AMBER Archive (2008)

Subject: Re: AMBER: configure_amber (10) for pg compilers

From: Robert Duke (
Date: Fri Jul 11 2008 - 07:27:02 CDT

I think the philosophy here is that unless there is a really good reason to
choose the matching vendor c compiler, we choose gcc because it is widely
available, widely tested, and free. I think at some point there were
potential issues with mixing ifort with gcc, but they went away. In pmemd I
typically don't worry about the quality of the c code (in terms of
optimization) because there is very little c code and none of it is
performance-critical, at least so far. If you are having screwball
compatibility problems, it may be something worth trying, but the critical
issue would be the intersection of the libraries being referenced, most
likely, assuming that nothing stupid was done at the function call interface
in the code. I am currently only using c to get some addresses to determine
data type --> byte conversions and do fine-grained timing I believe, and the
call interfaces are strictly call by reference, though there COULD be
mismatch between default datatype problems (eg., if c thinks an int is 8
bytes and fortran thinks the default integer type is 4 bytes, one will be
surprised). I have specifically avoided anything where c and fortran might
expect different initialization but be accessing the same underlying
objects, like mixed i/o (these sorts of things can be done, but they tend to
be portability deathtraps, so I steer clear of them if at all possible).
Regards - Bob Duke

----- Original Message -----
From: "Vlad Cojocaru" <>
To: "AMBER list" <>
Sent: Friday, July 11, 2008 7:51 AM
Subject: AMBER: configure_amber (10) for pg compilers

> Dear Ambers,
> I was wondering why in the configure_amber script provided with amber10 at
> lines 634 to 640, for the PG compilers, the flags cc and cplusplus point
> to gcc and g++ rather than pgcc and pgcpp.
> Thanks for answering
> Best wishes
> vlad
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
> e-mail:Vlad.Cojocaru[at]
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> Amtgericht Mannheim / HRB 337446
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> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
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