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3.0.2 (2023-02-20)

Features

  • Moved from travis to github-actions (PR 181) (#181)
  • Add test to CI to verify distribution with pip. (PR 182) (#182)
  • Make scaling projection show optimal scaling. (PR 193) (#193)

Bugfixes

  • Pin markupsafe to 2.0.1 to fix incompatibility with jinja2 ^2.10. (PR 184) (#184)
  • Fix bug when plotting cpu-/gpu-data only with 'version3-categories'. (PR 192) (#192)
  • Don't use deprecated kwarg 'type' in matplotlib.pyplot.savefig. (PR 195) (#195)

3.0.1 (2020-10-09)

Features

  • Add ability to scan number of MPI ranks and OpenMP threads. (#165)
  • Add support to run multiple simulations on single nodes (GROMACS-only). (#168)

3.0.0

This version was skipped intentionally. Version 3.0.1 is the first release of the major version 3.

2.0.1 (2020-03-04)

Features

  • Add GPUs to cobra template. (#142)
  • Lower startup time of the CLI. (#153)

Bugfixes

  • Already submitted benchmarks are now hidden in the summary of mdbenchmark submit. (#139)
  • Plotting will now work, even when some benchmarks are unfinished. (#140)
  • Restarting benchmarks with mdbenchmark submit --force works again. (#141)

Misc

  • Use poetry to manage Python dependencies and the project in general. (#155)

2.0.0 (2018-10-29)

Features

  • Updated plotting interface. mdbenchmark analyze --plot is not deprecated. Use mdbenchmark plot instead.

    The new workflow for plotting data is as follows:

    1. Use mdbenchmark analyze --save-csv results.csv to generate a CSV output file.
    2. Use mdbenchmark plot --csv results.csv to plot the data.

    Consult mdbenchmark <command> --help for options to filter your data accordingly. (#52)

  • mdbenchmark generate now accepts --cpu / --no-cpu and --gpu / --no-gpu. The default is --cpu and --no-gpu. (#69)

  • Added user prompts to mdbenchmark generate and mdbenchmark submit. (#90)

  • Added --yes flag to mdbenchmark generate and mdbenchmark submit to bypass user prompt. (#90)

  • Added -nc and -ng options to mdbenchmark generate. These are short hand for --no-cpu and --no-gpu, respectively. (#93)

  • Added template for MPCDF cluster cobra. (#104)

  • Added --template and -t option to mdbenchmark generate, to specify a job template. The --host option still works. (#106)

  • Standarize the CLI options across all mdbenchmark calls. (#107)

  • Added mdbenchmark plot --dpi option to change the plot DPI. (#108)

  • Added mdbenchmark plot --font-size to change the plot font size. (#108)

  • Linear scaling fit can now be hidden with --no-fit. (#108)

  • Updated ylim, xtick and ytick defaults. The steps for xtick can be overwritten with mdbenchmark plot --xtick-step. (#108)

  • Added a watermark in the top left corner for every plot. Can be easiliy disabled with mdbenchmark plot --no-watermark. (#108)

  • mdbenchmark analyze no longer writes CSV files by default. --save-csv flag added to write csv files. (#119)

  • Added mdbenchmark generate --job-name to change the job name submitted to the queuing system. (#125)

Bugfixes

  • Fixed a bug where benchmark creation with files ending in .namd did not work. (#124)
  • Fixed a bug where benchmark creation would fail when the input file was not in the current directory. (#124)

Misc

  • Replaced mdsynthesis with datreant and upgraded to the new datreant>=1.0 format. (#110)

1.3.3 (2018-09-24)

Bugfixes

  • Fixed a bug where the user was unable to call mdbenchmark analyze --plot. (#86)

1.3.2 (2018-07-20)

Bugfixes

  • We now print all rows when running mdbenchmark analyze. (#68)
  • Suppress UserWarning caused by MDAnalysis==0.18. (#71)

Misc

  • Added new error message when running mdbenchmark generate [...] --skip-validation without providing a supported MD engine. (#74)

1.3.1 (2018-05-17)

Bugfixes

  • Module name validation is now performed case insensitive. (#61)

Misc

  • Consolidate common functions from mdengines.gromacs and mdengines.namd into mdengines.utils, removing code duplication. (#57)
  • Refactor unit tests. Make everything more concise and use some more pytest functionality. (#58)

1.3.0 (2018-04-08)

Features

  • Add functionality to perform benchmarks with NAMD. (#29)
  • Consolidated internal API to output messages to the console. (#42)
  • Module name is now validated against available modules on host. Can be skipped with --skip-validation. (#49)

Bugfixes

  • The option --min-nodes needs to be bigger than --max-nodes. (#46)
  • Fixed edge-case in input filename parsing. (#54)

Misc

  • Fixed display of the number of benchmarks to-be generated. (#46)

1.2.0 (2018-02-19)

Features

  • Added Makefile to the project. Updated default strings. (#36)
  • GROMACS .tpr files can now be referenced with and without the file extension. (#32)

Bugfixes

  • Fixed crash during analyze, if some simulations have not started/finished yet. (#26)
  • Suppress FutureWarning caused by h5py. (#35)

Improved Documentation

  • Update and add more unit tests. (#36)

1.1.1 (2018-01-20)

Misc

  • Show benchmark png on PyPI.

1.1.0 (2018-01-19)

Features

  • Enable to run on macOS. (#10)
  • Read number of cores from simulation log. (#19)

Bugfixes

  • Ensure MPI environment is loaded on draco after a purge. (#17)

Improved Documentation

  • Fix readme usage docs for the module argument. (#20)

1.0.1 (2017-12-03)

Misc

  • Fixup MANIFEST.in. (#9)

1.0.0 (2017-12-03)

Initial release.