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Hi,<br><br>This is plain 4.0 code is presume?<br>This problem should be fixed then.<br><br>But I now also made vacuum without cut-off working with domain decomposition in CVS head.<br>Compared to a not-unbalanced PD (for instance only a protein, no water) DD is slightly slower.<br>But DD will be faster than a badly balanced PD system.<br><br>Berk<br><br>> Date: Wed, 27 May 2009 11:04:49 +0200<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Strange assignment of atoms to processors with pd<br>> <br>> Erik Marklund wrote:<br>> > David van der Spoel skrev:<br>> >> Erik Marklund wrote:<br>> >>> I should add that this problem only seem to arise when the analyte is <br>> >>> covered with a thin sheet of water. When simulating a dry analyte I <br>> >>> get good scaling. In the latter case the charges, and therefore the <br>> >>> topology, is slightly different.<br>> >> How about vsites? Did you happen to turn them off as well in the <br>> >> vacuum case?<br>> > Turned off in all cases. The VSites mentioned in the log file is the <br>> > 4:th particle on the tip4p-water molecules.<br>> OK. Did you try a one step run with -debug?<br>> It may give more info on the partitioning.<br>> <br>> >>><br>> >>> /Erik<br>> >>><br>> >>> Erik Marklund skrev:<br>> >>>> Hi,<br>> >>>><br>> >>>> I'm simulating non-periodic systems in vacuo, using constrained <br>> >>>> h-bonds and particle decomposition. For some of my simulations the <br>> >>>> cpu-usage seem far from optimal. The first cpu gets no atoms, while <br>> >>>> the second one gets plenty and the remaining cpus get less than I <br>> >>>> expected. Is this a bug?<br>> >>>><br>> >>>><br>> >>>> An excerpt from the log file:<br>> >>>><br>> >>>> There are: 2911 Atoms<br>> >>>> There are: 317 VSites<br>> >>>> splitting topology...<br>> >>>> There are 999 charge group borders and 318 shake borders<br>> >>>> There are 318 total borders<br>> >>>> Division over nodes in atoms:<br>> >>>> 0 1960 212 212 212 212 212 208<br>> >>>> Walking down the molecule graph to make constraint-blocks<br>> >>>> CPU= 0, lastcg= -1, targetcg= 499, myshift= 1<br>> >>>> CPU= 1, lastcg= 681, targetcg= 182, myshift= 0<br>> >>>> CPU= 2, lastcg= 734, targetcg= 235, myshift= 7<br>> >>>> CPU= 3, lastcg= 787, targetcg= 288, myshift= 6<br>> >>>> CPU= 4, lastcg= 840, targetcg= 341, myshift= 5<br>> >>>> CPU= 5, lastcg= 893, targetcg= 394, myshift= 4<br>> >>>> CPU= 6, lastcg= 946, targetcg= 447, myshift= 3<br>> >>>> CPU= 7, lastcg= 998, targetcg= 499, myshift= 2<br>> >>>> pd->shift = 7, pd->bshift= 0<br>> >>>> Division of bonded forces over processors<br>> >>>> CPU 0 1 2 3 4 5 6 7<br>> >>>> Workload division<br>> >>>> nnodes: 8<br>> >>>> pd->shift: 7<br>> >>>> pd->bshift: 0<br>> >>>> Nodeid atom0 #atom cg0 #cg<br>> >>>> 0 0 0 0 0<br>> >>>> 1 0 1960 0 682<br>> >>>> 2 1960 212 682 53<br>> >>>> 3 2172 212 735 53<br>> >>>> 4 2384 212 788 53<br>> >>>> 5 2596 212 841 53<br>> >>>> 6 2808 212 894 53<br>> >>>> 7 3020 208 947 52<br>> >>>><br>> >>>> …<br>> >>>> Total Scaling: 18% of max performance<br>> >>>><br>> >>><br>> >>><br>> >><br>> >><br>> > <br>> > <br>> <br>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
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