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].
