:) 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 <dur...@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 <dur...@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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