Re: AMBER: Installation problem. .

From: Andreas Svrcek-Seiler <>
Date: Wed, 15 Jun 2005 14:31:46 +0200 (CEST)

> 2.6 Linux kernel is already installed in my PC.
....That's the default, probably even since FC2 (?)

> My intel fortran compiler for linux is version 8.1. Was this the
> critical problem in installing AMBER 8?
....No problem at all (more or less).
The best way for the intel compiler and opterons:
do a:
../configure -p4 ifort

then edit config.h:
Optimization recommended for athlon 64 CPUs are '-O3 -ip -xW'
'-xW' turns on specific optimizations for Intel pentium4s and compatible
processors (e.g. Athlon 64).
Then (if present) set the path to the correct MKL library
(e.g. /opt/intel/mkl721/lib/em64t on my machine).

Now, everything should work like a charm (not charmm :-).
When compiling xleap, I found one issue: In one Makefile,
/usr/X11R6/lib should be changed to /usr/X11R6/lib64, otherwise
compilation fails.

There's one caveat: If you want 64 bit, choose the right compiler.
Many people might have 32 and 64 bit compilers installed (me, too).
Just make sure to source the right ${BLA}/bin/ifortvars.csh.
Per default, 64 bit compilers are under /opt/intel_fce_80 (fortran)
and opt/intel_cce_80.

One more thing: On my machine, All "Run.(...)" scripts must start
with #!/bin/csh -f (mind the '-f'), otherwise sander and colleagues don't
find the needed shared libs. This might not be a problem on other
machines (?).

I've attached 'my' config.h, which leads to a flawless 'make test'.

> Version 9.0 will be available for free from Auguest based on anouncement
> in Intel website.
....The C/C++ compiler is already available (and works - giving a
noticeable performance gain in the benchmarks I did, again on an athlon
64). Curiously, the install script doesn't allow installation,
but a manual install works just fine. I wonder whether
that happened on purpose (assuming it might take users till August to
find out how to do the installation manually) or someone simply messed
things up.

> I would really appreciate if anybody give me an advice to intall AMBER 8
> in a 64bit machine with FC3 x86_64 or FC4 x86_64. I don't want to buy a
> compiler just to install AMBER...
....No need to, obviously. I'd just recommend *not* to install FC4 right
now. FC3 with all updates and bug fixes might be the better choice
until FC4 has matured a little bit - but that's solely my personal

Good luck,

            ( O O )
               o        Wolfgang Andreas Svrcek-Seiler
               o        (godzilla)
       .oooO            Tel.:01-4277-52733
       (   )   Oooo. 
-------\ (----(   )--------------------------------------------------------
         \_)    ) /

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Received on Wed Jun 15 2005 - 13:53:00 PDT
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