vivek sharma wrote:


2008/11/11 Justin A. Lemkul <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>



    vivek sharma wrote:

        HI MArtin,
        I am using here the infiniband having speed more than 10
        gbps..Can you suggest some option to scale better in this case.


    What % imbalance is being reported in the log file?  What fraction
    of the load is being assigned to PME, from grompp?  How many
    processors are you assigning to the PME calculation?  Are you using
    dynamic load balancing?


Everybody thanks for your usefull suggestions..
What do you mean by % imbalance reported in log file. I don't know how to assign the specific load to PME, but I can see that around 37% of the computation is being used by PME. I am not assigning PME nodes separately. I have no idea of dynamic load balancing and how to use it ?

For the moment, you just need to look for information in your grompp output and your log file, like Justin asked.

To find out how to use things, check out mdrun -h and the version 4 manual. There's some relevant discussion in this thread http://www.gromacs.org/pipermail/gmx-users/2008-October/036856.html

Mark
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