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
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