From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Dec 10 2018 - 12:10:06 CST
The +devices argument isn't needed here, and should probably instead be looking at only the +p argument to specify the number of processors. NAMD's error message is saying that because only 1 video card (device) was found, it can't use the 6th one to run NAMD, so it errors out. My typical GPU call looks like this:
/PATH/TO/GPU/NAMD/namd2 +p8 input.namd > input.log
Only if you have multiple GPUs on the hardware and you want to only use a subset (maybe because you want to run two simulations on the same machine) do you need to specify +devices.
-Josh
On 2018-12-10 08:20:35-07:00 owner-namd-l_at_ks.uiuc.edu wrote:
Hello,
What is the output of 'nvidia-smi' ?
Best,
Victor
On Sun, Dec 9, 2018 at 3:03 AM 李耀 <liyao17_at_mails.tsinghua.edu.cn> wrote:
>
> Dear NAMD users,
>
> I'm running namd2 on GPU server with NAMD_Git-2017-12-25_Linux-x86_64-multicore-CUDA and this is the command:
> ./namd2 +devices 5 ~/4ntw/string_eq_5ns/f1t10/win_f1/win5_f1.conf > ~/4ntw/string_eq_5ns/f1t10/win_f1/win5_f1.log
>
> It came out the following error:
> Charm++ fatal error:
> FATAL ERROR: Pe 0 unable to bind to CUDA device 5 on omnisky because only 1 devices are present
>
> Aborted (core dumped)
>
> Then I declare 8 CPUs:
> ./namd2 +p 8 +devices 5 ~/4ntw/string_eq_5ns/f1t10/win_f1/win5_f1.conf > ~/4ntw/string_eq_5ns/f1t10/win_f1/win5_f1.log
>
> The coming message is:
> Charm++ fatal error:
> FATAL ERROR: Pe 4 unable to bind to CUDA device 5 on omnisky because only 1 devices are present
>
> Aborted (core dumped)
>
> I have a few questions:
> 1) Do I need to declare the number of CPU to use(+p num) in this version of NAMD?
> 2) How to make all the calculation(configuration and energy calculation) run with GPU but not with GPU and CPU?
> 3) How to explain those errors? There seems no problem about the GPU devices.
>
> Thank you for reading my mail.
>
> Best,
> Yao Li
>
</liyao17_at_mails.tsinghua.edu.cn>
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