Building mothur-1.39.5 with MPI on CentOS

mothur bugs
1

I am trying to build 1.39.5 mothur with MPI enabled on a CentOS cluster but I just can not work out how to build it with MPI. The https://www.mothur.org/wiki/Installation guide says to change USEMPI to yes for Mac but this line does not exist in the linux source code makefile?

Or is the Linux version automatically MPI? What about the prebuild one?

I have looked through this forum, but could not find any information regarding my problem.

I am feeling very silly, I hope someone can enlighten me.

Thank you

Mana

2

You don’t need MPI. None of the algoirthms we have actually benefit from using MPI over the normal “processors=” option.

Pat

3

Thank you for the information. We had just seen that running mothur with the normal processor option had resulted in mothur using only one processor independent of how many processors we had specified. I had read that can happen if it had been build with MPI so I wanted to test it.

If, as I assume, the prebuild is not MPI build than the problem should be somewhere else and I will check other options.

Kind regards,

Mana

4

Not all of the commands use multiple processors and even when they do, some processors may end earlier than others.

Pat