Your run is probably GPU-bound because you have a rather slow GPU and as
per new mdrun defaults both PME and nonbondeds are offloaded which may not
be ideal for your case. Try the different offload modes to see which one is
best on your hardware.

Additionally, you still have not provided the *mdrun log file* I requested.
top output is not what I asked for.




--
Szilárd

On Wed, Feb 28, 2018 at 4:47 PM, Mahmood Naderan <nt_mahm...@yahoo.com>
wrote:

> I forgot to say that gromacs reports
>
> No option -multi
> Using 1 MPI thread
> Using 16 OpenMP threads
>
> 1 GPU auto-selected for this run.
> Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
>   PP:0,PME:0
>
> NOTE: GROMACS was configured without NVML support hence it can not exploit
>       application clocks of the detected Quadro M2000 GPU to improve
> performance.
>
>
>
>
>
>
> Regards,
> Mahmood
>
>
> On Wednesday, February 28, 2018, 7:15:13 PM GMT+3:30, Mahmood Naderan <
> nt_mahm...@yahoo.com> wrote:
>
>
> By runing
>
> gmx mdrun -nb gpu -deffnm md_0_1
>
>
> I see the following outputs
>
>
> $ top -b  | head -n 10
> top - 19:14:10 up 7 min,  1 user,  load average: 4.54, 1.40, 0.54
> Tasks: 344 total,   1 running, 343 sleeping,   0 stopped,   0 zombie
> %Cpu(s):  7.1 us,  0.5 sy,  0.0 ni, 91.9 id,  0.4 wa,  0.0 hi,  0.0 si,
> 0.0 st
> KiB Mem : 16438496 total, 13462876 free,  1968196 used,  1007424 buff/cache
> KiB Swap: 31250428 total, 31250428 free,        0 used. 14054796 avail Mem
>
>   PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
>  3604 mahmood   20   0 30.519g 525812 128788 S 918.8  3.2   6:58.38 gmx
>  1180 root      20   0  324688  69384  49712 S   6.2  0.4   0:14.41 Xorg
>  1450 mahmood   20   0  210228   7856   7192 S   6.2  0.0   0:00.17
> ibus-engin+
>
>
>
> $ nvidia-smi
> Wed Feb 28 19:14:35 2018
> +-----------------------------------------------------------
> ------------------+
> | NVIDIA-SMI 384.81                 Driver Version:
> 384.81                    |
> |-------------------------------+----------------------+----
> ------------------+
> | GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr.
> ECC |
> | Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute
> M. |
> |===============================+======================+====
> ==================|
> |   0  Quadro M2000        Off  | 00000000:23:00.0  On |
> N/A |
> | 65%   64C    P0    58W /  75W |    292MiB /  4035MiB |     93%
> Default |
> +-------------------------------+----------------------+----
> ------------------+
>
>
> +-----------------------------------------------------------
> ------------------+
> | Processes:                                                       GPU
> Memory |
> |  GPU       PID   Type   Process name
> Usage      |
> |===========================================================
> ==================|
> |    0      1180      G   /usr/lib/xorg/Xorg
> 141MiB |
> |    0      1651      G   compiz
> 46MiB |
> |    0      3604      C   gmx
> 90MiB |
> +-----------------------------------------------------------
> ------------------+
>
>
>
>
>
> Any idea?
>
>
> Regards,
> Mahmood
>
>
> On Monday, February 26, 2018, 10:52:40 PM GMT+3:30, Szilárd Páll <
> pall.szil...@gmail.com> wrote:
>
>
> Hi,
>
> Please provide details, e.g. the full log so we know what version, on what
> hardware, settings etc. you're running.
>
>
>
> --
> Szilárd
>
>
-- 
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