AMBER Archive (2009)

Subject: Re: [AMBER] amber9 serial compilation issues

From: Francesco Pietra (
Date: Fri Apr 03 2009 - 17:04:17 CDT

Unless it involves substantial work in answering, are any flags to

./configure ifort_x86_64

in order that xleap is not involved and make finds a clean territory?
I don't need xleap in this context, simply a fully patched code to
modify in sander.

I noticed the issue about X, but X in lenny is the same as in etch,
and the computers are the same (old stuff of many years ago). At any
event, my mail was not addressed to any particular individual. One can
simply skip my mail if of no interest.

francesco pietra

On Fri, Apr 3, 2009 at 10:01 PM, David A. Case <> wrote:
> On Fri, Apr 03, 2009, Francesco Pietra wrote:
>> Following failure to compile serial amber9 with debian linux amd64
>> lenny, intel 10.1.015 compilers, on supermicro quad socket
>> dual-opteron, I have tried  with a tyan 2-socket dual-opteron, same OS
>> and compilers. mkl support. In the recent past, on both computers with
>> previous debian linux amd64 etch I had no problems, even with pmemd.
> I don't think that people on the list will be motivated to spend time to
> help you without some idea of why you think you need to do all this.  I
> can't think of any real reason why you (or we) should struggle to compile an
> old version of xleap on today's 64-bit machines and current OSes.  We
> struggle to have enough manpower to keep current releases working, and
> don't have resources to backport old codes.  An updated version of
> xleap, which has its own version of yacc and which the new organization
> of X11 files, is available for free in AmberTools.
> And, it's too bad that you have not yet learned to understand error
> messages from the compilation.  For your case, the key line is this:
> gcc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -m64 -O2 -o WcActCB.o WcActCB.c
> WcActCB.c:22:28: error: X11/IntrinsicP.h: No such file or directory
> WcActCB.c:29:24: error: X11/ShellP.h: No such file or directory
> This indicates that you do not have the proper X11 development libraries
> installed on the machine you are using, or that they are not in the place
> that was standard back when Amber9 was being developed.  Note that this
> has nothing to do with the intel compilers, nor with mkl, nor with quad
> sockets, or dual opterons, etc.
> You may find it quite frustrating to get old X11 code to run on modern
> Linux distributions: the x11-org people recently moved all their files
> around, and many (most) distributions will no longer have a
> /usr/X11R6/include directory that was standard (and expected) at the
> time Amber9 was released.
> ....dac
> _______________________________________________
> AMBER mailing list

AMBER mailing list