[gmx-users] problem with gpu performance
Peter Kroon
p.c.kroon at rug.nl
Fri Sep 4 15:15:06 CEST 2015
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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