Re: AMBER: AMBER8 Build on Linux x64 running Opterons

From: Mark Rance <>
Date: Wed, 11 May 2005 11:02:05 -0400

I encountered the same problem Thomas has reported, with xleap compiling
but giving a segmentation fault on start-up (after it prints out four
lines of
text stating it was adding entries to the search path). This was on an
opteron system
runniing SuSE Enterprise Server 9 and the pathscale compilers. The only
I had made in the supplied software was to change the entry in the
for leap for the XALEAP_LIB environment variable from -L$(XHOME)/lib
to -L$(XHOME)/lib64 so that it could find libraries like Xt. For the
file, since there is no option in configure for the pathscale compilers, I
made some
best guesses as to compiler flags, but if anyone has an optimized config.h
for an opteron/pathscale system, I'd be interested to see it.

The only other problem I had with the amber8 install was that the
fantasian program
(in nmr_aux) would not compile, due to not finding a subroutine/function
named rand.


Thomas Patko wrote:

> AMBER Users:
> For those of you that have had trouble getting AMBER8 to
> compile correctly on a 64-bit Opteron Linux system (I have
> RHEL 4.0 AS) with the old PGI 5.2 compiler (as I certainly
> did), there is a new instruction set of how to build
> AMBER8 on the PGI website for 64-bit Opteron and Intel
> processors.
> I upgraded my PGI compiler to 6.0-2 and followed the PGI
> directions after applying the latest bugfixall. Everything
> compiled correctly and passed the tests (with some minor
> numerical differences that can be expected). xleap
> compiles and links correctly (or so it would seem) but
> gives a segmentation fault upon start, so I an still using
> the 32-bit binary from my previous ifc 8.1 32-bit build
> (no problem there). PGI support said that they were
> unaware of the issue and are looking into it.
> Cheers,
> Thomas
> -- Graduate Student
> Department of Chemistry & Biochemistry
> California State University, Long Beach
> Dr. Marco Lopez Research Group
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Dr. Mark Rance
Associate Professor
Dept. of Molecular Genetics, Biochemistry and Microbiology
University of Cincinnati College of Medicine
231 Albert Sabin Way
Cincinnati, Ohio 45267-0524
phone: 513-558-0066
  fax: 513-558-8474
e-mail: mark.rance.UC.Edu
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Received on Wed May 11 2005 - 16:53:00 PDT
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