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

[Mark Abraham]

Did you try this yourself before asking? You have mix-precision runs you
could restart with double-precision mdrun.

As you will see when you try it, mdrun will notice the change and report it
in the log file, only.

Mark

On Wed, Sep 17, 2014 at 4:18 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Is it possible to run equilibration with mdrun of mixed precision, then run
> production md with mdrun of double precision?
>
> On Tue, Sep 16, 2014 at 8:24 PM, 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?
> > 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?
> >
> >
> > 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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