AMBER Archive (2007)

Subject: Re: AMBER: is possible to compile pmemd using scali MPI?

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Fri Mar 30 2007 - 14:21:39 CST

Hi Andrea,

Congrats! You might also consider posting to the list what
changes/tweaks you needed to make (and of course also pass this info to
Bob Duke, as he mentioned), so that future users can benefit benefit
from your experience.

Best regards,

Gustavo.

Andrea Bortolato wrote:
> thanks a lot, I fought a bit, but finally it worked
> best
> Andrea
>
> On Thu, 29 Mar 2007 12:36:01 -0400
> "Robert Duke" <rduke_at_email.unc.edu> wrote:
>
>> Undoubtedly, but I have never had access to a machine with scali. You may
>> want to look at how it is being done in sander and see if that gives you
>> some clues as to what is required in pmemd. I presume it is mostly a matter
>> of picking up the headers and libraries correctly. Try doing a fake
>> configure of mpich (ie., run the pmemd configure command, and act like you
>> have mpich instead of scali), and then do the following to the config.h for
>> pmemd (in the pmemd subdir):
>> 1) remove -DSLOW_NONBLOCKING_MPI from the MPI_DEFINES = line
>> 2) for the MPI_LIBS line, change -lmpich to -lfmpi -lmpi
>>
>> Please let me know how this works.
>>
>> Regards - Bob Duke
>>
>> ----- Original Message -----
>> From: "Andrea Bortolato" <andrea.bortolato.1_at_unipd.it>
>> To: <amber_at_scripps.edu>
>> Sent: Thursday, March 29, 2007 12:17 PM
>> Subject: AMBER: is possible to compile pmemd using scali MPI?
>>
>>
>>> Dear all,
>>>
>>> I installed successfully amber serial and parallel in our cluster with
>>> scali MPI.
>>>
>>> however I cannot compile pmemd: is possible to compile it using scali MPI?
>>>
>>> Thank you very much and best regards
>>> Andrea
>>>
>>> ---------------------------------------

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