GroLogs: A log reader for the software GROMACS

GroLogs was started out of a need to quickly check thet status update of molecular dynamic simulations using GROMACS. By reading the log files and the steps within the log files we can calculate the time in nanoseconds of the simulation using this simple formula

nanoseconds = steps / 500,000

and output to a beautiful table.

Quick Start

First you will need authentication to the cluster or server running the Molecular Dynamics simulation for GROMACS.

First is simple

1. Register your RSA key with the dedicated server so you don't have to be password prompted when SSH'ing into the server

GroLogs class takes 4 arguments

• target_directory - target directory where all your log files for this particular experiment will be
• log_file_name - the name of the log file. Traditionally, I have everything called as md_3.log
• username - the username registered on the cluster or particular machine
• hostname - the hostname or ip address of the target server that we want to extrapolate information.

Initialize the class like so:

log_reader = GroLogs('target_directory/*', 'md_3.log', username, hostname)

and then generate a table to output the results

log_reader.generate_table()

and here is an example of the output:

+-------------------------------------------------------+----------+-----------+
|                   --- File Path ---                   |   Step   | Time (ns) |
+-------------------------------------------------------+----------+-----------+
|  file/path/to/experiment/trial_2/                     | 60947999 |  121.896  |
+-------------------------------------------------------+----------+-----------+
|  file/path/to/experiment/trial_3/                     | 68454999 |  136.91   |
+-------------------------------------------------------+----------+-----------+
|  file/path/to/experiment/trial_3/                     | 28107999 |  56.216   |
+-------------------------------------------------------+----------+-----------+

Announcements

• Work has began! Dec 4th
• 0.0.1 version released Dec 4th LogReader
• 0.0.2 version released -> authentication can be passed in and name changed to GroLogs, more documentation!

Installation

GroLogs is going to be distribute via PyPi and as the content store grows we can expand it to other pieces of software making it accessible to all regardless of what you use. Alternatively, you could have a glance at the source code and copy/paste it yourself.

To install the reader

python -m pip install grologs

Structure ofGroLogs

Currently, the main subpackages are:

• grologs: logreader main class.

Genesis

LogReader was created because I noticed I was using the same variable across multiple scripts and figure it would be useful for folk to have.

• Lead Developer Suliman Sharif

External links