Hi Szilad, thank You for your response, I attach the log file 2017-09-19 15:19 GMT+02:00 Szilárd Páll <[email protected]>:
> PS: A bit of extrapolation from my standard historical benchmark data > shows that regular cut-off kernels should run at ~3.0 ms/step, so > force shift will be ~3.5-4 ms/step (with nstlist=20 and 2 fs step); > assuming 70% CPU-GPU overlap that's 5-5.5 ms/step which corresponds to > ~35 ns/day (with 2 fs). > > That's just a rough estimate, though, and it assumes that you have > enough CPU cores for a balanced run. > > -- > Szilárd > > > On Tue, Sep 19, 2017 at 3:16 PM, Szilárd Páll <[email protected]> > wrote: > > On Tue, Sep 19, 2017 at 2:20 PM, Tomek Stępniewski > > <[email protected]> wrote: > >> Hi everybody, > >> I am running gromacs 5.1.4 on a system that uses NVIDIA Tesla K40m, > >> surprisingly I get a speed of only 15 ns a day when carrying out nvt > >> simulations, my colleagues say that on a new GPU like this with my > system > >> size it should be around 60 ns a day, > >> are there any apparent errors in my input files that might hhinder the > >> simulation? > > > > 15 ns/day seems a bit low, but I can't say for sure if it's far too > > low. Can you share logs? > > > >> input file: > >> integrator = md > >> dt = 0.002 > >> nsteps = 100000000 > >> nstlog = 10000 > >> nstxout = 50000 > >> nstvout = 50000 > >> nstfout = 50000 > >> nstcalcenergy = 100 > >> nstenergy = 1000 > >> ; > >> cutoff-scheme = Verlet > >> nstlist = 20 > >> rlist = 1.2 > >> coulombtype = pme > >> rcoulomb = 1.2 > >> vdwtype = Cut-off > >> vdw-modifier = Force-switch > >> rvdw_switch = 1.0 > >> rvdw = 1.2 > >> ; > >> tcoupl = Nose-Hoover > >> tc_grps = PROT MEMB SOL_ION > >> tau_t = 1.0 1.0 1.0 > >> ref_t = 310 310 310 > >> ; > >> constraints = h-bonds > >> constraint_algorithm = LINCS > >> continuation = yes > >> ; > >> nstcomm = 100 > >> comm_mode = linear > >> comm_grps = PROT MEMB SOL_ION > >> ; > >> refcoord_scaling = com > >> > >> the system has around 70,000 atoms, > >> > >> can this issue depend on the CUDA drivers?: > > > > A bit, but not to a factor of 4. > > > >> CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda > compiler > >> driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on > >> Tue_Jan_10_13:22:03_CST_2017;Cuda compilation tools, release 8.0, > V8.0.61 > >> CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch= > >> compute_30,code=sm_30;-gencode;arch=compute_35,code= > >> sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch= > >> compute_50,code=sm_50;-gencode;arch=compute_52,code= > >> sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch= > >> compute_61,code=sm_61;-gencode;arch=compute_60,code= > >> compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;; > >> ;-march=core-avx2;-Wextra;-Wno-missing-field- > initializers;-Wpointer-arith;- > >> Wall;-Wno-unused-function;-O3;-DNDEBUG;-funroll-all-loops;- > >> fexcess-precision=fast;-Wno-array-bounds; > >> CUDA driver: 8.0 > >> CUDA runtime: 8.0 > >> GPU info: > >> Number of GPUs detected: 1 > >> #0: NVIDIA Tesla K40m, compute cap.: 3.5, ECC: yes, stat: compatible > >> > >> NOTE: GROMACS was configured without NVML support hence it can not > exploit > >> application clocks of the detected Tesla K40m GPU to improve > >> performance. > >> Recompile with the NVML library (compatible with the driver used) > or > >> set application clocks manually. > >> > >> > >> Using GPU 8x8 non-bonded kernels > >> > >> I will be extremely grateful for any help, > >> best > >> > >> -- > >> Tomasz M Stepniewski > >> Research Group on Biomedical Informatics (GRIB) > >> Hospital del Mar Medical Research Institute (IMIM) > >> -- > >> 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]. > -- > 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]. > -- Tomasz M Stepniewski Research Group on Biomedical Informatics (GRIB) Hospital del Mar Medical Research Institute (IMIM)
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