AMBER Archive (2009)

Subject: Re: [AMBER] amber9 serial compilation issues

From: David A. Case (
Date: Fri Apr 03 2009 - 15:01:02 CDT

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.


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