FYI, the Docker installation for FiPy: https://github.com/wd15/fipy-dockerize
On Wed, Mar 30, 2016 at 3:32 PM, Guyer, Jonathan E. Dr. (Fed) <[email protected]> wrote: > No worries. If building trilinos doesn't blindside you with something > unexpected and unpleasant, you're not doing it right. > > I have a conda recipe at > https://github.com/guyer/conda-recipes/tree/trilinos_upgrade_11_10_2/trilinos > that has worked for me to build 11.10.2 on both OS X and Docker (Debian?). I > haven't tried to adjust it to 12.x, yet. > > > On Mar 30, 2016, at 2:42 PM, Michael Waters <[email protected]> wrote: > >> Hi Jon, >> >> I was just reviewing my version of Trilinos 11.10 and discovered that there >> is no way that I compiled it last night after exercising. It has unsatisfied >> dependencies on my machine. So I must apologize, I must have been more tired >> than I thought. >> >> Sorry for the error! >> -Mike Waters >> >> On 3/30/16 11:52 AM, Guyer, Jonathan E. Dr. (Fed) wrote: >>> It looked to me like steps and accuracy were the way to do it, but my runs >>> finish in one step, so I was confused. When I change to accuracy = >>> 10.0**-6, it takes 15 steps, but still no leak (note, the hiccup in RSS and >>> in ELAPSED time is because I put my laptop to sleep for awhile, but VSIZE >>> is rock-steady). >>> >>> The fact that things never (or slowly) converge for you and Trevor, in >>> addition to the leak, makes me wonder if Trilinos seriously broke something >>> between 11.x and 12.x. Trevor's been struggling to build 12.4. I'll try to >>> find time to do the same. >>> >>> In case it matters, I'm running on OS X. What's your system? >>> >>> - Jon >>> >>> On Mar 29, 2016, at 3:59 PM, Michael Waters <[email protected]> wrote: >>> >>>> When I did my testing and made those graphs, I ran Trilinos in serial. >>>> Syrupy didn't seem to track the other processes memory. I watched in >>>> real time as the parallel version ate all my ram though. >>>> >>>> To make the program run longer while not changing the memory: >>>> >>>> steps = 100 # increase this, (limits the number of self-consistent >>>> iterations) >>>> accuracy = 10.0**-5 # make this number smaller, (relative energy >>>> eigenvalue change for being considered converged ) >>>> initial_solver_iterations_per_step = 7 # reduce this to 1, (number of >>>> solver iterations per self-consistent iteration, to small and it's slow, >>>> to high and the solutions are not stable) >>>> >>>> I did those tests on a machine with 128 GB of ram so I wasn't expecting >>>> any swapping. >>>> >>>> Thanks, >>>> -mike >>>> >>>> >>>> On 3/29/16 3:38 PM, Guyer, Jonathan E. Dr. (Fed) wrote: >>>>> I guess I spoke too soon. FWIW, I'm running Trilinos version: 11.10.2. >>>>> >>>>> >>>>> On Mar 29, 2016, at 3:34 PM, Guyer, Jonathan E. Dr. (Fed) >>>>> <[email protected]> wrote: >>>>> >>>>>> I'm not seeing a leak. The below is for trilinos. VSIZE grows to about >>>>>> 11 MiB and saturates and RSS saturates at around 5 MiB. VSIZE is more >>>>>> relevant for tracking leaks, as RSS is deeply tied to your system's >>>>>> swapping architecture and what else is running; either way, neither >>>>>> seems to be leaking, but this problem does use a lot of memory. >>>>>> >>>>>> What do I need to do to get it to run longer? >>>>>> >>>>>> >>>>>> >>>>>> On Mar 25, 2016, at 7:16 PM, Michael Waters <[email protected]> >>>>>> wrote: >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I still have a large memory leak when using Trilinos. I am not sure >>>>>>> where to start looking so I made an example code that produces my >>>>>>> problem in hopes that someone can help me. >>>>>>> >>>>>>> But! my example is cool. I implemented Density Functional Theory in >>>>>>> FiPy! >>>>>>> >>>>>>> My code is slow, but runs in parallel and is simple (relative to most >>>>>>> DFT codes). The example I have attached is just a lithium and hydrogen >>>>>>> atom. The electrostatic boundary conditions are goofy but work well >>>>>>> enough for demonstration purposes. If you set use_trilinos to True, the >>>>>>> code will slowly use more memory. If not, it will try to use Pysparse. >>>>>>> >>>>>>> Thanks, >>>>>>> -Michael Waters >>>>>>> <input.xyz><fipy-dft.py>_______________________________________________ >>>>>>> fipy mailing list >>>>>>> [email protected] >>>>>>> http://www.ctcms.nist.gov/fipy >>>>>>> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >>>>>> >>>>>> <attachment.png> >>>>>> _______________________________________________ >>>>>> fipy mailing list >>>>>> [email protected] >>>>>> http://www.ctcms.nist.gov/fipy >>>>>> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >>>>> >>>>> _______________________________________________ >>>>> fipy mailing list >>>>> [email protected] >>>>> http://www.ctcms.nist.gov/fipy >>>>> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >>>> >>>> _______________________________________________ >>>> fipy mailing list >>>> [email protected] >>>> http://www.ctcms.nist.gov/fipy >>>> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >>> <Mail Attachment.png> >>> >>> >>> _______________________________________________ >>> fipy mailing list >>> >>> [email protected] >>> http://www.ctcms.nist.gov/fipy >>> >>> [ NIST internal ONLY: >>> https://email.nist.gov/mailman/listinfo/fipy >>> ] >>> >> >> _______________________________________________ >> fipy mailing list >> [email protected] >> http://www.ctcms.nist.gov/fipy >> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > > > _______________________________________________ > fipy mailing list > [email protected] > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] -- Daniel Wheeler _______________________________________________ fipy mailing list [email protected] http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
