[gmx-users] Slow MDRUN performance

[Syed Azeem]

>
> 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
>> --