Re: namd2.7b1 slower with openmpi 1.3.2 than namd2.6 with openmpi 1.2.6

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jul 03 2009 - 13:42:08 CDT

dear vlad,

> Both openmpi and mvapich2 I compiled myself with infiniband support
> using same compiler. the flags used for the compilation of openmpi 1.3.2
> were exactly the same as those used for the old compilation of openmpi
> 1.2.6.
>
> Is there a reason for the drop in performance when compiled with openmpi
> 1.3.2 ?

i've heard similar reports with other codes. perhaps openmpi 1.3
and 1.2 have somewhat different default settings and efficiencies for
the choice of some algorithms (particularly collectives). depending on
hardware (OpenMPI does adjust some of its settings to the individual
 HCA) you may just run into less optimal algorithms for your particular
 usage and hardware. there are a large number of parameters in the
 openib layer of OpenMPI that can be used to tweak the algorithms.
check out: ompi_info -a

cheers,
   axel.

> Best wishes
> Vlad
>
>

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
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