[gmx-users] Slow MDRUN performance

[Mark Abraham]

Hi,

OK. The build system will choose these defaults correctly for you if you
just leave things alone ;-)

Mark

On Wed, Jun 21, 2017 at 1:17 PM Syed Azeem <syedazeemullah186 at gmail.com>
wrote:

> >
> > Hi,
> >
> > On Wed, Jun 21, 2017 at 12:47 PM Syed Azeem <syedazeemullah186 at gmail.com
> >
> > wrote:
> >
> >> Hi all,
> >>
> >> I installed gromacs 5.1.2 on a new machine.
> >> Config: Intel Core i5 6500 3.20 GHz Quad Core Skylake with 8 GB DDR4.
> >>
> >> Then I started a NVT simulation for 500ps with ~250000 atom system.
> >> Surprisingly, the estimated time was 4 days and 3 hours.
> >>
> >> There was a note stating consider rebuilding gmx with the
> >> GMX_USE_RDTSCP=ON CMake option, as follows:
> >>
> >> GROMACS:      gmx mdrun, VERSION 5.1.2
> >> Executable:   /usr/local/gromacs/bin/gmx
> >> Data prefix:  /usr/local/gromacs
> >> Command line:
> >>   gmx mdrun -v -deffnm nvt
> >>
> >>
> >> Running on 1 node with total 4 cores, 4 logical cores
> >> Hardware detected:
> >>   CPU info:
> >>     Vendor: GenuineIntel
> >>     Brand:  Intel(R) Core(TM) i5-6500 CPU @ 3.20GHz
> >>     SIMD instructions most likely to fit this hardware: AVX2_256
> >>     SIMD instructions selected at GROMACS compile time: None
> >>
> >> Compiled SIMD instructions: None, GROMACS could use AVX2_256 on this
> >> machine, which is better
> >>
> >>
> >> The current CPU can measure timings more accurately than the code in
> >> gmx was configured to use. This might affect your simulation
> >> speed as accurate timings are needed for load-balancing.
> >> Please consider rebuilding gmx with the GMX_USE_RDTSCP=ON CMake option.
> >>
> >> Reading file em.tpr, VERSION 5.1.2 (single precision)
> >> Using 1 MPI thread
> >> Using 4 OpenMP threads
> >>
> >>
> >> WARNING: Using the slow plain C kernels. This should
> >> not happen during routine usage on supported platforms.
> >>
> >> Then, I rebuilt gromacs with the CMAKE GMX_USE_RDTSCP=ON, as suggested.
> >>
> >> Again the performance is slow with the same note being generated.
> >>
> >> PS: For comparison, I ran 500 ps NVT simulation of the same ~250000
> >> atom system on another machine of the same config and finished within
> >> 7 hours.
> >>
> >> What mistake am I making in the installation?
> >>
> >
> > We can't tell, because you didn't tell us about how the installation was
> > done. ;-) But somehow everything useful got turned off, so don't do that.
> > You should use the quick and dirty guide at
> > http://manual.gromacs.org/documentation/5.1.4/install-guide/index.html,
> > configure on the node you'll run on, and install the latest in the 5.1
> > series, not an older one with extra bugs ;-)
> >
> > Mark
> Thanks for the reply, Mark.
>
> I followed the quick and dirty installation from the gromacs
> installation documentation.
>
> Now I rectified the problem by rebuilding GMX with GMX_USE_RDTSCP=ON
> and -DGMX_SIMD=AVE2_256, which gromacs suggested would be better for
> my machine.
>
> Azeem
> >
> >
> >> Thanks in advance,
> >>
> >> Azeem
> >> --
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