Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)

2006-09-14 Thread Qiao Baofu
2006/9/14, Mark Abraham <[EMAIL PROTECTED]>: Probably your interconnects between nodes are using carrier pigeons orsomething :-) I expect that 1 cpu on machine A will require around fourtimes as long as 1 4-cpu node, which you can presumably test for yourself. It is forbidden to  run only one cpu o

Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)

2006-09-14 Thread Florian Haberl
On Thursday 14 September 2006 09:53, Mark Abraham wrote: > Qiao Baofu wrote: > > Hi, > > > > Thanks. I have test different cpus. Our institute has two clusters: one > > is each node has 4 cpu (A), one is one node has only 1 cpu (B). I made > > different tests on the two clusters and my local comp

Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)

2006-09-14 Thread Mark Abraham
Qiao Baofu wrote: Hi, Thanks. I have test different cpus. Our institute has two clusters: one is each node has 4 cpu (A), one is one node has only 1 cpu (B). I made different tests on the two clusters and my local computer using the same system. See the following result: A (For 1 hou

Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)

2006-09-14 Thread Qiao Baofu
Hi,Thanks. I have test different cpus. Our institute has two clusters: one is each node has 4 cpu (A), one is one node has only 1 cpu (B).   I made different tests on the two clusters and my local computer using the same system. See the following result:  A     (For 1 hour)    # of cpus   ;    MD s

Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)

2006-09-13 Thread Mark Abraham
> You have to > find your optimum making some tests with your settings. To do that you can > start your simulation and interrupt after a while to have some data logged > in the log file. Then, from the information in that log file you can > estimate the time that the whole task will take and compar

[gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)

2006-09-13 Thread Cesar Araujo
Well, there is a common misconception with parallel computing. Usually, you will have an optimun number of processors that guarantees the best performance. More or less than that number will result in a decreased performance and longer computation times. The optimum number of processors will de