[gmx-users] compiling gromacs on powerpc64

[David van der Spoel]

On Wed, 2005-08-03 at 19:54 -0700, Martin Siegert wrote:
> On Wed, Aug 03, 2005 at 06:30:47AM -0500, Nathan Moore wrote:

> 
> 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?
We'd be delighted to hear of any 64-bit incompatibilities, we're not
aware of any. Have you tried double precision in 64 bit? Most likely it
is a compiler thing anyway.


> 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?

     I. It is no problem, tpr files are portable, you can make them on
        your desktop computer as well. The only difference is between
        single and double precision.

> 
> 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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-- 
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://xray.bmc.uu.se/~spoel
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