mdbenchmark 1.3.0

mdbenchmark gromacs simulations

---

MDBenchmark — quickly generate, start and analyze benchmarks for your molecular dynamics simulations.

MDBenchmark is a tool to squeeze the maximum out of your limited computing resources. It tries to make it as easy as possible to set up systems on varying numbers of nodes and compare their performances to each other.

You can also create a plot to get a quick overview of the possible performance (and also show of to your friends)! The plot below shows the performance of an molecular dynamics system on up to five nodes with and without GPUs.

Installation

You can install mdbenchmark via pip or conda:

$ pip install mdbenchmark

$ conda install -c conda-forge mdbenchmark

Usage with a virtual environments

We recommend to install the package inside a conda environment. This can easily be done with conda. The following commands create an environment called benchmark and then installs mdbenchmark and its dependencies.

$ conda create -n benchmark
$ conda install -n benchmark -c conda-forge mdsynthesis click mdbenchmark

Before every usage of mdbenchmark, you need to first activate the conda environment. After doing this once, you can use the tool for the whole duration of your shell session.

$ source activate benchmark
# mdbenchmark should now be usable!
$ mdbenchmark
Usage: mdbenchmark [OPTIONS] COMMAND [ARGS]...

  Generate and run benchmark jobs for GROMACS simulations.

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  analyze   analyze finished benchmark.
  generate  Generate benchmark queuing jobs.
  submit    Start benchmark simulations.

Features

• Generates benchmarks for GROMACS and NAMD simulations (contributions for other MD engines are welcome!).

• Automatically detects the queuing system on your high-performance cluster and submits jobs accordingly.

• Grabs performance from the output logs and creates a fancy plot.

• Can benchmark systems either with or without GPUs.

Usage

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!

Benchmark generation for GROMACS

Assuming your TPR file is called protein.tpr and you want to run benchmarks with the module gromacs/5.1.4-plumed2.3 on up to ten nodes, run the following command:

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

To run benchmarks on GPUs simply 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 of GROMACS:

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

Benchmark generation for NAMD

NAMD support is experimental. If you encounter any problems or bugs, we would appreciate to hear from you.

Generating benchmarks for NAMD follows a similar process to GROMACS. Assuming the NAMD configuration file is called protein.namd, you will also need the corresponding protein.pdb and protein.psf inside the same folder. Warning: Please be aware that all paths given in the protein.namd file must be absolute paths. This ensures that MDBenchmark does not destroy paths when copying files around during benchmark generation.

In analogy to the GROMACS setup, you can execute the following command to generate benchmarks for a module named namd/2.12:

$ mdbenchmark generate --name protein --module namd/2.12 --max-nodes 10

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

$ mdbenchmark generate --name protein --module namd/2.12-gpu --max-nodes 10 --gpu

Be aware that you will need to specify NAMD modules when running GPU and non-GPU benchmarks! To work with GPUs, NAMD needs to be compiled separately and will be probably named differently on the host of your choice. Using the --gpu option on non-GPU builds of NAMD may lead to poorer performance and erroneous results.

Usage with multiple modules

It is possible to generate benchmarks for different MD engines with a single command:

$ mdbenchmark generate --name protein --module namd/2.12 --module gromacs/2016.3 --max-nodes 10

Benchmark submission

After you generated all benchmarks, you can submit them at once:

$ mdbenchmark submit

To start specific benchmarks separately, use the --directory option and specify the corresponding folder:

$ mdbenchmark submit --directory draco_gromacs/5.1.4-plumed2.3

Benchmark analysis

As soon as the benchmarks have been submitted you can run the analysis script via mdbenchmark analysis. When at least one system has finished, the script will produce a .csv output file or a plot for direct usage (via the --plot option).

Note: The plotting function currently only allows to plot a CPU and GPU benchmark from the same module. We are working on fixing this. If you want to compare different modules with each other, either use the --directory option to generate separate plots or create your own plot from the provided CSV file.

$ mdbenchmark analyze
                   gromacs  nodes  ns/day  run time [min]    gpu        host  ncores
0  gromacs/5.1.4-plumed2.3      1  10.878              15  False       draco      32
1  gromacs/5.1.4-plumed2.3      2   21.38              15  False       draco      64
2  gromacs/5.1.4-plumed2.3      3  34.033              15  False       draco      96
3  gromacs/5.1.4-plumed2.3      4  40.274              15  False       draco     128
4  gromacs/5.1.4-plumed2.3      5   51.71              15  False       draco     160

Defining Host Templates

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. Otherwise you can point MDBenchmark to a specific template by providing its name via the --host option.

Assuming you created a new host template in your home directory ~/.config/MDBenchmark/my_custom_hostfile:

$ mdbenchmark generate protein --host my_custom_hostfile --module gromacs/5.1.4-plumed2.3

Here is an example job template 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 passes the following variables to each template:

Value	Description
name	Name of the TPR file
gpu	Boolean that is true, if GPUs are requested
module	Name of the module to load
n_nodes	Maximal number of nodes to run on
time	Benchmark run time in minutes
formatted_time	Run time for the queuing system in human readable format (HH:MM:SS)

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

MDBenchmark will look for user templates in the xdg config folders defined by the environment variables XDG_CONFIG_HOME and XDG_CONFIG_DIRS which by default are set to $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.

Contributing

Contributions to the project are welcome! Information on how to contribute to the project can be found in CONTRIBUTING.md and DEVELOPER.rst.