RE: RE: Re: RE: NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance

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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