Software Open Access
Michael Gecht; Max Linke; Marc Siggel
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.
mdbenchmark analyze --plot
command was replaced with mdbenchmark plot
.--dpi
, --font-size
, --xtick-step
, --no-fit
and --no-watermark
options.mdbenchmark
commands (generate
, analyze
, submit
and plot
) now use consistent option names, when handling similar functions.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.mdbenchmark generate --cpu --gpu
.--job-name
option when using mdbenchmark 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. 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)mdbenchmark generate
and mdbenchmark submit
. (#90)--yes
flag to mdbenchmark generate
and mdbenchmark submit
to bypass user prompt. (#90)-nc
and -ng
options to mdbenchmark generate
. These are short hand for --no-cpu
and --no-gpu
, respectively. (#93)cobra
. (#104)--template
and -t
option to mdbenchmark generate
, to specify a job template. The --host
option still works. (#106)mdbenchmark
calls. (#107)mdbenchmark plot --dpi
option to change the plot DPI. (#108)mdbenchmark plot --font-size
to change the plot font size. (#108)--no-fit
. (#108)ylim
, xtick
and ytick
defaults. The steps for xtick
can be overwritten with mdbenchmark plot --xtick-step
. (#108)mdbenchmark plot --no-watermark
. (#108)mdbenchmark analyze
no longer writes CSV files by default. --save-csv
flag added to write csv files. (#119)mdbenchmark generate --job-name
to change the job name submitted to the queuing system. (#125).namd
did not work. (#124)mdsynthesis
with datreant
and upgraded to the new datreant>=1.0
format. (#110)Name | Size | |
---|---|---|
bio-phys/MDBenchmark-v2.0.0.zip
md5:7246c9e4794218fc9722896741e05646 |
178.7 kB | Download |
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