Re: [gmx-users] why it is so slow in Blue gene?

2012-04-25 Thread Mark Abraham
On 25/04/2012 3:24 PM, Albert wrote: hello: it is blue gene P. And the gromacs is single precision in the cluster. Getting Loaded...And the administrator told me that I have to use the multiples of 32 in the bg_size parameter. The number specified in "-np" should be 4 times bg_size. Yes,

Re: [gmx-users] why it is so slow in Blue gene?

2012-04-24 Thread Albert
hello: it is blue gene P. And the gromacs is single precision in the cluster. Getting Loaded...And the administrator told me that I have to use the multiples of 32 in the bg_size parameter. The number specified in "-np" should be 4 times bg_size. It is even slower than my own workstation

Re: [gmx-users] why it is so slow in Blue gene?

2012-04-24 Thread Hannes Loeffler
On Tue, 24 Apr 2012 15:42:15 +0200 Albert wrote: > hello: > >I am running a 60,000 atom system with 128 core in a blue gene > cluster. and it is only 1ns/day here is the script I used for You don't give any information what exact system that is (L/P/Q?), if you run single or double pr

Re: [gmx-users] why it is so slow in Blue gene?

2012-04-24 Thread Justin A. Lemkul
On 4/24/12 9:42 AM, Albert wrote: hello: I am running a 60,000 atom system with 128 core in a blue gene cluster. and it is only 1ns/day here is the script I used for submitting jobs: # @ job_name = gmx_test # @ class = kdm-large # @ error = gmx_test.err # @ output = gmx_test.out # @ wall_

[gmx-users] why it is so slow in Blue gene?

2012-04-24 Thread Albert
hello: I am running a 60,000 atom system with 128 core in a blue gene cluster. and it is only 1ns/day here is the script I used for submitting jobs: # @ job_name = gmx_test # @ class = kdm-large # @ error = gmx_test.err # @ output = gmx_test.out # @ wall_clock_limit = 00:20:00 # @ job_t