Running on GPU

From: Mahmood Naderan (mahmood.nt_at_gmail.com)
Date: Mon Mar 12 2018 - 14:22:31 CDT

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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