Re: AMBER: Leap compilation issues

From: Andreas Svrcek-Seiler <>
Date: Mon, 11 Jul 2005 12:43:39 +0200 (CEST)

Hi All,
> I know this is question that mainly reflects by ignorance, but is "Athlon 64
> running FC4" a 64-bit OS (where pointers are 64-bit). xleap is probably
> broken on such a platform. See the comments in $AMBERHOME/src/Makefile
> on how to compile for tleap only (which seems to be 64-bit clean).
....I recommend against using ifort on a FC4 machine. There are some
compatibility issues between gcc4 and the intel compilers (and even
between gcc4 and gfortran).

> If any amber users know the answers to the following questions, please post
> them:
> 1. Has anyone gotten xleap to run in 64-bit mode? How?
....pointers are 4 bytes in 32 bit mode and 8 bytes in 64 bit mode,
so replacing all occurances of int =(=) pointer with
long int =(=) pointer should fix things (provided there are no other
pitfalls lurking). However, doing this would mean fiddling with quite a
lot of .c and header files. In principle, pointers should be stored in pointers
and integers in ints (Though I've never done that).

> 2. Are there compile/load options that can force a 32-bit build?
....Yes, see the attached ${AMBERHOME}/src/leap/Makefile.
the '-m32' flag must be set for compiling and linking, then all output is
32 bit clean.

> 3. If you take an xLeap executable from an IA-32 machine, and try to run it
> on a 64-bit machine, will it work?
.... It will work on common red-hat-like and most other x86_64 machines,
since the default kernel does suppurt running 32 bit executables (without
speed loss) and these distributions come with both 32 and 64 bit
(shared) libraries installed. I've read about one '64 bit clean'
distribution, but forgotten it's name (definitely not "main-stream").

> 4. Has anyone used gcc 4 to compiler xaLeap on a 32-bit system?
....I've just compiled amber8 using gcc4 and ifort (9.0) on an FC4 machine
(using the attached Makefile - (xa)Leap in 32 bit mode). It worked.
Since ifort 9.0 uses inter-obect file optimization per default and this
(for an unknown reason) fails with gcc4 as standard-compiler,
one has to link without optimizations:

config.h:LOADPTRAJ= ifort -O0 -nofor_main $(LOCALFLAGS) $(AMBERBUILDFLAGS)

....'-O0' fixes the above problem. The result passed a 'make test' without
problems and xleap opens a pretty window. I don't know enough of xleap to
do a more in-depth test of xaLeap, but the result looks promising.

I hope that helps,
best regards

            ( O O )
               o        Wolfgang Andreas Svrcek-Seiler
               o        (godzilla)
       .oooO            Tel.:01-4277-52733
       (   )   Oooo. 
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Received on Mon Jul 11 2005 - 11:53:01 PDT
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