[gmx-users] problem with gpu performance

Fri Sep 4 15:58:37 CEST 2015

Hi Peter
  Thanks for your response. I also realized that GTX-610 is not able to
catch up with the faster cpu ( Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz). I
tried cpu-gpu combination for -nb option. It improves it slightly but not
by much. So, we are planning to go for a replacement of GPU cards.
At this point, we have two plans: either go for single 4 GB GTX-970 or two
2 GB GTX-960 . I was wondering whether you can comment on which options
will be better as far as performance is concerned.
Thanks for your input
jagannath

On Fri, Sep 4, 2015 at 6:45 PM, Peter Kroon <p.c.kroon at rug.nl> wrote:

> Hi Jagannath,
>
> AFAIK GT610's are rather slow. What you could try is using both cpu and
> gpu for non-bonded interactions (-nb gpu_cpu)
>
> Peter
>
> On 04/09/15 15:01, jagannath mondal wrote:
> > Dear Gromacs Users
> >
> >   I am trying to run gpu version of gromacs5.0.6 in a work-station which
> is
> > a hexacore processor that can be multithreaded to 12. The workstation
> has 2
> > Geforce GT  610 GPUs . I am finding the simulation using -nb gpu is
> > exceedingly slower than -nb cpu ( i,e turning off gpu)
> >
> > I installed cuda-7.0 and using this I could install gpu version of
> gromacs
> > 5.0.6 as follows.
> >
> > cmake ../ -DGMX_BUILD_OWN_FFTW=ON
> > -DCMAKE_INSTALL_PREFIX=/home/jmondal/UTIL/GROMACS_5.0.6_gpu/
> > -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++  -DGMX_GPU=ON
> > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/
> >
> >
> > However,  the performance with gpu is very weird. If I do mdrun using
> > following command:
> > 1) gmx mdrun -s topol. -nb gpu -v &>log_run
> >
> > and then repeat the same thing by turning of gpu usage
> >
> > 2) gmx mdrun -s topol -nb cpu -v >& log_run
> >
> > using gpus, the performance drops about 3 times !! Using both the GPUs
> > along with CPUs, the performance is: 1.620 ns/day
> >   using only CPUs, the performance is 4.6 ns/day... usage of GPUs is
> > frustratingly slowing down the performance.
> >
> > when using -nb gpu option, gromacs md.log correctly detects gpu and cpu
> as
> > follows:
> >
> > Using 2 MPI threads
> > Using 6 OpenMP threads per tMPI thread
> >
> > Detecting CPU SIMD instructions.
> > Present hardware specification:
> > Vendor: GenuineIntel
> > Brand:  Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
> > Family:  6  Model: 63  Stepping:  2
> > Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm mmx
> > msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2
> > sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> > SIMD instructions most likely to fit this hardware: AVX2_256
> > SIMD instructions selected at GROMACS compile time: AVX2_256
> >
> >
> > 2 GPUs detected:
> >   #0: NVIDIA GeForce GT 610, compute cap.: 2.1, ECC:  no, stat:
> compatible
> >   #1: NVIDIA GeForce GT 610, compute cap.: 2.1, ECC:  no, stat:
> compatible
> >
> > 2 GPUs auto-selected for this run.
> > Mapping of GPUs to the 2 PP ranks in this node: #0, #1
> >
> >
> > However, when I look at the performance at the end of the simulation, the
> > 'wait GPU nonlocal' takes awfully long time.
> > I also tried few other options ( such as using only 1 gpu using gpu_id 0
> ).
> > Also played with ntmpi and ntomp option. But GPUs performance is
> > drastically poor ( surprisingly 3 times slower than only cpu-based
> > simulation),
> >
> > I am struggling to figure out whether it is a hardware issue or
> GPU-driver
> > issue or whether I am not using best optimal option.
> > Your suggestion will be useful in solving the issue.
> > Jagannath
> >
> >
> >    R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
> >
> > On 2 MPI ranks, each using 6 OpenMP threads
> >
> >  Computing:          Num   Num      Call    Wall time         Giga-Cycles
> >                      Ranks Threads  Count      (s)         total sum    %
> >
> -----------------------------------------------------------------------------
> >  Domain decomp.         2    6         63       0.270         11.322
>  0.2
> >  DD comm. load          2    6         13       0.000          0.002
>  0.0
> >  Neighbor search        2    6         63       0.311         13.062
>  0.2
> >  Launch GPU ops.        2    6       5002       0.205          8.614
>  0.2
> >  Comm. coord.           2    6       2438       0.239         10.016
>  0.2
> >  Force                  2    6       2501       1.358         57.011
>  1.0
> >  Wait + Comm. F         2    6       2501       0.404         16.954
>  0.3
> >  PME mesh               2    6       2501       9.734        408.587
>  7.3
> >  Wait GPU nonlocal      2    6       2501     117.798       4944.651
> 88.3
> >  Wait GPU local         2    6       2501       0.005          0.206
>  0.0
> >  NB X/F buffer ops.     2    6       9878       0.255         10.683
>  0.2
> >  Write traj.            2    6          4       0.180          7.558
>  0.1
> >  Update                 2    6       2501       0.807         33.886
>  0.6
> >  Constraints            2    6       2501       1.216         51.025
>  0.9
> >  Comm. energies         2    6        126       0.001          0.055
>  0.0
> >  Rest                                           0.609         25.573
>  0.5
> >
> -----------------------------------------------------------------------------
> >  Total                                        133.392       5599.205
> 100.0
>
>
>
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