I know this been posted befor but not sure if here was a solution.
I just downloaded and compiled the MPI version of mothur v.1.24.1
and tried running the following command
mpirun -np 8 mothur.mpi "#shhh.flows(file=03092012Lanoil.flow.files)"
It seems to get submitted ok (see below) but hangs when calculating distances. All 8 processors are showing 100% usage.
I am running it on a Debian 6.0.1 (Squeeze) cluster with dual 8 Core AMD64 processors with openMPI installed.
--------------------------------------------------------------------------
[[30899,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:
Module: OpenFabrics (openib)
Host: bioinfor1
Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
mothur v.1.24.1
Last updated: 3/16/2012
by
Patrick D. Schloss
Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org
When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.
Distributed under the GNU General Public License
Type 'help()' for information on the commands that are available
Type 'quit()' to exit program
mothur > shhh.flows(file=03092012Lanoil.flow.files)
Unable to open LookUp_Titanium.pat. Trying default /usr/bin/LookUp_Titanium.pat
Getting preliminary data...
>>>>> Processing /home/bioinfor1/lleclair/mothur.bat/sff/03092012Lanoil.ResH.flow (file 1 of 1) <<<<<
Reading flowgrams...
Identifying unique flowgrams...
Calculating distances between flowgrams...
If the run the command on a single processor then it seem work to work ok
mpirun -np 1 mothur.mpi “#shhh.flows(file=03092012Lanoil.flow.files)”