bio-phys/MDBenchmark: Release 2.0.0

After lots of work, MDBenchmark 2.0 is finished. This new release includes major improvements to the plotting functionality and user experience in general. But it also comes with breaking changes to the command-line interface and requires an update to your Python environment.

If you have any workflows that rely on the function of specific calls to mdbenchmark, please check the latest CLI reference to make sure everything works as expected.

• Revamped plotting functionality, making it possible to plot many different benchmark combinations (modules, hosts, other settings) at once.
  • The old mdbenchmark analyze --plot command was replaced with mdbenchmark plot.
  • Plots can now be easily customized with the --dpi, --font-size, --xtick-step, --no-fit and --no-watermark options.
• All calls to the main mdbenchmark commands (generate, analyze, submit and plot) now use consistent option names, when handling similar functions.
• Running mdbenchmark analyze will not produce CSV output files, until asked to with the --save-csv option.
• mdbenchmark generate and mdbenchmark submit will now ask for confirmation, before performing any operations. The confirmation can be skipped with the --yes option.
• CPU and GPU benchmarks can now be generated at once, without the need to run two separate commands: mdbenchmark generate --cpu --gpu.
• The job name for the queuing system can be customized with the --job-name option when using mdbenchmark generate.

Please refer to our documentation on how to install the package from your favorite package manager.

When upgrading from a previous version, you need to remove three packages that were previously installed alongside of MDBenchmark: datreant.core, datreant.data and mdsynthesis. Refer to our upgrading guide, if you need assistance.

To upgrade, use the appropriate command for your Python package manager.

If you are using conda and your conda environment is called benchmark, simply run:

conda update -n benchmark mdbenchmark

Users of pip run the following:

pip install mdbenchmark --upgrade

A full list of changes, both user facing and behind the scenes, can be found below.

• 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)

• 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)

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