[gmx-users] Compatibility of Files Between Version, Precision, and Compilation

[Mark Abraham]

On Wed, Sep 17, 2014 at 2:24 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Will gromacs 4.5 double precision (which has altivec support) run faster on
> the power7 cluster than 4.6.7 or 5.0.1?
>

Maybe. You'll have to use the group scheme (which was the only scheme
then), but that scheme got substantial upgrades in 4.6 which you'd be
losing.


> Are there any bugs that I have look out if I use gromacs 4.5 double
> precision mdrun on a cluster that only has cpu?
>

Yep, lots of them, in particular any bug fix in the release notes of the
4.6 and 5 series.

Mark


> On Tue, Sep 16, 2014 at 11:20 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > On Tue, Sep 16, 2014 at 4:19 PM, Johnny Lu <johnny.lu128 at gmail.com>
> wrote:
> >
> > > that machine without sse2 is a power7 cluster.
> > > It has altivec 128 simd. I wonder if gromacs can use that?
> > >
> >
> > Not right now. Maybe in future GROMACS versions.
> >
> >
> > > Where can I find the official compilation switches for power7 (xlc or
> > gcc)?
> > >
> >
> > -O3 and hope the compiler is better than any ever made.
> >
> > Mark
> >
> >
> > > On Tue, Sep 16, 2014 at 10:03 AM, Mark Abraham <
> mark.j.abraham at gmail.com
> > >
> > > wrote:
> > >
> > > > On Tue, Sep 16, 2014 at 3:06 PM, Johnny Lu <johnny.lu128 at gmail.com>
> > > wrote:
> > > >
> > > > > Hi.
> > > > >
> > > > > For cpt, gro, edr, and trr files, can I continue from one version
> > (4.66
> > > > or
> > > > > 5.01) and precision (single or double), with gromacs of another
> > version
> > > > > (4.6.6, or 5.0.1), precision,
> > > >
> > > >
> > > > Yes, if the relevant features are implemented in both versions. But
> you
> > > > should never want to do that.
> > > >
> > > > > and on another machine?
> > > >
> > > > Always
> > > >
> > > > So far, it seems that tpr file compiled on a machine with sse2 and
> > > gromacs
> > > > > 4.6.6 double precision causes segmentation fault on another machine
> > > > without
> > > > > sse2 and with gromacs 4.6.6 double precision.
> > > > >
> > > >
> > > > Extremely unlikely. The .tpr file format has been no-problems
> portable
> > > for
> > > > about a decade ;-) But if the machine doesn't even have SSE2, then it
> > is
> > > > only good for warming your coffee.
> > > >
> > > > Mark
> > > >
> > > > Thank you (again).
> > > > > --
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