Note that pmemd calls a (very) few system-level functions in pmemd_clib.c -
all the interfaces to potentially extraneous things are through c. These
are needed - there is no equivalent fortran functionality (so this is stuff
like accurate wallclock times and setting stack limits, if memory serves).
There have been no portability problems to speak of with this stuff (I
probably aimed for posix compliance).
- Bob
----- Original Message -----
From: "Ross Walker" <ross.rosswalker.co.uk>
To: "'AMBER Developers Mailing List'" <amber-developers.ambermd.org>
Sent: Monday, March 16, 2009 3:07 PM
Subject: RE: [AMBER-Developers] Amber coding standards
> Hi Joe,
>
>> That is why we need a list of allowed extension routines. Sander appears
>> to only use IARGC, GETARG and EXIT. Maybe those 3 are the complete list.
>
> Yes although I think right now we are okay with all of those. The original
> idea though was that we have wrappers for all the extension routines that
> deal with exceptions. For example people should ONLY be using mexit (or
> through sander_bomb) and NOT calling exit directly. The routine mexit is
> defined in mexit.f (although there is one in both src/lib/ and src/sander/
> which is somewhat confusing) and deals with cases where exit is not
> supported. E.g.
>
> #ifdef XLF90
> if (status /= 0) then
> stop 1
> else
> stop 0
> end if
> #else
> call exit(status)
> #endif
>
> Note the one in src/sander/ does not seem to correctly deal with calling
> exit when MPI is defined. Here it always seems to call exit regardless of
> the definition.
>
> The same is true for getarg - you are supposed to call getarg_wrap (same
> for
> iargc). However, I think what is generally happening these days is that
> everything (as far as most users are concerned) is converging on a single
> operating system (Linux) or variations thereof and a single instruction
> set
> (x86_64) hence nothing else (bsd etc etc) is being properly tested. So
> people just add the extension calls to the code, find it compiles on their
> machine and then assume all is good.
>
> We should probably organise a retreat for a select group of coders to get
> together (no presentations allowed etc) and decide on a series of
> standards
> etc and then go through the code and clean it up / enforce those
> standards.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
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>
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Received on Wed Mar 18 2009 - 01:11:37 PDT
