VMD-L Mailing List

From: João Ribeiro KS (jribeiro_at_ks.uiuc.edu)
Date: Thu Mar 09 2017 - 07:29:49 CST

Hi Kanishk,

I'm glad that the problem is solved. You can check the output created by
NAMD, in the <QwikMD output folder>/run/*.log files. If you find a message
like the one below, that means NAMD is using the GPU, and you can even see
if it detected your GPU correctly.

Best wishes

Joao Ribeiro

"Info: Built with CUDA version 7000
Did not find +devices i,j,k,... argument, using all
Pe 0 physical rank 0 will use CUDA device of pe 4
Pe 7 physical rank 7 will use CUDA device of pe 4
Pe 3 physical rank 3 will use CUDA device of pe 4
Pe 6 physical rank 6 will use CUDA device of pe 4
Pe 2 physical rank 2 will use CUDA device of pe 4
Pe 5 physical rank 5 will use CUDA device of pe 4
Pe 4 physical rank 4 binding to CUDA device 0 on <Machine name>: 'GeForce
GT 750M' Mem: 2047MB Rev: 3.0
Pe 1 physical rank 1 will use CUDA device of pe 4"

On Wed, Mar 8, 2017 at 7:12 PM Kanishk Jain <kjain_at_ucla.edu> wrote:

> Axel, thanks for the advice!
>
> Joao, your question prompted me to update my CUDA driver to 8.0.63 and my
> NVIDIA driver is 367.15.10.35f01. After updating the CUDA driver, I tried
> my simulation again and I didn't get that error anymore. I'm assuming this
> means that my GPU was recognized and is being used now?
>
> -Kanishk
>
> On Wed, Mar 8, 2017 at 1:32 PM, João Ribeiro KS <jribeiro_at_ks.uiuc.edu>
> wrote:
>
> Dear Kanishk,
>
> can you tell us the CUDA Driver Version that you installed and the GPU
> Driver Version? You can find this in your System Preferences/CUDA.
>
>
> Best
>
> Joao
>
> On Wed, Mar 8, 2017 at 3:26 PM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> On Wed, Mar 8, 2017 at 3:48 PM, Kanishk Jain <kjain_at_ucla.edu> wrote:
>
> I double checked and noticed there was indeed an initial error which may
> explain why I'm not able to connect to NAMD:
>
> Reason: FATAL ERROR: CUDA error cudaGetDeviceCount(&deviceCount) in file
> src/DeviceCUDA.C, function initialize
>
> on Pe 3 (Kanishks-iMac.local): CUDA driver version is insufficient for
> CUDA runtime version
>
> Does this mean that my GPU (NVIDIA GeForce GT 750M 1024 MB) isn't good
> enough? I updated the NVIDIA web drivers as well, but still nothing.
>
> I've used the non-CUDA version of NAMD (NAMD_2.12_MacOSX-x86_64-multicore)
> succesfully, but I was hoping that the CUDA version would allow me to
> utilize my GPU and make the MD calcs much faster.
>
>
> ​i cannot comment on the driver issue, but i suggest you carefully study
> the NAMD release notes which should reference GPU compatibility.
>
> ​also, ​you seem to have quite inflated expectations about how much
> speedup you can get from your ​GPU. your GPU appears to be a laptop model
> with a limited number of CUDA cores. it also will have a lower clock and
> heat budget than high-end desktop models. so i would be surprised, if you
> get more than 20% of the CUDA performance of a high-end desktop or server
> GPU. if you are also going to share the GPU across multiple CPUs, there is
> not much speedup left.
>
> ​axel.​
>
> -Kanishk
>
> On Tue, Mar 7, 2017 at 3:08 PM, Kanishk Jain <kjain_at_ucla.edu> wrote:
>
> Hello all,
>
> I'm an MD novice, starting out on QwikMD. I'm using a mac with the
> following versions of VMD and NAMD, respectively: vmd193macx86nocuda
> and NAMD_2.12_MacOSX-x86_64-multicore-CUDA.
>
> My problem is that when I try to start a simulation, I keep getting the
> following error:
>
> ERROR) Error connecting to localhost on port 3000
>
> I've seen a similar question to mine as it applies to Linux machines, but
> as I'm a novice, I'm not quite sure how to implement the solutions
> mentioned in those threads to my situation. Any help would be appreciated!
>
> -Kanishk
>
> --
> Sincerely,
> Kanishk Jain
> Steven G. Clarke Laboratory, PhD Candidate
> Biochemistry and Molecular Biology Program
> Department of Chemistry and Biochemistry
> University of California, Los Angeles
>
>
>
>
> --
> Sincerely,
> Kanishk Jain
> Steven G. Clarke Laboratory, PhD Candidate
> Biochemistry and Molecular Biology Program
> Department of Chemistry and Biochemistry
> University of California, Los Angeles
>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3000380 <(217)%20300-0380>
>
>
>
>
> --
> Sincerely,
> Kanishk Jain
> Steven G. Clarke Laboratory, PhD Candidate
> Biochemistry and Molecular Biology Program
> Department of Chemistry and Biochemistry
> University of California, Los Angeles
> 

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
jribeiro_at_ks.uiuc.edu
+1 (217) 3000380