[gmx-developers] compilation of current gmx cvs head code
Axel Kohlmeyer
akohlmey at cmm.chem.upenn.edu
Tue Aug 29 18:30:03 CEST 2006
On 8/29/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
[...]
> Thanks Axel, we'll implement it. The gmxprefix is most in line with
> coding we are implementing now, either gmxfio or gmx_fio.
ok. i think gmx_fio_XXX is more readable. i'll send in the patch for that
later. along with a few other changes needed for that machine.
> 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.
i'm using the assembly code (and in fact, we'll be needing to hack this
a little for the project we're currently working on here at the CMM), but
if you link with the default scripts provided by cray you run a high chance
of getting the fortran runtime pulled in regardless. shawn and i had been
falling back on the fortran code because we were chasing some weird
bug that finally turned out to be a bug in a library that gets pulled
in indirectly
thanks to the combined 'intelligence' of cray software engineers and
gnu libtool. it also depends a little bit on how you handle the fact of
basically needing to do a cross-compile even though you have the same
hardware on front end and compute node.
i have some more changes that are needed and one workaround
that will hopefully only be needed for a while to make the
code work at all and quite well on that kind of hardware.
more later,
axel.
>
> >
> >
> > ------------------------------------------------------------------------
> >
> > 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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> > gmx-developers at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-developers
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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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>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
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