[gmx-users] compiling gromacs on powerpc64

[Martin Siegert]

On Wed, Aug 03, 2005 at 06:30:47AM -0500, Nathan Moore wrote:
> Martin,
> 
> I've been able to compile Gromacs on PowerPC64 systems in the past with
> normal functionality, but I'm wary of the -O5 flag you included.  Have you
> tried installing a vanilla version?  Here's the configure script I used a
> few months ago which worked,
> 
> ./configure \
>         --prefix="/bglhome/usr2/ntmoore/GROMACS/bin/bglfen3.double" \
>         --disable-float \
>         F77='f77' \
>         CC='xlc' \
>         CXX='xlC' \
>         CFLAGS="-g -O2
> -I/bglhome/usr2/ntmoore/lib/fftw-double-bglfen3/include/" \
>         CPPFALGS="-I/bglhome/usr2/ntmoore/lib/fftw-double-bglfen3/include/"\
>         LIBS="-L/bglhome/usr2/ntmoore/lib/fftw-double-bglfen3/lib/"\
>         LDFLAGS="-lfftw -lrfftw"\
>         --disable-fftw \
>         --without-xml \
>         --without-x

Nathan: this turned out to be very helpful:

compiling with "-O2" works, i.e., the resulting grompp generates a
topol.tpr file that works with mdrun.

compiling with "-q64 -O2" does not work, i.e., the problem is with
the 64bit compilation.

Could there be some variable conversion in the code that fails in 64bit
mode?
Also: is it possible to use a 32bit grompp together with a 64bit mdrun,
particularly for problems that require 64bit due to the size of the
problem? In other words: if the size of the problem is such that mdrun
requires more than 2GB of memory, can I still use a 32bit grompp to
generate the topol.tpr file?

Thanks for your help!
Martin

> > On Sun, Jul 31, 2005 at 09:29:21PM +0200, David wrote:
> >> On Sun, 2005-07-31 at 11:59 -0700, Martin Siegert wrote:
> >> > Hi,
> >> >
> >> > On Sat, Jul 30, 2005 at 03:55:20PM -0700, Martin Siegert wrote:
> >> >
> >> > > I then try to run the d.dppc test case:
> >> > > grompp -c conf.gro -f grompp.mdp -p topol.top
> >> > > mdrun -s topol.tpr -nice 0
> >> > >
> >> > > The grompp command completes fine, but the mdrun command fails with
> >> > >
> >> > > Fatal error: Can not read file topol.tpr,
> >> > >              this file is from a Gromacs version which is older than
> >> 2.0
> >> > >              Make a new one with grompp or use a gro or pdb file, if
> >> possible
> >> > >
> >> > > Thus, mdrun cannot read the topol.tpr file although both are
> >> definitely
> >> > > compiled from the same gromacs-3.2.1 source tree.
> >> > >
> >> > > It gets really strange when I ran the grompp command on a different
> >> platform,
> >> > > Linux 64-bit Opteron, copied the so-generated topol.tpr file over to
> >> the
> >> > > PPC machine and ran mdrun using that topol.tpr file. That works!
> >> > >
> >> > > But that really shouldn't work, should it? X86_64 is little endian
> >> and
> >> > > PowerPC is big endian. Thus, is there an endian issue that configure
> >> > > is not resolving correctly on the PPC platform or what is going
> >> wrong here?
> >> >
> >> > By now I succeeded compiling gromacs-3.2.1 using the --disable-shared
> >> > configure option. This avoids all the libtool problems and compiles
> >> > cleanly. It nevertheless generates a grompp that produces topol.tpr
> >> > files that cannot be read by mdrun which lets me conclude that this
> >> > problem has nothing to do with the libtool problems reported in my
> >> > previous email. Thus:
> >> >
> >> > How do I compile grompp on powerpc64?
> >> Maybe there is a problem with the xdr libraries, used for the platform-
> >> independent file formats that gromacs uses (edr, tpr, trr). Check which
> >> libraries gromacs uses for these.
> >>
> >> Have you tried moving a powerpw64 tpr file to another machine and
> >> reading it there (using e.g. gmxdump)?
> >
> > I tried that on the X86_64 platform and it give the same error message.
> > I spent the day getting gromacs to compile with libxml2 (libtool screws
> > that up as well) but even with libxml2 support the result remains the
> > same.
> >
> > You are probably right when suggesting that something goes wrong
> > with the compilation of those gromacs libraries. But if those file
> > formats are supposed to be platform indenpendent then there ought to
> > be some code that makes a decision to compile these libraries
> > differently on big endian and little endian machines. Does anybody
> > know where that code is and where the code is that detects whether
> > a platform is little endian or big endian?
> >
> > Cheers,
> > Martin
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