Hi all, Could Ian's issue be related to the issues I came across at the end of March? Trevor Keller seems to have isolated my memory leak to versions of Trilinos newer than 12.0.
Trevor, It seems that I never got around to testing an older version of Trilinos, I'll do that now. -Mike On 10/11/2016 10:36 AM, Guyer, Jonathan E. Dr. (Fed) wrote: > I have access to their code. Ian, please provide an explicit recipe for > demonstrating the leak with the code in your github repo. > > - Jon > >> On Oct 11, 2016, at 11:15 AM, Daniel Wheeler <daniel.wheel...@gmail.com> >> wrote: >> >> Hi Ian, >> >> Could you possible post your code or a version of the code that demonstrates >> the problem? Also, do you have the same issue with different solver suites? >> >> Cheers, >> >> Daniel >> >> >> >> On Fri, Sep 30, 2016 at 12:41 PM, Campbell, Ian >> <i.campbel...@imperial.ac.uk> wrote: >> Hi All, >> >> >> >> We are sweeping six PDEs in a time-stepping loop. We’ve noticed that as CPU >> time progresses, the duration of each time-step increases, although the >> sweep count remains constant. This is illustrated in the Excel file of data >> logged from the simulation, which is available at the first hyperlink below. >> >> >> >> Hence, we suspected a memory leak may be occurring. After conducting >> memory-focused line-profiling with the vprof tool, we observed a linear >> increase in total memory consumption at a rate of approximately 3 MB per >> timestep loop. This is evident in the graph at the second link below, which >> illustrates the memory increase over three seconds of simulation. >> >> >> >> As a further step, we used Pympler to investigate the source of RAM >> consumption increase for each timestep. The table below is an output from >> Pympler’s SummaryTracker().print_diff(), which describe the additional >> objects created within every time-step. Clearly, there are ~3.2 MB of >> additional data being generated with every loop – this correlates perfectly >> with the total rate of increase of memory consumption reported by vprof. >> Although we are not yet sure, we suspect that the increasing time spent per >> loop is the result of this apparent memory leak. >> >> >> >> We suspect this is the result of the calls to .sweep, since we are not >> explicitly creating these objects. Can the origin of these objects be >> traced, and furthermore, is there a way to avoid re-creating them and >> consuming more memory with every loop? Without some method of unloading or >> preventing this object build-up, it isn’t feasible to run our simulation for >> long durations. >> >> >> dict >> >> 2684 >> >> 927.95 >> >> KB >> >> type >> >> 1716 >> >> 757.45 >> >> KB >> >> tuple >> >> 9504 >> >> 351.31 >> >> KB >> >> list >> >> 4781 >> >> 227.09 >> >> KB >> >> str >> >> 2582 >> >> 210.7 >> >> KB >> >> numpy.ndarray >> >> 396 >> >> 146.78 >> >> KB >> >> cell >> >> 3916 >> >> 107.08 >> >> KB >> >> property >> >> 2288 >> >> 98.31 >> >> KB >> >> weakref >> >> 2287 >> >> 98.27 >> >> KB >> >> function (getName) >> >> 1144 >> >> 67.03 >> >> KB >> >> function (getRank) >> >> 1144 >> >> 67.03 >> >> KB >> >> function (_calcValue_) >> >> 1144 >> >> 67.03 >> >> KB >> >> function (__init__) >> >> 1144 >> >> 67.03 >> >> KB >> >> function (_getRepresentation) >> >> 1012 >> >> 59.3 >> >> KB >> >> function (__setitem__) >> >> 572 >> >> 33.52 >> >> KB >> >> SUM >> >> 3285.88 >> >> KB >> >> >> >> >> >> https://imperialcollegelondon.box.com/s/zp9jj67du3mxdcfgbc4el8cqpxwnv0y4 >> >> >> >> https://imperialcollegelondon.box.com/s/ict9tnswqk9z57ovx8r3ll5po5ccrib9 >> >> >> >> With best regards, >> >> >> >> - Ian & Krishna >> >> >> >> P.S. Daniel, thank you very much for the excellent example solution you >> provided in response to our question on obtaining the sharp discontinuity. >> >> >> >> Ian Campbell | PhD Candidate >> >> Electrochemical Science & Engineering Group >> >> Imperial College London, SW7 2AZ, United Kingdom >> >> >> >> >> _______________________________________________ >> fipy mailing list >> fipy@nist.gov >> http://www.ctcms.nist.gov/fipy >> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >> >> >> >> >> -- >> Daniel Wheeler >> _______________________________________________ >> 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 ]
