[gmx-users] does gromacs-4.6 support intel core Quad Q9550 cpu?

[Mark Abraham]

On Thu, Sep 25, 2014 at 4:19 PM, Vedat Durmaz <durmaz at zib.de> wrote:

>
> i guess that's it, mark. thanks. following mirco's hint and checking the
> log file indeed reveals that "rdtscp" was used upon compiling the binaries.
>
> so i will compile it myself on the affected machine. you say i don't
> need to set any special cmake variable?


"Nothing is required if building on the target machine - GROMACS cmake
configuration does all the required detection"


> shouldn't i at least set the
> "GMX_USE_RDTSCP" variable the website you've linked below mentions?


Not if GROMACS cmake is doing the required detection - which it does. (We
did improve the implementation of the detection after 4.6.5, but that is an
issue only if you tried to do a source-based install of 4.6.5 or earlier
with a build host that has rdtscp and a target machine that does not - so
do the build on the target machine and stop worrying about it ;-) ).

and
> if so, how would i do that? like this?:
>
> cmake ... -DGMX_USE_RDTSCP=OFF
>

Yes, but you don't need if it you are building on the target machine,
because GROMACS cmake configuration does all the required detection, and
this gets turned off automatically if appropriate.


> and what about using SSE4.1? you've written: "Yes, and use the SSE4.1
> speed advantages ..." do i need to set some proper cmake variable in
> order to use this feature?
>

No, if you are building on the target machine, because GROMACS cmake
configuration does all the required detection, and turns on SSE4.1 support
if that would suit the build host.

:-)

Mark


> vedat
>
>
>
> Am 25.09.2014 um 15:28 schrieb Mark Abraham:
> > On Thu, Sep 25, 2014 at 12:16 PM, Vedat Durmaz <durmaz at zib.de> wrote:
> >
> >> hi guys,
> >>
> >> sorry for disturbing!
> >>
> >> the pc of a student here has ubuntu 14.04 installed on it along with the
> >> gromacs version 4.6.5 debian/ubuntu binaries from the ubuntu
> repositories.
> >>
> >> when we start mdrun, we get an german error message saying:
> >>
> >> "ungültiger maschinenbefehl" (something like "invalid machine command").
> >> when searching the internet i got the feeling that this has something to
> >> do with the cpu.
> >>
> >> cat /proc/cpuinfo yields (among others):
> >>
> >> ...
> >> flags        : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
> >> cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall
> >> nx lm constant_tsc arch_perfmon pebs bts rep_good nopl aperfmperf pni
> >> dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm sse4_1 xsave
> >> lahf_lm dtherm tpr_shadow vnmi flexpriority
> >> ...
> >>
> >> can anybody confirm that this cpu with the given properties/flag is not
> >> supported by gromacs 4.6 debian binaries?
> >
> > That cpu does not appear to support an instruction (rdtscp) that is used
> by
> > GROMACS in doing timing if that instruction was supported on the build
> > machine (mentioned at
> >
> http://www.gromacs.org/Documentation/Installation_Instructions_4.6#4.3.1._Portability_aspects
> > ).
> >
> >
> >> if so, would compiling it from
> >> the sources remedy the problem?
> >
> > Yes, and use the SSE4.1 speed advantages that the cpu does have, unlike
> the
> > least-common-denominator build that is targeted by the
> > ubuntu-gromacs-package maintainer. If you want mdrun to run optimally,
> > compile it on the machine you want to run it on.
> >
> >
> >> if so, which flag must be set for
> >> builing/compiling gromacs accordingly?
> >>
> > Nothing is required if building on the target machine - GROMACS cmake
> > configuration does all the required detection, but it can't detect the
> > capabilities of a machine it hasn't yet seen...
> >
> > Mark
> >
> > thanks a lot & take care
> >> vedat
> >>
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