[gmx-users] problem with Threading during run

Sanku M msanku65 at yahoo.com
Mon Oct 31 02:28:52 CET 2011

 I just compiled gromacs 4.5.4 in a cluster. But, I find that if I try to make use of threading introduced in gromacs 4.5.x series, it does not work. 
 After issuing command like mdrun -v -s , I expected that for my 8-core processor which is not running any other jobs, the threading will show one job with 800 % cpu usage. But, it is showing 100 % cpu usage hence using only 1 of the 8 processors. I was wondering whether there is any command line I need to use to ensure the gromacs understands that there is 8 processors in a core and force make full use of the entire machine.

I have tried the same thing in another different cluster where I found that threading works with showing 800 % cpu usage . But, for this cluster , the threading does not work.

Any help will be appreciated.

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