Re: AMBER: sander and mpich (which compilers/mpich work)

From: Jerry Grooms <>
Date: Sat, 31 Jan 2004 15:44:30 -0500

At 08:23 PM 1/30/2004 -0500, Viktor Hornak wrote:

Hi, thanks for the reply. The comments below are for the general community.

>The amber PC cluster page has not been updated since last
>September/October but the information should be still more or less valid.
>As Jarry noted, the problem almost always resides in a compiler/mpich
>combination. Serial versions of amber7 work with most compilers. Amber7
>was not well tested with intel ifc compiler (serial should work fine and
>fast, but you may encounter problems with parallel runs:
>from my experience, ifc compiles amber7 with mpich but crashes when
>running the executable). Therefore, I recommend to stick to g77+mpich
>combination for parallel runs.

I would be ok with this if I can find a combination that works with my
OS. Although in our experience with other applications, the Intel
compilers give better performance.

>Even then, I recall having problems on RH8/9. They were related to
>compilation problems of mpich with new g77/gcc-3.x series, which was
>introduced for the first time in RH8. However, I need to verify this
>because I don't remember which version of mpich I was dealing with at the

>In summary, RH7.3+g77+mpich is a safe combination for amber7.

The problem is that for a new installation, RH7.3 is not a choice some of
us can make. In my case, for these reasons:

o) another application will not work (at least is not supported by the
vendor) with RH7.3
o) no more security updates, etc from RH for 7.3 (or soon 8/9 for that matter).

>For the future, I'd be focusing on linux distributions which are supported
>by intel compilers (their latest release is version 8 and supported glibc
>libraries and distributions are listed on intel wesite as well).

It would be nice if we could publish compiler/mpich versions known to work
with Amber on their respective distributions. In my specific case, I need
a combination that works on SuSE 8.2. I have the option of the Portland
or the Intel 7/8 compiler.

RH 7.3 has been a stable platform, but it's time to move on in my
opinion. Are there any known working combinations for gcc 3.3./mpich 1.2.x
that anyone would care to comment on? Any Suse 8.2 Amber users?



The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sat Jan 31 2004 - 20:53:05 PST
Custom Search