VMD-L Mailing List

From: yp sun (sunyeping_at_yahoo.com.cn)
Date: Sun May 26 2013 - 04:00:43 CDT

 Dr. Kohlmeyer,  You are right, VMD load dcd file slowly because I am performing a NAMD simulation. and the CPU of the machine is completely occupied. Best Regards!    Yeping Sun CAS Key Laboratory of Pathogenic Microbiology & Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china ________________________________ 发件人： Axel Kohlmeyer <akohlmey_at_gmail.com> 收件人： yp sun <sunyeping_at_yahoo.com.cn> 抄送： "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu> 发送日期： 2013年5月26日, 星期日, 2:24 下午 主题: Re: vmd-l: why does VMD load dcd file so slowly? On Sun, May 26, 2013 at 3:40 AM, yp sun <sunyeping_at_yahoo.com.cn> wrote: > Dear VMD users, > >    I find the VMD program installed in my computer with two tesla c2050 > cards loads dcd file very slowly, the FPS is about 3. Even in my laptop with > the video card  ATI Mobility Radeon HD 4300 Series, VMD load dcd file with > FPS of 45. Do you also have such experience? Why vmd works so bad in > computer with GPU? because loading files has *nothing* to do with GPUs. tesla GPUs in particular are only used for certain highly compute bound operations. just sticking a GPU into a machine doesn't make it faster. as for the file i/o speed, it sounds a lot like you have your data on your desktop not on a local disk, but on a networked file system, which is orders of magnitude slower than a local (spinning) disk and especially SSDs. VMD has highly optimized code for reading dcd format files, so the conclusion is that it is not a VMD problem, but how *you* are using it. axel. > > Best regards! > > Yeping Sun > CAS Key Laboratory of Pathogenic Microbiology & Immunology > INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES > NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china -- Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.