[gmx-users] compiling gromacs on powerpc64

[Nathan Moore]

Dear Martin,

I'm glad to hear that "-O2" worked.  As I recall, many copilers (SGI for
sure, not sure about XL) will compile in 32 bit mode when you turn up the
optimization flags.  I'm guessing (don't know for sure) that if things are
done in 32 bit then maybe you can vectorize some of the operations - this
is just a flat-out guess though on my part.  What I mean to encourage
though is to try -O5 without the -q64.

Do you really need 64-bit memory availability though?  Even the largest
benchmark systems I've run (dppc level, 120K atoms) will fit on 1 node of
the proto-Blue Gene (256MB).

Nathan

> 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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