Re: Re: 答复: compilation of namd

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed May 11 2011 - 10:53:59 CDT

I meant more conservative in the sense of not breaking code, but Axel's
suggestion is correct. Changing -O3 to -O2 and adding -no-vec improves
performance on newer compilers without hurting it on the old ones. I also
bumped -march up from pentiumpro to pentium4 on 32-bit builds to enable
some explicit SSE2 code. I think ten years is long enough to wait.

-Jim

On Tue, 10 May 2011, Axel Kohlmeyer wrote:

> On Tue, May 10, 2011 at 9:32 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>>
>> I have also observed that the Intel 11.1 compilers produce slower NAMD
>> builds than the old 9.0 compilers, even for the latest processors.  I'm
>> guessing the compiler is now more conservative in some optimization, but I
>> don't know what it is or how to work around it yet.
>
> jim, i believe the opposite is the case. the newer intel compilers
> are optimizing much more aggressively and particularly seem to
> try utilizing the vector instructions much more aggressively,
> often seems to be enefficient, since the data they operate on
> is not properly aligned. i often get faster executables by lowering
> optimization levels and optimizing for pentium pro (on 32-bit)
> and pentium 4 instruction set, but using core2 or nehalem heuristics
> (-march / -mtune).
>
> cheers,
> axel
>>
>> You must use the same compiler and version for Charm++ and NAMD or you are
>> likely to see errors like those below because of incompatibilities in the
>> C++ application binary interface (ABI), which is not standardized.
>>
>> -Jim
>>
>> On Mon, 9 May 2011, TAO WANG wrote:
>>
>>> 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
>>>>
>>>>
>>>
>>
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:55 CST