Re: compiler flags.

From: gengbin (gzheng_at_ks.uiuc.edu)
Date: Wed Jul 14 2004 - 23:58:54 CDT

Certain optimizations may use more memory for speed, but doubling memory
usage seems to be too much.
I am interested to see how -O2 goes with both memory and speed.
Also, use "top" to see if the memory usage agrees to what NAMD reports.

Gengbin

Brian Bennion wrote:

>Hi Gengbin and Jim and others
>
>I just finished a compile of tcl, fftw, charm++ and namd all using the -xN
>-O3 icc8.0 compiler flags.
>
>Compared to the previous executable I get about a 13% gain in speed for
>the same exact namd.config. I did notice that memory usage more than
>doubled and this is troubling.
>Some log snippets are below. Every second line is the same run....sorry
>for the confusion. The first line is the newest binary.
>any ideas what I might have done (wrong)?
>Regards
>Brian
>Info: Entering startup phase 0 with 15024 kB of memory in use | 00: Info:
>Entering startup phase 0 with 7139 kB of memory in
>Info: Entering startup phase 1 with 15024 kB of memory in use | 00: Info:
>Entering startup phase 1 with 7139 kB of memory in
>Info: Entering startup phase 2 with 17456 kB of memory in use | 00: Info:
>Entering startup phase 2 with 9572 kB of memory in
>Info: Entering startup phase 3 with 17699 kB of memory in use | 00: Info:
>Entering startup phase 3 with 9816 kB of memory in
>Info: PATCH GRID IS 5 (PERIODIC) BY 5 (PERIODIC) BY 4 (PERIOD | 00: Info:
>PATCH GRID IS 5 (PERIODIC) BY 5 (PERIODIC) BY 4 (PE
>Info: REMOVING COM VELOCITY -0.000221351 -0.00606466 0.000429 | 00: Info:
>REMOVING COM VELOCITY -0.000221351 -0.00606466 0.00
>Info: LARGEST PATCH (33) HAS 402 ATOMS | 00: Info:
>LARGEST PATCH (33) HAS 402 ATOMS
>Info: Entering startup phase 4 with 22092 kB of memory in use | 00: Info:
>Entering startup phase 4 with 14208 kB of memory in
>Info: PME using 40 and 40 processors for FFT and reciprocal s | 00: Info:
>PME using 40 and 40 processors for FFT and reciproc
>Creating Strategy 4 | 00:
>Creating Strategy 4
>Creating Strategy 4 | 00:
>Creating Strategy 4
>Info: PME GRID LOCATIONS: 1 3 5 7 9 11 13 14 15 17 ... | 00: Info:
>PME GRID LOCATIONS: 1 3 5 7 9 11 13 14 15 17 ...
>Info: PME TRANS LOCATIONS: 1 3 5 7 9 11 13 14 15 17 ... | 00: Info:
>PME TRANS LOCATIONS: 1 3 5 7 9 11 13 14 15 17 ...
>Info: Entering startup phase 5 with 22098 kB of memory in use | 00: Info:
>Entering startup phase 5 with 14215 kB of memory in
>Info: Entering startup phase 6 with 18266 kB of memory in use | 00: Info:
>Entering startup phase 6 with 10382 kB of memory in
>Info: Entering startup phase 7 with 18270 kB of memory in use | 00: Info:
>Entering startup phase 7 with 10387 kB of memory in
>Info: COULOMB TABLE R-SQUARED SPACING: 0.0625 | 00: Info:
>COULOMB TABLE R-SQUARED SPACING: 0.0625
>Info: COULOMB TABLE SIZE: 705 POINTS | 00: Info:
>COULOMB TABLE SIZE: 705 POINTS
>
>
>On Tue, 13 Jul 2004, Gengbin Zheng wrote:
>
>
>
>>I guess you just need these switches for NAMD. If you also want them for
>>charm, you can add them to build script like:
>>./build charm++ net-linux -O3 ...
>>
>>Gengbin
>>
>>Brian Bennion wrote:
>>
>>
>>
>>>okay. now that I am going to do some testing...where do I put these
>>>switches if i use the build script in charm?
>>>
>>>
>>>On Tue, 13 Jul 2004, Gengbin Zheng wrote:
>>>
>>>
>>>
>>>
>>>
>>>>yes, i was using the default. No luck with it. -O1 or -O0 may work. I am
>>>>not aware of -xWNP flags.
>>>>
>>>>Gengbin
>>>>
>>>>Brian Bennion wrote:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>So you where using the default -O2 optimization and not and -xWNP flags?
>>>>>
>>>>>
>>>>>
>>>>>On Tue, 13 Jul 2004, Gengbin Zheng wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>unforturantely so far I have no luck with Intel 8 compiler. Get rid of
>>>>>>all optimization flags let it work as I remember, however, very very bad
>>>>>>performance. I have not tried to selectively get rid of some of the
>>>>>>optimization flags and see the impact of the performance though. For
>>>>>>example, remove some of the -f flags, or lower the optimization level.
>>>>>>
>>>>>>Gengbin
>>>>>>
>>>>>>Brian Bennion wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>Hi Gengbin,
>>>>>>>
>>>>>>>I know I sent an email through the namd-l list, but I really could use a
>>>>>>>quick answer either way. I need to get NAMD and charm running at their
>>>>>>>best and soon. If I need to experiment with different options then I can,
>>>>>>>but I really don't want to reinvent the wheel here.
>>>>>>>
>>>>>>>Tell me what you think.
>>>>>>>brian
>>>>>>>
>>>>>>>
>>>>>>>*****************************************************************
>>>>>>>**Brian Bennion, Ph.D. **
>>>>>>>**Computational and Systems Biology Division **
>>>>>>>**Biology and Biotechnology Research Program **
>>>>>>>**Lawrence Livermore National Laboratory **
>>>>>>>**P.O. Box 808, L-448 bennion1_at_llnl.gov **
>>>>>>>**7000 East Avenue phone: (925) 422-5722 **
>>>>>>>**Livermore, CA 94550 fax: (925) 424-6605 **
>>>>>>>*****************************************************************
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>*****************************************************************
>>>>>**Brian Bennion, Ph.D. **
>>>>>**Computational and Systems Biology Division **
>>>>>**Biology and Biotechnology Research Program **
>>>>>**Lawrence Livermore National Laboratory **
>>>>>**P.O. Box 808, L-448 bennion1_at_llnl.gov **
>>>>>**7000 East Avenue phone: (925) 422-5722 **
>>>>>**Livermore, CA 94550 fax: (925) 424-6605 **
>>>>>*****************************************************************
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>*****************************************************************
>>>**Brian Bennion, Ph.D. **
>>>**Computational and Systems Biology Division **
>>>**Biology and Biotechnology Research Program **
>>>**Lawrence Livermore National Laboratory **
>>>**P.O. Box 808, L-448 bennion1_at_llnl.gov **
>>>**7000 East Avenue phone: (925) 422-5722 **
>>>**Livermore, CA 94550 fax: (925) 424-6605 **
>>>*****************************************************************
>>>
>>>
>>>
>>>
>>
>>
>
>*****************************************************************
>**Brian Bennion, Ph.D. **
>**Computational and Systems Biology Division **
>**Biology and Biotechnology Research Program **
>**Lawrence Livermore National Laboratory **
>**P.O. Box 808, L-448 bennion1_at_llnl.gov **
>**7000 East Avenue phone: (925) 422-5722 **
>**Livermore, CA 94550 fax: (925) 424-6605 **
>*****************************************************************
>
>

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