[gmx-developers] compilation of current gmx cvs head code

[David van der Spoel]

Axel Kohlmeyer wrote:
> hi everybody,
> 
> FYI,
> please find attached a patch that contains changes needed to compile the
> current gmx-cvs code.
> 
> i'm also currently revising the changes made by shawn brown and me
> to run gromacs on cray xt3 machines and could use recommendations
> on a name change.
> 
> the current fio_XXXX() routines collide with internal routines in the
> PGI compiler fortran(?) runtime. since this machine only allows static
> linkage, there is a high chance of getting a messed up link (unless one
> uses manual partial linking with ld -r). i'd thus propose to change the
> names of those subroutines into something less common, e.g.
> gmx_fio_XXX, gmxfio_XXX, gmxio_XXX, fio_XXX_gmx, or...
> suggestions are highly welcome.



> 
> cheers,
>    axel.

Thanks Axel, we'll implement it. The gmxprefix is most in line with 
coding we are implementing now, either gmxfio or gmx_fio.

I'm only wondering, whether you are using the Fortran compiler... As far 
as I know the Cray is an Opteron box, so Fortran won't help you since we 
can use the assembly code.

> 
> 
> ------------------------------------------------------------------------
> 
> Index: configure.ac
> ===================================================================
> RCS file: /home/gmx/cvs/gmx/configure.ac,v
> retrieving revision 1.68
> diff -c -u -r1.68 configure.ac
> --- configure.ac	19 Jul 2006 13:31:20 -0000	1.68
> +++ configure.ac	28 Aug 2006 22:23:52 -0000
> @@ -8,7 +8,7 @@
>  AC_CONFIG_AUX_DIR(config)
>  AC_CANONICAL_HOST
>  
> -AM_INIT_AUTOMAKE(tar-ustar)
> +AM_INIT_AUTOMAKE
>  AC_PREFIX_DEFAULT(/usr/local/gromacs)
>  
>  AM_CONFIG_HEADER(src/config.h)
> Index: src/kernel/Makefile.am
> ===================================================================
> RCS file: /home/gmx/cvs/gmx/src/kernel/Makefile.am,v
> retrieving revision 1.22
> diff -c -u -r1.22 Makefile.am
> --- src/kernel/Makefile.am	24 Sep 2005 19:55:51 -0000	1.22
> +++ src/kernel/Makefile.am	28 Aug 2006 22:23:53 -0000
> @@ -20,7 +20,8 @@
>  	toputil.c	topdirs.c	grompp.c	add_par.h	\
>  	topio.h		toputil.h	convparm.h		\
>  	sorting.h	topdirs.h	toppush.h	vsite_parm.h	\
> -	readir.h	topcat.h	topexcl.h	topshake.h
> +	readir.h	topcat.h	topexcl.h	topshake.h	\
> +	compute_io.c	compute_io.h
>  
>  
>  tpbconv_SOURCES = \
> @@ -74,7 +75,8 @@
>  	ionize.c 	ionize.h 	xmdrun.h	\
>  	do_gct.c 	relax_sh.c	repl_ex.c	repl_ex.h	\
>  	xutils.c		\
> -	md.c		mdrun.c		genalg.c	genalg.h
> +	md.c		mdrun.c		genalg.c	genalg.h	\
> +	compute_io.c	compute_io.h
>  
>  ffscan_SOURCES = \
>  	ffscan.c	\
> @@ -82,7 +84,7 @@
>  	ionize.c 	ionize.h 	\
>  	do_gct.c 	relax_sh.c	repl_ex.c	repl_ex.h	\
>  	xutils.c	\
> -	md.c		genalg.c
> +	md.c		genalg.c	compute_io.c	compute_io.h
>  
>  
>  # shortcut to install only mdrun
> Index: src/tools/addconf.c
> ===================================================================
> RCS file: /home/gmx/cvs/gmx/src/tools/addconf.c,v
> retrieving revision 1.66
> diff -c -u -r1.66 addconf.c
> --- src/tools/addconf.c	12 May 2006 10:09:27 -0000	1.66
> +++ src/tools/addconf.c	28 Aug 2006 22:23:53 -0000
> @@ -299,8 +299,10 @@
>    search_neighbours(fp,fr,x,box,top,grps,cr,nsb,&nrnb,md,lambda,&dvdlambda,
>  		    TRUE,FALSE);
>  
> +#if 0
>    if (debug)
>      dump_nblist(debug,fr,0);
> +#endif
>  
>    if (bVerbose)    
>      fprintf(stderr,"Succesfully made neighbourlist\n");
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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