[gmx-users] compiling gromacs on powerpc64
nmoore at physics.umn.edu
Wed Aug 3 13:30:47 CEST 2005
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,
> 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
>> > > Make a new one with grompp or use a gro or pdb file, if
>> > >
>> > > Thus, mdrun cannot read the topol.tpr file although both are
>> > > compiled from the same gromacs-3.2.1 source tree.
>> > >
>> > > It gets really strange when I ran the grompp command on a different
>> > > Linux 64-bit Opteron, copied the so-generated topol.tpr file over to
>> > > 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
>> > > 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
> 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?
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