Re: namd-l digest V1 #2289

From: Zahra Mohammadi (mohammadizahra94_at_gmail.com)
Date: Wed Oct 25 2017 - 02:58:36 CDT

Hi everyone,

And thank you

Abhi for replying me. I did the "

+idlepoll" in my command line. The command line is:

/home/.../NAMD_2.11_Linux-x86_64-multicore-CUDA/charmrun *++local* *+p24 *
 /home/.../NAMD_2.11_Linux-x86_64-multicore-CUDA/namd2 *+idlepoll*
File.conf > File.log

1- Another question is the syntax of above command, is it correct? Because
you said add the "

+idlepoll" *next to charmrun*, while in mine it is written *next to namd2*.
Would it make any difference?

*2- Also the problem still exist, so any advice, suggestion or solution by
anyone is deeply appreciated.*

Thanks,
Zahra

On Wed, Oct 25, 2017 at 9:37 AM, namd-l digest <
owner-namd-l-digest_at_ks.uiuc.edu> wrote:

>
> namd-l digest Wednesday, October 25 2017 Volume 01 : Number
> 2289
>
>
>
> In this issue:
>
> Re: namd-l: FATAL ERROR: cuda_check_progress polled 1000000 times over
> ...
>
> ----------------------------------------------------------------------
>
> Date: Tue, 24 Oct 2017 11:42:32 +0000
> From: Abhishek TYAGI <atyagiaa_at_connect.ust.hk>
> Subject: Re: namd-l: FATAL ERROR: cuda_check_progress polled 1000000 times
> over ...
>
> Hi,
>
> It seems to me that on hpc you need to add +idlepoll next to charmrun
>
> Best
> Abhi
>
> Get Outlook for Android<https://aka.ms/ghei36>
>
>

> ________________________________
> From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
> Zahra
> Mohammadi <mohammadizahra94_at_gmail.com>
> Sent: Tuesday, October 24, 2017 7:12:55 PM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: FATAL ERROR: cuda_check_progress polled 1000000 times over
> ...
>
> Hi eveyone,
> I was wondering if anybody who knows about my problem or has any related
> experiences, help me with my problem.
>
> I am runnig a common MD simulation of a protein in a water box. My
> simulation
> is running on High Performance Computer Cluster (HPCC). After the
> minimization
> process (3000 steps) when it ends my problem occurs which is at the
> beginning
> of MD simulation process. I get this FATAL error which is below:
>
> Charm++ fatal error:
> FATAL ERROR: cuda_check_progress polled 1000000 times over 100.825342 s on
> step 1181
>
> I searched and found nothing about it to solve my problem. In advance, I
> appreciate all of the help.
>
> Thanks
> Zahra
>
> ------------------------------
>
> End of namd-l digest V1 #2289
> *****************************
>
>

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