Hi Daniel, Thanks for all your suggestions. I also believe 80*80*80 is a pretty large problem for the machine. I really appreciate your help!
Have a nice day! Regards, Zhiwen On Fri, Nov 14, 2008 at 5:36 PM, Daniel Wheeler <[EMAIL PROTECTED]>wrote: > > On Fri, Nov 14, 2008 at 2:52 PM, Zhiwen Liang <[EMAIL PROTECTED]> wrote: > > > > From the "top", the program takes a vsize of around 2G while the > available > > physical RAM is >20G for the server. So I think I have enough resource. > > Okay. How much memory is the machine slated to have in the specs? The > machine has a 64 bit OS, I assume. The question is whether you are > running out of memory. The error statement certainly seems to be > suggesting that. It's possible, 80 * 80 * 80 is a fairly large > problem. > > > I got the memory error when defining one of the source terms for the > > equation. I have a second order diffusion term and several coupled source > > terms (You probably might have seen those long long equations I sent you > > before). I don't know if the source terms cause the trouble. > > It could be that you have an array multiplication that is leading to > an (Ncells, Ncells) array which is huge, although you would probably > notice that in top. Go to where the thing is failing "line 80 in > variables/gaussCellGradVariable.py" and print > numerix.shape(orientations) and numerix.shape(contributions) just to > check that "orientations * contributions" is not somehow making a > weird shaped massive array. Also, put a raw_input() statement right > before this line and check how much memory is used right before that > statement. > > > Yes I am using the uniform grid. All the meshes I use so far are created > by > > Grid3D. I am thinking to use GMSH though. > > Won't be as memory efficient at the moment. > > > I am now using the GMRES solver from pysparse. What do you recommend? > > That's fine. > > > When I look at the top, the memory usage for the program doesn't change > much > > throughout the definition of the equations, and it crashes somehow in > > It won't change much. The equations are mostly empty objects. > > > between. And I am solving for an equilibrium state without any time > > evolution (just one time step). But I will check the variables. > > yeah, but you are doing some sort of sweeping to convergence, which is > the same in this context. > > > -- > Daniel Wheeler > >
