Re: Running on GPU

From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Mon Mar 12 2018 - 14:33:58 CDT

Hi Mahmood,

As I understand it, the GPU only does some of the calculations, a good
amount of the simulation is still on the CPU's and is CPU dependent. The
GPU utilization will change depending on which cycle of the simulation is
occurring. It would appear to me that your simulation is running fine,
however I am not an expert.

~Bassam

On Mon, Mar 12, 2018 at 12:22 PM, Mahmood Naderan <mahmood.nt_at_gmail.com>
wrote:

> Hi,
> Previously I asked about gpu utilization of my namd run. Still I have
> problem and I need some hints to see what is what. According to the
> manual [1], I used the following command
>
>
> namd2 +idlepoll +p4 +devices 0 ubq_ws_eq.conf
> >namd2_idlepoll_p4_devices_0.txt
>
>
> The full output is available at https://pastebin.com/Mbp8N2h4
>
> As you can see in the log the GPU is detected. During the run, I see
> 400% CPU utilization, while nvidia-smi reports about 15% GPU
> utilization while a namd2 process with 100MB is there on the gpu.
>
> Any idea? Any idea is appreciated. I have stuck!
>
>
> +-----------------------------------------------------------
> ------------------+
> | Processes: GPU
> Memory |
> | GPU PID Type Process name Usage
> |
> |===========================================================
> ==================|
> | 0 1137 G /usr/lib/xorg/Xorg
> 158MiB |
> | 0 1616 G compiz
> 47MiB |
> | 0 3687 C namd2
> 104MiB |
> +-----------------------------------------------------------
> ------------------+
> Mon Mar 12 22:46:23 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 |
> | 56% 46C P0 26W / 75W | 324MiB / 4035MiB | 11%
> Default |
> +-------------------------------+----------------------+----
> ------------------+
>
>
>
>
> [1] http://www.ks.uiuc.edu/Research/namd/2.9/ug/node88.html
>
>
>
> Regards,
> Mahmood
>
>

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