Yes
On Wed, Mar 4, 2009 at 3:45 PM, David van der Spoel <sp...@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 <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-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-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
