PFLOTRAN options

[Chunhui He]

Hi,

There are many options in PFLOTRAN makefile, such as hdf5-vamsi, uo2, glenn ......

What is the meaning of these options? When do I need to turn on these options?

( I have found chuan_co2,coll,temp,dasvyat  in user manual, but I still do not very clear.)

Thanks,

Chunhui

[sw wang]

I have same questions,what's the meaning of those options? and in what situations should i turn on those options?

anyone  knows?

2012/10/2 Chunhui He <iuhn...@gmail.com>

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[Richard Tran Mills]

Hello All,

Whenever we are adding code to PFLOTRAN that is deemed "experimental", we protect that code with preprocessor directives.  Yes, there are a lot... we are probably overdue to go through the code and make some of those currently optional bits of cod part of the regular code base.

The only option that teams may want to explore is enabling the 'hdf5-vamsi' option:

  make hdf5-vamsi=1 pflotran

This will enable two-phase collective IO, which is very briefly described in the paper at

  http://climate.ornl.gov/~rmills/pubs/Mills_SciDAC2010.pdf

This speeds up IO very dramatically on some large machines and tends not to make much of a difference on smaller ones.

(By the way, I do know that I need to look into a bug that causes a crash of the 5-spot example when scaling up the problem size sometimes.  At the default size, it is really a single-core example and IO optimizations certainly won't matter.)

Best regards,
Richard

-- 
Richard Tran Mills, Ph.D.
Computational Earth Scientist      | Joint Assistant Professor
Hydrogeochemical Dynamics Team     | EECS and Earth & Planetary Sciences
Oak Ridge National Laboratory      | University of Tennessee, Knoxville
E-mail: rmi...@ornl.gov  V: 865-241-3198 http://climate.ornl.gov/~rmills