AMBER Archive (2008)

Subject: Re: AMBER: Amber9 Installation Problem

From: David A. Case (
Date: Wed Mar 19 2008 - 20:37:57 CDT

On Wed, Mar 19, 2008, wrote:
> I am currently trying to install Amber 9 on a 64 bit Xeon machine with
> RHEL 5.1 as the operating system. I used gcc [version: gcc (GCC) 4.1.2
> 20070626 (Red Hat 4.1.2-14) ] and g95 [version: G95 (GCC 4.0.3 (g95
> 0.90!) Jul 27 2006)] (./configure g95) and the compilation was
> succesful, and I did not notice any errors along the way. But, when I
> ran the test suite, several of the tests gave results that were
> significantly far from what was expected, and in particular the ptraj
> module completely crashed with the following errors:
> ----------------------------------------
> # make test.ptraj
> cd ptraj_matrix; ./Run.matrix
> ptraj: analyze fluctuation matrices
> Segmentation fault
> ./Run.matrix: Program error

Are you sure you are planning to analyze fluctuation matrices in ptraj? (This
is a very specialized calculation.)

If not, you should probably just move on to something else...a newly rewritten
ptraj (all in C) will be released in a few weeks. So, people are not likely
to be highly motivated to try to track down your bug.

As to the "other tests" that failed, we would need to see details. I note
that your g95 is 20 months old: it *might* be worth downloading a newer version
from But it might also be that your installation is (almost)
fully functional as is.

> ifort -c -w95 -mp1 -O0 -o new2oldparm.o _new2oldparm.f
> ifort: error #10149: option '-cxxlib-gcc' not supported with the
> current installed GCC

This has nothing to do with Amber code: errors in new2oldparm.f are invariably
problems with the compiler installation. Make sure that you can compile
simple fortran programs on your machine.

Others on the list may know the answer to how to install ifort on Xeons.
Did you Google on the error message listed above?


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