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 <lind...@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 >>> _______________________________________________ >>> gmx-users mailing list gmx-us...@gromacs.org >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> -- >> 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. >> sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >> _______________________________________________ >> gmx-users mailing list gmx-us...@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
