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Ensemble Algebra Call 29 Nov 2016

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Vivekanandan (Vivek) Balasubramanian edited this page Nov 27, 2018 · 2 revisions

MSM usecase

After looking into the references from Peter's email, some new experiment parameters:

  • Number of simulations = 1000
  • Duration = 20ps
  • Machine = (Stampede, Comet)

Currently working through some gromacs parameter issue on stampede for a smaller test case.

EE usecase

After moving to larger parameters (timesteps=80000, iterations=50), hitting two issues consistently:

  • simulation/gromacs error:
-------------------------------------------------------
: Unknown error 255

-------------------------------------------------------
Program gmx mdrun, VERSION 5.1.2
Source code file: /home1/02875/micbuild/rpms/BUILD/gromacs-5.1.2/src/gromacs/pulling/pull.cpp, line: 520

Fatal error:
Distance between pull groups 1 and 2 (2.818957 nm) is larger than 0.49 times the box size (2.876175).
You might want to consider using "pull-geometry = direction-periodic" instead.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Even the resubmitted tasks are falling into this issue.

  • another condition (possibly new) where new tasks are not being submitted -- investigating more before I can comment further on why.

Todos

  • MSM: Once verified, go to the above scale and plot results similar to existing plots.
  • EE: Investigate the above issues and resume experiment.
  • Paper: Will be addressing comments on the paper and adding pseudographs to the experiment section
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