[gmx-users] gromacs on itanium2

[Marius Retegan]

Yes

On Wed, Mar 4, 2009 at 3:45 PM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> Marius Retegan wrote:
>>
>> Hi,
>>
>> Thank you for the suggestions. I've managed to get the version 4.0.4
>> compiled by using --enable-fortran and --disable-ia64-asm.
>> Nevertheless some of the kernel tests still fail.
>
> Did you use the new test set?
>
>>
>> FAILED. Check files in kernel020
>> FAILED. Check files in kernel120
>> FAILED. Check files in kernel121
>> FAILED. Check files in kernel122
>> FAILED. Check files in kernel123
>> FAILED. Check files in kernel124
>> FAILED. Check files in kernel220
>> FAILED. Check files in kernel221
>> FAILED. Check files in kernel222
>> FAILED. Check files in kernel223
>> FAILED. Check files in kernel224
>> FAILED. Check files in kernel320
>> FAILED. Check files in kernel321
>> FAILED. Check files in kernel322
>> FAILED. Check files in kernel323
>> FAILED. Check files in kernel324
>> 16 out of 63 kernel tests FAILED
>>
>> Is this due to the fact that I've disable the assembly loops for ia64?
>> I also have some problems with the parallel version.
>>
>> Testing acetonitrilRF . . . FAILED. Check files in acetonitrilRF
>> Testing aminoacids . . . FAILED. Check files in aminoacids
>> Testing argon . . . FAILED. Check files in argon
>> Testing butane . . . PASSED but check mdp file differences
>> Testing dec+water . . . PASSED but check mdp file differences
>> Testing ethyleenglycol . . . PASSED but check mdp file differences
>> Testing fe_test . . . PASSED but check mdp file differences
>> Testing field . . . PASSED but check mdp file differences
>> Testing nacl . . . PASSED but check mdp file differences
>> Testing sw . . . FAILED. Check files in sw
>> Testing tip4p . . . FAILED. Check files in tip4p
>> Testing tip4pflex . . . PASSED but check mdp file differences
>> Testing urea . . . FAILED. Check files in urea
>> Testing water . . . FAILED. Check files in water
>> 7 out of 14 complex tests FAILED
>>
>> For the failed test I get the following error
>>
>> -------------------------------------------------------
>> Program mdrun_mpi_d, VERSION 4.0.4
>> Source code file: domdec.c, line: 5444
>>
>> Fatal error:
>> ns type Simple is not supported with domain decomposition,
>> use particle decomposition: mdrun -pd
>> -------------------------------------------------------
>>
>> Also in the gmxtest.pl script the option -np for the grompp should be
>> removed.
>> Finally, I was wondering if the use of mkl in place of fftw3 would
>> improve performance.
>>
>> Thanks,
>> Marius
>>
>>
>>
>>
>> On Tue, Mar 3, 2009 at 10:02 PM, Erik Lindahl <lindahl at cbr.su.se> wrote:
>>>
>>> Hi,
>>>
>>> There have been some reports on newer ia64 processors being quite fast
>>> with
>>> the Fortran kernels instead (even faster than asm!), so I would try that.
>>>
>>> This has to do with the brain-dead architecture on ia64. The asm kernels
>>> were written for original itanium2 timings, but with the register
>>> rotation
>>> loops and lack of dynamic instruction scheduling you would get lots of
>>> pipeline stalls/bubbles if Intel ever changed their instruction
>>> latencies,
>>> and that might have happend now.
>>>
>>> Considering the limited adoption of ia64 I don't think we're very likely
>>> to
>>> keep updating those kernels - the first thing on the agenda right now
>>> will
>>> rather be improved performance of x86 SSE kernels for Gromacs 4.1.
>>>
>>> Cheers,
>>>
>>> Erik
>>>
>>>
>>> On Mar 3, 2009, at 8:14 PM, David van der Spoel wrote:
>>>
>>>> Marius Retegan wrote:
>>>>>
>>>>> Hello
>>>>> Since I was unable to get a working version for Gromacs 4.0.4 on a
>>>>> Itanium 2 machine with the ia64 nonbonded kernel, I was wondering what
>>>>> would be the lost in speed if I would disable the assembly loops?
>>>>
>>>> About a factor of two. What's the problem with compiling?
>>>>
>>>>> Thanks,
>>>>> Marius
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>>>>
>>>> --
>>>> David van der Spoel, Ph.D., Professor of Biology
>>>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
>>>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
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>