thanks- Dan will fix this now. We will leave rem available in serial
so we can write a useful error message, but REMD will only work in MPI.
should be fixed later today.
I have no idea what the ncsu code does or how it fits into REMD.
carlos
On Dec 21, 2007 1:17 PM, David A. Case <case.scripps.edu> wrote:
> I've checked in changes from Volodymyr, and for me, both serial and
> parallel
> codes now compile. But I had to make some tweaks, and there seems to be
> cross-purposes about the "rem" variable:
>
> In multisander (and elsewhere in Dan's code I think), rem gets set and
> passed
> around only when MPI is set. It's not clear to me what happens when MPI
> is not set (it's in the code: I just haven't studied carefully enough to
> figure it out.) There clearly seem to be places where it is assumed that
> rem
> and remd variables are only available under MPI.
>
> There is a comment in remd.f that indicates that some variables might be
> available without MPI, but I'm not yet convinced that this is consistently
> handled.
>
> The force.f routine uses the rem variable when LES is turned on, even if
> MPI
> is not set. I put in a declaration just to make the code compile, but
> this
> needs to be looked at -- if the intent is to disable simulatneous rem and
> LES
> (?), that should be done once (presumably in mdread.f) and not everywhere
> inside force.f. If there is some other intent, things should be commented
> and
> fixed.
>
> The ncsu stuff uses the "rem" variable, but in serial mode this is
> probably
> not available. I haven't taken the time to try to grok the connection
> between
> remd and ncsu, since I figure others understand the code much better than
> I
> do.
>
> My bias (based on what I know now): replica exchange seems to require MPI,
> and
> we should not try to be using those variables in serial code. But I'm
> open
> to alternatives. We certainly could have an "rem" variable that was set
> to 0
> (but still visible) in serial code, [somewhat like we define master=.true.
> in serial code so that code like "if(master)" will work in both serial and
> parallel.]
>
> So, please look at what is there, and make appropriate fixes.
>
> ...thanks!...dave
>
> --
>
> ==================================================================
> David A. Case | e-mail: case.scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | skype: dacase
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
>
--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
Received on Sun Dec 23 2007 - 06:07:33 PST
