From: sunyeping (sunyeping_at_aliyun.com)
Date: Wed Mar 12 2014 - 09:42:34 CDT
Dear Dong,I searched the namdenergy.tcl and found namd2 appeared in two places:
-path [file join /usr/local/bin/namd2] namd2]set job(biocore_cmd) [list "namd2"]I added +idlepoll to after all the namd2, so the two lines become:-path [file join /usr/local/bin/namd2 +idlepoll] namd2 +idlepoll]set job(biocore_cmd) [list "namd2 +idlepoll"]However when I ran NAMDEnergy plugin in VMD, the same error appeared:Reason: FATAL ERROR: Please add +idlepoll to command line for proper performance.
Charm++ fatal error:
FATAL ERROR: Please add +idlepoll to command line for proper performance.Could you explain how to modify to script so as to enable the plugin work properly? Thank you very much.
Yeping
------------------------------------------------------------------
发件人：Dong Luo <us917_at_yahoo.com>
发送时间：2014年2月25日(星期二) 01:24
收件人：孙业平 <sunyeping_at_aliyun.com>
主 题：Re: namd-l: RE：namd-l: Re: RE：namd-l: NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance
Hi sunyeping,
Let me try explain it to you. nameenergy.tcl is a script file comes with NAMDEnergy plugin of VMD. The execution of this plugin is just a call to this script. You can find it under plugins/noarch/tcl/namdenergy1.4 of VMD folder.Using any text editor to open the tcl file and find where "namd2" is called, and change it into "namd2 +idlepoll".
FYI, all VMD plugins are built by tcl files.
Dong
On Monday, February 24, 2014 4:40 AM, sunyeping <sunyeping_at_aliyun.com> wrote:
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
------------------------------------------------------------------
发件人：Axel Kohlmeyer <akohlmey_at_gmail.com>
发送时间：2014年2月24日(星期一) 11:26
收件人：孙业平 <sunyeping_at_aliyun.com>
抄 送：namd-l <namd-l_at_ks.uiuc.edu>
主 题：namd-l: Re: RE：namd-l: NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance
On Sun, Feb 23, 2014 at 10:13 PM, sunyeping <sunyeping_at_aliyun.com> wrote:
>
> 发件人：Axel Kohlmeyer <akohlmey_at_gmail.com>
> 发送时间：2014年2月24日(星期一) 10:57
> 收件人：孙业平 <sunyeping_at_aliyun.com>
> 抄 送：namd-l <namd-l_at_ks.uiuc.edu>
> 主 题：Re: namd-l: NAMDEnergy: FATAL ERROR: Please add
+idlepoll to command
> line for proper performance
>
> On Sun, Feb 23, 2014 at 9:29 PM, sunyeping <sunyeping_at_aliyun.com> wrote:
>> Dear NAMD user,
>>
>> I am using CUDA accelerated VMD and trying to run NAMD Energy using NAMD
>> Energy Plugin graphical interface. I am getting this error:
>> FATAL ERROR: Please add +idlepoll to command line for proper
>> performance.
>>
>> In namd mail list here Dr. Axel Kohlmeyer used to give comment to the
>> error.
>> He suggest changing the namdenergy.tcl script and insert it everywhere
>> namd
>> is executed, But I cann't understand it. Should I put the vmd scrpit
>> namdenergy.tcl into the directory which contains namd2 command? I have
>> tried
>> it but it doesn't work?
>
> of *course* it doesn't work. you have to put the modified version
>
where you took the original version from. or is that too obvious?
>
> axel.
>
>
>>Hi, axel,
>
> I would be very appreciated if you could explain how to modify the
> namdenergy.tcl script.
you load it into a text editor, change the text and save it. done.
axel.
>
>> Yeping Sun
>
>>Hi, axel,
>> Sorry I mean I don't know where to insert "+idlepoll" in the namdenergy.tcl script. Could you explain this to me?
>>
>Best regards.
>
>
> --
> 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.
--
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.
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