bio-phys/MDBenchmark: Release 2.0.0
Creators
- 1. MPI of Biophysics
- 2. Max Planck Institute of Biophysics
Description
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 withmdbenchmark plot
. - Plots can now be easily customized with the
--dpi
,--font-size
,--xtick-step
,--no-fit
and--no-watermark
options.
- The old
- All calls to the main
mdbenchmark
commands (generate
,analyze
,submit
andplot
) 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
andmdbenchmark 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 usingmdbenchmark generate
.
Please refer to our documentation on how to install the package from your favorite package manager.
MigratingWhen 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.
conda
If you are using conda
and your conda environment is called benchmark
, simply run:
conda update -n benchmark mdbenchmark
pip
Users of pip
run the following:
pip install mdbenchmark --upgrade
Full changelog
A full list of changes, both user facing and behind the scenes, can be found below.
FeaturesUpdated plotting interface.
mdbenchmark analyze --plot
is not deprecated. Usemdbenchmark 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) Usemdbenchmark 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
andmdbenchmark submit
. (#90) - Added
--yes
flag tomdbenchmark generate
andmdbenchmark submit
to bypass user prompt. (#90) - Added
-nc
and-ng
options tomdbenchmark 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 tomdbenchmark 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
andytick
defaults. The steps forxtick
can be overwritten withmdbenchmark 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
withdatreant
and upgraded to the newdatreant>=1.0
format. (#110)
Files
bio-phys/MDBenchmark-v2.0.0.zip
Files
(178.7 kB)
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Additional details
Related works
- Is supplement to
- https://github.com/bio-phys/MDBenchmark/tree/v2.0.0 (URL)