[gmx-users] Slow MDRUN performance

[Mark Abraham]

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 in advance,
>
> Azeem
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