Hi Trevor, I am seeing the same behavior as you regarding Pysparse vs Trilinos.
I compiled Trilinos version 12.4.2 on our machine running Ubuntu 14.04. But! when I get the PyTrilinos version from PyTrilinos, it says: 12.3;(;Dev;) I see there is a new version of Trilinos out (12.6), I'll compile that and report back. Thanks for investigating, -Mike On 3/29/16 2:41 PM, Keller, Trevor (Fed) wrote: > Hi Mike, > > I can confirm the leak in this code/solver system using FiPy on a Linux box. > Some details: > FiPy: 3.1-dev131-g77851ef > PyTrilinos: 12.1;(;Dev;) > PySparse: 1.1.1 > > I commented out the solver and preconditioner specifications, using the > default behavior when launching the script with --pysparse or --trilinos > flags instead. I also disabled garbage collection. Memory use was monitored > using memory-profiler, launching the script using > OMP_NUM_THREADS=6 mprof run mod-fipy-dft.py --trilinos > or > OMP_NUM_THREADS=6 mprof run mod-fipy-dft.py --pysparse > > For 100 steps, the pysparse solver plateaued around 8GB, with regular spikes > in RAM consumption while solving the equations. > For 100 steps, the pytrilinos solver just keeps gobbling up RAM -- it had > about 37GB at the last step. > Using the solver (LinearBicgstabSolver) and preconditioner > (JacobiPreconditioner) you specified for Trilinos, it's a little better, > ramping up to just 24GB after 100 steps. > > > Digging around a little bit, there was a patch to PyTrilinos (for v. 12.4) > in October meant to address some memory leaks -- I'm cloning and re-building > the project now. Can you report your PyTrilinos version, please, using > >>> from PyTrilinos import __version__ as PyTriVer > >>> print PyTriVer > > Thank you, > Trevor > > > > Trevor Keller, Ph.D. > Materials Science and Engineering Division > National Institute of Standards and Technology > 100 Bureau Dr. MS 8550; Gaithersburg, MD 20899 > Office: 223/A131 or (301) 975-2889 > > > ________________________________________ > From: fipy-boun...@nist.gov <fipy-boun...@nist.gov> on behalf of Michael > Waters <waters.mik...@gmail.com> > Sent: Monday, March 28, 2016 2:10 PM > To: FIPY > Subject: Re: Memory Leaks with Trilinos > > Thanks, If you think DFT in FiPy is strange, you should see how I make > isosurfaces in POV-Ray. :) > > That said, If anyone is tinkering with my example and has questions, I > am glad to answer them! > > Cheers, > -Mike Waters > > > > On 03/28/2016 01:46 PM, Guyer, Jonathan E. Dr. (Fed) wrote: >> Mike, thanks for the example, and for the rather perverse application of >> FiPy! >> >> I'll fiddle with this and see what I get. >> >> - Jon >> >> On Mar 25, 2016, at 7:16 PM, Michael Waters <waters.mik...@gmail.com> 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 >>> fipy@nist.gov >>> http://www.ctcms.nist.gov/fipy >>> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >> _______________________________________________ >> fipy mailing list >> fipy@nist.gov >> http://www.ctcms.nist.gov/fipy >> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > _______________________________________________ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > _______________________________________________ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] _______________________________________________ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
