On 31/10/2011 3:36 PM, lina wrote:
On Mon, Oct 31, 2011 at 9:28 AM, Sanku M<msank...@yahoo.com> wrote:
Hi,
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
mdrun -t number_of_processors
No, mdrun -nt will specify a number of processors, but I have never
heard of any system where the default (0 meaning to guess) does not lead
to a correct result.
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.
and make sure during your compile process, enable --threads
configure --enable-threads works, but this is enabled by default.
Mark
Any help will be appreciated.
Sanku
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