Re: [gmx-users] why it is so slow

2012-11-02 Thread Justin Lemkul
On 11/2/12 11:08 AM, Albert wrote: On 11/02/2012 04:02 PM, Justin Lemkul wrote: I wasn't suggesting that you use NPT, I was merely pointing out that you made an statement that wasn't true and thought I would mention it. It looks like you have other issues to deal with. -Justin Hello Just

Re: [gmx-users] why it is so slow

2012-11-02 Thread Albert
On 11/02/2012 04:02 PM, Justin Lemkul wrote: I wasn't suggesting that you use NPT, I was merely pointing out that you made an statement that wasn't true and thought I would mention it. It looks like you have other issues to deal with. -Justin Hello Justin: thanks a lot for such kind rep

Re: [gmx-users] why it is so slow

2012-11-02 Thread Justin Lemkul
On 11/2/12 10:56 AM, Albert wrote: On 11/01/2012 06:15 PM, Justin Lemkul wrote: On 11/1/12 12:55 PM, Albert wrote: hello: I am running a 40ns REMD with GBSA solvent NPT simulations. It is exchange for 16 different temperature with exchange step 300. Based on your .mdp file, you're not

Re: [gmx-users] why it is so slow

2012-11-02 Thread Albert
On 11/01/2012 06:15 PM, Justin Lemkul wrote: On 11/1/12 12:55 PM, Albert wrote: hello: I am running a 40ns REMD with GBSA solvent NPT simulations. It is exchange for 16 different temperature with exchange step 300. Based on your .mdp file, you're not doing NPT (pcoupl = no). Hello J

Re: [gmx-users] why it is so slow

2012-11-01 Thread Justin Lemkul
On 11/1/12 12:55 PM, Albert wrote: hello: I am running a 40ns REMD with GBSA solvent NPT simulations. It is exchange for 16 different temperature with exchange step 300. Based on your .mdp file, you're not doing NPT (pcoupl = no). mpiexec -n 384 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb

[gmx-users] why it is so slow

2012-11-01 Thread Albert
hello: I am running a 40ns REMD with GBSA solvent NPT simulations. It is exchange for 16 different temperature with exchange step 300. mpiexec -n 384 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s remd_.tpr -multi 16 -replex 300 I found that it will require 1 months to be finished whi

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