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
_______________________________________________
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
