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

Mark Abraham mark.j.abraham at gmail.com
Thu Sep 25 15:28:17 CEST 2014

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

> 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...


thanks a lot & take care
> vedat
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