Hi Carsten and Justin, I am interrupting here as I tried with the option u suggested.. I tried cut-off instead of PME as coulombtype option it is running well for 24 processor, then I tried with 60 processor , following is the result I am getting
Result1: When tried for 50 ps of run on 24 processors, with PME took 12:29 in comparison to 7:54 with cut-off Result2: When tried for 500 ps of run on 60 processors, with PME it is giving same segmentation fault again and with cut-off it is giving LINCS warning and exiting with writing the intermediate step.pdb Can you suggest some more option that I can try for scaling experiment... Also I tried with shuffle and sort option it didn't worked for me as my system is simply one protein molecule in a ater box (around 45000 no. of atoms) connected Gromacs version I am using is 3.3.3 and the hardware is like all nodes contain quad-core 3.0 GHz Intel Xeon processors connected via infiniband. With Thanks, Vivek 2008/9/26 Carsten Kutzner <[EMAIL PROTECTED]> > Hi Tiago, > > if you swith off PME and suddenly your system scales, then the > problems are likely to result from bad MPI_Alltoall performance. Maybe > this is worth a check. If this is the case, there's a lot more information > about this in the paper "Speeding up parallel GROMACS on high- > latency networks" from 2007 to which you will also find link on the > gromacs webpage. > > What you can also do to track down the problem is to compile gromacs with > MPE logging, for which you have to enable the #define USE_MPE macro at the > begin of mpelogging.h (you will have to use gmx version 4, though). You > will get a logfile which you can view with jumpshot then. The MPE tools > come with the MPICH MPI distribution. > > Carsten > > > Tiago Marques wrote: > >> We currently have no funds available to migrate to infiniband but we will >> in the future. >> >> I thought on doing interface bonding but I really think that isn't really >> the problem here, there must be something I'm missing, since most >> applications scale well to 32 cores on GbE. I can't scale any application to >> more than 8 though. >> >> Best regards, >> Tiago Marques >> >> >> On Tue, Sep 23, 2008 at 6:30 PM, Diego Enry <[EMAIL PROTECTED]<mailto: >> [EMAIL PROTECTED]>> wrote: >> >> Tiago you can try merging two network interfaces with "channel >> bonding" it's native on all new (2.6.x) linux kernels. You only need >> two network adapters (most dual socket boards come with then), two >> network switches ( or two VPN on the same switch). >> >> To tell you the truth, you will not much improvement even with the >> latest gromacs version (4beta). However other software that may be >> used by your group like NAMD, GAMESS, will benefit a lot from this >> approach. (it almost doubles network bandwidth) >> >> The best solution for gromacs is to migrate to infiniband. Go for it, >> it is not super expensive anymore. >> >> >> On Tue, Sep 23, 2008 at 1:48 PM, Jochen Hub <[EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]>> wrote: >> > Tiago Marques wrote: >> >> I don't know how large the system is. I'm the cluster's system >> administrator >> >> and don't understand much of what's going on. The test was given >> to me by a >> >> person who works with it. I can ask him or look at it, if you >> can point me >> >> how to do it. >> > >> > Hi, >> > >> > you can count the nr of atoms in the structure: >> > >> > grep -c ATOM protein.pdb >> > >> > Jochen >> > >> >> >> >> Thanks, I will look at some of his posts. >> >> >> >> Best regards, >> >> >> >> Tiago Marques >> >> >> >> >> >> On Tue, Sep 23, 2008 at 4:03 PM, Jochen Hub <[EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]>> wrote: >> >> Tiago Marques wrote: >> >>> Hi! >> >>> >> >>> I've been using Gromacs on dual-socket quad-core Xeons with >> 8GiB of RAM, >> >>> connected with Gigabit Ethernet and I always seem to have >> problems scaling >> >>> to more than a node. >> >>> >> >>> When I run a test on 16 cores, it does run but the result is >> often slower >> >>> than when running on only 8 cores on the same machine. The best >> result >> >> I've >> >>> managed is not being slower than 8 cores on 16. >> >>> >> >>> What am I missing here, or are the tests inappropriate to run >> over more >> >> than >> >>> one machine? >> >> >> >> How large is your system? Which gromacs version are you using? >> >> >> >> And have a look at the messages by Carsten Kutzner in this list, he >> >> wrote a lot on gromacs scaling. >> >> >> >> Jochen >> >> >> >>> Best regards, >> >>> >> >>> Tiago Marques >> >>> >> >>> >> >>> >> >>> >> >> ------------------------------------------------------------------------ >> >>> >> >>> _______________________________________________ >> >>> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >>> 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 [EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]>. >> >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> >> -- >> >> ************************************************ >> >> Dr. Jochen Hub >> >> Max Planck Institute for Biophysical Chemistry >> >> Computational biomolecular dynamics group >> >> Am Fassberg 11 >> >> D-37077 Goettingen, Germany >> >> Email: jhub[at]gwdg.de <http://gwdg.de> >> >> Tel.: +49 (0)551 201-2312 >> >> ************************************************ >> >> _______________________________________________ >> >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> 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 [EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> >> >> _______________________________________________ >> >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> 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 [EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >> > >> > -- >> > ************************************************ >> > Dr. Jochen Hub >> > Max Planck Institute for Biophysical Chemistry >> > Computational biomolecular dynamics group >> > Am Fassberg 11 >> > D-37077 Goettingen, Germany >> > Email: jhub[at]gwdg.de <http://gwdg.de> >> > Tel.: +49 (0)551 201-2312 >> > ************************************************ >> > _______________________________________________ >> > gmx-users mailing list [email protected] >> <mailto:[email protected]> >> > 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 [EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]>. >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >> >> >> >> -- >> Diego Enry B. Gomes >> Laboratório de Modelagem e Dinamica Molecular >> Universidade Federal do Rio de Janeiro - Brasil. >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> 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 [EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > Dr. Carsten Kutzner > Max Planck Institute for Biophysical Chemistry > Theoretical and Computational Biophysics Department > Am Fassberg 11 > 37077 Goettingen, Germany > Tel. +49-551-2012313, Fax: +49-551-2012302 > www.mpibpc.mpg.de/home/grubmueller/ > www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne/ > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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