Re: [gmx-users] Error in BlueGene

2013-02-14 Thread Cintia C. Vequi-Suplicy
Hello, I am writing just to tell how the problem was solved. I contact a person that works with the BlueGene cluster and he installed the Gromacs 4.6 in the cluster. And all my problems were solved. I did not get the same error over and over again. Apparently, it was some problem with the 4.

Re: [gmx-users] Error in BlueGene

2013-02-05 Thread Cintia C. Vequi-Suplicy
Mark, Thank you for your answer. I have already tried to run with several numbers of processors from 8 to 512 and I always got the same error. And I transfer the simulation to the BlueGene in two different ways. In both ways, I got the same error. They were the following: 1) only using the

Re: [gmx-users] Error in BlueGene

2013-02-05 Thread Mark Abraham
On Mon, Feb 4, 2013 at 5:18 PM, Cintia C. Vequi-Suplicy wrote: > > > > Hello David, > > I think it is the pressure. > I would think the mentions of pressure are just one of the symptoms. See http://www.gromacs.org/Documentation/Terminology/Blowing_Up. You seem to have somewhat more than 100K ato

Re: [gmx-users] Error in BlueGene

2013-02-04 Thread Cintia C. Vequi-Suplicy
Hello David, I think it is the pressure. Because the error starts with the message below. But this only happens in the BlueGene cluster. In my local cluster it is running fine for 60 ns. Thank you, Cintia vol 0.71 imb F 1% vol 0.74 imb F 1% vol 0.73 imb F 1% vol 0.75 imb F 1% vol 0.7

Re: [gmx-users] Error in BlueGene

2013-02-04 Thread Ricardo O. S. Soares
Hello Cíntia, On 02/01/2013 04:19 PM, Cintia C. Vequi-Suplicy wrote: Hello Ricardo, I tried to decrease the integration time but I got the same error. The system is running fine in my local core. I have two questions: 1) What do you mean by "I balance the domain decomposition for the la

Re: [gmx-users] Error in BlueGene

2013-02-01 Thread Cintia C. Vequi-Suplicy
Hello Ricardo, I tried to decrease the integration time but I got the same error. The system is running fine in my local core. I have two questions: 1) What do you mean by "I balance the domain decomposition for the larger number of core"? 2) Are you running simulations at Bluegene P at Rice

Re: [gmx-users] Error in BlueGene

2013-01-31 Thread David van der Spoel
On 2013-01-30 23:48, Ricardo Soares wrote: Hello, before submitting to Bluegene, I always test the system in my local 8 core cpu, and if it works, it will also work in Bluegene, as long as I balance the domain decomposition for the larger number of cores. If your system insists in exploding, eve

Re: [gmx-users] Error in BlueGene

2013-01-30 Thread Ricardo Soares
Hello, before submitting to Bluegene, I always test the system in my local 8 core cpu, and if it works, it will also work in Bluegene, as long as I balance the domain decomposition for the larger number of cores. If your system insists in exploding, even after energy minimization, you could try to

Re: [gmx-users] Error in BlueGene

2013-01-30 Thread Cintia C. Vequi-Suplicy
Mark, Thank you for your answer. I did an energy minimization with the file em.mdp (below) and then I did a 40 ns simulation with the same md.mdp I send before. These two steps were done in my local cluster. After that I took the configuration for the simulation in the bluegene and I got th

[gmx-users] Error in BlueGene

2013-01-30 Thread Cintia C. Vequi-Suplicy
Hello, I am having some problems to run my system in a bluegene cluster. I am running a bilayer simulation. The simulation runs very well in my local cluster. After 50ns of simulation on my local cluster with 8 nodes, I got the configurations and tried to run it in a bluegene with 512 nodes.