[gmx-users] gromacs on itanium2

[Marius Retegan]

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.

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.
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