AMBER Archive (2004)

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

From: Jerry Grooms (grooms_at_uky.edu)
Date: Sat Jan 31 2004 - 14:44:30 CST

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
>time.

>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?

Thanks,

Jerry

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