From: Gary M. Skinner (ga_skinner_at_hotmail.com)
Date: Mon May 09 2011 - 03:31:45 CDT
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> From: twang_at_ssc.net.cn
> To: johanstr_at_ks.uiuc.edu; norman.geist_at_uni-greifswald.de
> CC: namd-l_at_ks.uiuc.edu
> Subject: 答复: namd-l: compilation of namd
> Date: Mon, 9 May 2011 14:27:12 +0800
>
> Another question is when I user intel compilers 9.1 to compile NAMD_2.8b1,
> I got the following error
> ld: Cpv_iout_obj_: TLS reference in obj/main.o mismatches non-TLS reference in obj/common.o
> obj/main.o: could not read symbols: Bad value
>
> But I can not find Cpv_iout_obj in source files
>
> TAO
>
> ---------------------------------------------------------------------------------------
> Dr. Tao Wang
> Ph.D. @ University of Science and Technology of China, Computational Chemistry
>
> Manager
> Dept. of HPC Application Technology
> Shanghai Supercomputer Center
> No.585 Guoshoujing Rd., Pudong, Shanghai 201203, P.R.C.
> Phone: (86)-21-50802779
> Cell: 13601984020
> Fax: (86)-21-50801265
> e-mail: twang_at_ssc.net.cn
> http://www.ssc.net.cn
>
>
> -----邮件原件-----
> 发件人: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] 代表 johan strumpfer
> 发送时间: 2011年5月6日 22:10
> 收件人: Norman Geist
> 抄送: TAO WANG; Namd Mailing List
> 主题: Re: namd-l: compilation of namd
>
> Hi Tao,
>
> Jim would have to correct me here, but as far as I know there are no
> additional compiler flags specified (i.e. other than those in
> arch/*.arch) for the binaries on the website. According to my
> knowledge version 9.0.30 of the intel compilers were used for those
> builds.
>
> Cheers,
> Johan
>
> ------------------------------------------------------------------------------------------------------
> Johan Strumpfer: johanstr_at_ks.uiuc.edu www.ks.uiuc.edu/~johanstr
> Theoretical and Computational Biophysics Group
> 3115 Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews
> Urbana, IL 61801, USA
> ------------------------------------------------------------------------------------------------------
>
>
>
> On Fri, May 6, 2011 at 1:16 AM, Norman Geist
> <norman.geist_at_uni-greifswald.de> wrote:
> > Hi,
> >
> >
> >
> > no I don’t know their flags, but I think you could just ask them. I can’t
> > imagine any reason why they shouldn’t tell you. But it’s always better to
> > get a little into the things, to understand what the flags do and where they
> > could have an impact.
> >
> >
> >
> > Best regards
> >
> >
> >
> > Norman Geist.
> >
> >
> >
> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
> > von TAO WANG
> > Gesendet: Freitag, 6. Mai 2011 07:57
> > An: 'Norman Geist'
> > Cc: 'Namd Mailing List'
> > Betreff: ??: namd-l: compilation of namd
> >
> >
> >
> > Thank you
> >
> > But, do you know how namd’s guy compile the binary version
> > Linux-x86_64-ibverbs on namd’s website ?
> >
> > What is their compiler flags ?
> >
> > TAO
> >
> >
> >
> > 发件人: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] 代表 Norman
> > Geist
> > 发送时间: 2011年5月6日 13:46
> > 收件人: 'TAO WANG'
> > 抄送: Namd Mailing List
> > 主题: AW: namd-l: compilation of namd
> >
> >
> >
> > Hi,
> >
> >
> >
> > well, there are many compiler flags that can increase performance, and also
> > the opposite. You could try the auto optimization levels like –O3 for
> > example, I think the icc must have parameters like this. But to high
> > optimization levels can come with unstable binarys or bad portability. U can
> > also try to fit the compilation to your hardware, but that also restrict
> > portability, if you want to run the same binary on different architectures
> > like amd -> intel, or Xeon -> opteron. But you should really try the
> > optimization flags.
> >
> >
> >
> > Mit freundlichen Grüßen
> >
> >
> >
> > Norman Geist.
> >
> >
> >
> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
> > von TAO WANG
> > Gesendet: Freitag, 6. Mai 2011 04:09
> > An: namd-l_at_ks.uiuc.edu
> > Betreff: namd-l: compilation of namd
> >
> >
> >
> > Dear all,
> >
> > I have successfully compiled namd 2.8b1 by the following command
> >
> >
> >
> > ./build charm++ net-linux-x86_64 iccstatic ibverbs ifort --no-build-shared
> > --with-production
> >
> > ./config Linux-x86_64-icc --charm-arch
> > net-linux-x86_64-ibverbs-ifort-iccstatic --cxx icpc
> >
> >
> >
> > And this version run well.
> >
> >
> >
> > Then I download the binary version Linux-x86_64-ibverbs of namd 2.8b1
> >
> >
> >
> > I found this version is faster than my compiled version by 10%
> >
> >
> >
> > My complier is ifort and icc 11.1
> >
> >
> >
> > Is there anyone knows how they compile the binary version
> > Linux-x86_64-ibverbs on namd’s website, so that their version is faster than
> > mine ?
> >
> > Thanks
> >
> > TAO
> >
> >
>
>
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