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

From: liupeng012 (
Date: Sat Jul 04 2009 - 21:17:15 CDT

Dear alex:
  yes! i use the command: ompi_info -a, check the setting of opneib.
  there is a plenty of parameter.

  which one is significant ?



发件人: Axel Kohlmeyer
发送时间: 2009-07-04 18:56:06
收件人: Vlad Cojocaru
抄送: NAMD list
主题: Re: namd-l: namd2.7b1 slower with openmpi 1.3.2 than namd2.6 withopenmpi 1.2.6

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


> Best wishes
> Vlad

Axel Kohlmeyer
   Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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