Hi Jagannath, I don't dare comment on these specifics. There's probably some (gromacs specific) benchmarks out there *somewhere*, quite possibly on this list. But maybe someone else on the list knows what you should get :)
Peter On 04/09/15 15:58, jagannath mondal wrote: > 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 <[email protected]> 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 >> >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to [email protected]. >>
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