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

[Vedat Durmaz]

:)  well, you convinced me finally. after having had screwed up all my 
courage, i just gave it a try:

cmake .. -DCMAKE_INSTALL_PREFIX=$path

and everything worked surprisingly fine with make. i guess i was still 
traumatized by the attempt to install gromacs on some cray xc30 a couple 
of month ago!

vedat



Am 25.09.2014 um 18:09 schrieb 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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