorithms to find the best option, and Dnaclust (as you say) looked promising, but without running multi thread option it takes at least 1 hour to clust 1 milion reads...

[arnauvich]

I have been following the behaviour of the program with "top", and most of the time it use one core at 100%, but in short periods of time uses different numbers of cores but never using more than 100% of total CPU for the process ( f.e 2 cores at 60% and 40%). How can I make to use more than one core for this process?