[gmx-users] problem with Threading during run

Mark Abraham Mark.Abraham at anu.edu.au
Mon Oct 31 12:58:22 CET 2011

On 31/10/2011 3:36 PM, lina wrote:
> On Mon, Oct 31, 2011 at 9:28 AM, Sanku M<msanku65 at 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.


>> Any help will be appreciated.
>> Sanku
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