[gmx-users] does gromacs-4.6 support intel core Quad Q9550 cpu?
mark.j.abraham at gmail.com
Thu Sep 25 18:10:01 CEST 2014
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 ;-) ).
> 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.
> 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
> >> 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
> > GROMACS in doing timing if that instruction was supported on the build
> > machine (mentioned at
> > ).
> >> 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
> > 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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