use MPI for server and shhh.flows

Theory behind mothur
1

Hello,

Could you please tell me if it is possible run mothur with MPI option in a server (not cluster)? I am trying to run shhh.flows using your advice, use mpirun -np x “#shhh.flows(…)”. If this is possible, could you help me to interpret this error?

-bash: runmpi: command not found
sgaraycochea@INIA-LB-SLES11SP2:~/Metagenomica_suelos/Analisis_mothur> ./runmpi mothur_MPI
-bash: ./runmpi: No such file or directory
sgaraycochea@INIA-LB-SLES11SP2:~/Metagenomica_suelos/Analisis_mothur> ./mothur_MPI
librdmacm: couldn’t read ABI version.
librdmacm: assuming: 4
CMA: unable to get RDMA device list

WARNING: Failed to open “OpenIB-cma” [DAT_INTERNAL_ERROR:].
This may be a real error or it may be an invalid entry in the uDAPL
Registry which is contained in the dat.conf file. Contact your local
System Administrator to confirm the availability of the interfaces in
the dat.conf file.


Thank you very much
2

It looks like the error message is just a typo, http://linux.die.net/man/1/mpirun.

Here’s the basic format for mpirun:
mpirun -np

sgaraycochea@INIA-LB-SLES11SP2:~/Metagenomica_suelos/Analisis_mothur> ./runmpi mothur_MPI

As a side note, we have found our MPI version to slower than the NON-MPI version, and will be removing the source from mothur for our next version. You might try the regular version and use multiple processors, https://github.com/mothur/mothur/releases/tag/v1.36.1.