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

Vedat Durmaz durmaz at zib.de
Thu Sep 25 16:30:10 CEST 2014

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? shouldn't i at least set the
"GMX_USE_RDTSCP" variable the website you've linked below mentions? and
if so, how would i do that? like this?:


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?


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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