AMBER Archive (2005)

Subject: Re: AMBER: AMBER8 Build on Linux x64 running Opterons

From: Thomas Patko (tpatko_at_csulb.edu)
Date: Wed May 11 2005 - 10:34:18 CDT

I am not familiar with Pathscale compilers (at all) for
building pmemd, but pmemd is compiled and built completely
separately from the rest of the AMBER8 package in the new
PGI instructions for 6.0-2 (possibly incorporating many of
the recommendations from Robert Duke posted on the AMBER
website into their modified pmemd configuration scripts).
 Many files are also altered from their original forms.
 Read the PGI post very carefully for details if you are
trying the pmemd build. But finally, at least it works!

Regards,

Thomas

Graduate Student
Department of Chemistry & Biochemistry
California State University, Long Beach
Dr. Marco Lopez Research Group

On Wed, 11 May 2005 11:18:12 -0400
  "Robert Duke" <rduke_at_email.unc.edu> wrote:
> Sorry, in my last mail to the reflector (below) I forgot
>to state that the new pmemd config info is found on the
>amber.scripps.edu website...
> Regards - Bob
>
> ----- Original Message ----- From: "Robert Duke"
><rduke_at_email.unc.edu>
> To: <amber_at_scripps.edu>
> Sent: Wednesday, May 11, 2005 11:14 AM
> Subject: Re: AMBER: AMBER8 Build on Linux x64 running
>Opterons
>
>
>> You may want to look at the 'March 2005 configuration
>>update for PMEMD'.
>> The config files for pmemd are different than the ones
>>used by all the
>> rest of amber, mostly in that more aggressive
>>optimization is sometimes
>> used. However, I think that for pathscale compilers,
>>chances are good that
>> the compilers options/libraries listed here will get you
>>started (I think
>> that pathscale is easy in that you don't need to
>>reference the compiler
>> libraries explicitly); you should of course leave out
>>the pmemd
>> optimization defines (-D...), though I doubt that
>>including them is
>> harmful. I found pathscale to be very easy to use and
>>solid.
>> Regards - Bob Duke
>>
>> ----- Original Message -----
>> From: "Mark Rance" <rance_at_rabi.med.uc.edu>
>> To: <amber_at_scripps.edu>
>> Sent: Wednesday, May 11, 2005 11:02 AM
>> Subject: Re: AMBER: AMBER8 Build on Linux x64 running
>>Opterons
>>
>>
>>>I encountered the same problem Thomas has reported, with
>>>xleap compiling
>>> ok
>
>
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