Quickly generate, start and analyze benchmarks for GROMACS simulations. Below is an example of the scaling plots you can generate quickly with MDBenchmark.

You can install MDBenchmark via pip:

pip install mdbenchmark

If you are using conda:

conda install -c conda-forge mdbenchmark

After installation, the mdbenchmark command should be available to you globally. If you have installed the package in a virtual environment, make sure to activate that first!

Generate 10 benchmarks for our system with the GROMACS module gromacs/5.1.4-plumed2.3.

mdbenchmark generate --name protein --module gromacs/5.1.4-plumed2.3 --max-nodes 10

To run benchmarks on GPUs add the --gpu flag:

mdbenchmark generate --name protein --module gromacs/5.1.4-plumed2.3 --max-nodes 10 --gpu

You can also create benchmarks for different versions off GROMACS:

mdbenchmark generate --name protein --module gromacs/5.1.4-plumed2.3 --module gromacs/2016.4-plumed2.3 --max-nodes 10 --gpu

After you generated all the benchmarks, you can start them at once:

mdbenchmark start

When the benchmark simulations have finished, you can run the analysis to produce a CSV output file or a plot for direct usage (via --plot option).

mdbenchmark analyze

It is possible to define your own host templates in addition to the ones shipped with the package. A template file should have the same filename as the UNIX command hostname returns to be detected automatically. You can also specify the exact template you want to use with --host.

Here is an example template from for the MPG cluster hydra.

# @ shell=/bin/bash
#
# @ error = {{ name }}.err.$(jobid)
# @ output = {{ name }}.out.$(jobid)
# @ job_type = parallel
# @ node_usage = not_shared
# @ node = {{ n_nodes }}
# @ tasks_per_node = 20
{%- if gpu %}
# @ requirements = (Feature=="gpu")
{%- endif %}
# @ resources = ConsumableCpus(1)
# @ network.MPI = sn_all,not_shared,us
# @ wall_clock_limit = {{ formatted_time }}
# @ queue

module purge
module load {{ module }}

# run {{ module }} for {{ time }} minutes
poe gmx_mpi mdrun -deffnm {{ name }} -maxh {{ time / 60 }}

MDBenchmark provides the following values to a template

• name: name of benchmark
• gpu: boolean if GPUs are requested
• module: module to load
• n_nodes: number of nodes to run on
• time: program run-time in minutes
• formatted_time: queuing runtime in human readable format (HH:MM:SS)

To ensure correct termination of jobs formatted_time is 5 minutes longer then time.

MDBenchmark searches for user templates in the xdg config folders defined by XDG_CONFIG_HOME and XDG_CONFIG_DIRS which by default are $HOME/.config/MDBenchmark and /etc/xdg/MDBenchmark respectively. If the variable MDBENCHMARK_TEMPLATES is set, the script will also search in that directory.

MDBenchmark will first search in XDG_CONFIG_HOME and XDG_CONFIG_DIRS for a suitable template file. This means it is possible to overwrite system-wide installed templates or templates shipped with the package.