[gmx-developers] On integrating 'progrep' - a command-line utility to show live status, ETA etc. - with GROMACS
erik.lindahl at gmail.com
Mon Nov 30 16:10:38 CET 2020
Sounds like a useful tool - we've thought about adding something like this
However, unfortunately, if it's GPLv3, it means people cannot redistribute
binaries under the (much more permissive) GROMACS LGPLv2 license used by
GROMACS, so while I won't rule out adding optional support, we can't enable
it by default.
On Mon, Nov 30, 2020 at 4:01 PM sdphys_rs Calcutta University <
sdphys_rs at caluniv.ac.in> wrote:
> Hello all,
> I have recently released a command-line utility, called 'progrep'
> (DOI: 10.5281/zenodo.4294762), which is intended to show % completed,
> wall-time remaining (ETA), wall-time elapsed, number of threads, CPU
> usage and speed (Frames Per Second) for any molecular dynamics (MD)
> simulation. 'progrep' works in client+server model. The server can be
> installed in the simulation source code (such as md.cpp in
> src/gromacs/mdrun/) with only 4 extra lines, viz.
> # include <cprogrep.h> // The progrep header for C++ code
> progrep_installer(); //Installs SIGWINCH handler
> progrep_tot=<total number of MD steps>; //Before entering the main loop
> progrep_curr=<current MD step>; //Inside the main loop
> When the 'progrep' command is invoked through terminal, it queries this
> server by sending a SIGWINCH signal at 1s intervals. The server
> handles this signal by writing the current simulation state (just 16
> bytes) atomically to a binary pipe, which the user-invoked client then
> reads, processes and displays. 'progrep' does not interfere with or
> slow down the simulation when not invoked. Even when invoked, the
> overhead is insignificant (only 16 bytes stream output every second).
> The purpose of this mail is to inquire if integration of the
> progrep-server or driver in the official version of GROMACS would be
> useful in your opinion. If GROMACS ships with 'progrep', the end-user
> would be able to track the above-mentioned aspects of live GROMACS
> simulations easily in real-time, any time, without waiting for /
> depending on the md.log updates that only happen once in a while. In
> addition, with the command: progrep list, the user would be able to
> list all active GROMACS simulations with their respective process id,
> start time and login/user name - an empty list indicating all GROMACS
> jobs are complete/terminated.
> 'progrep' can be availed under GPL-v3-or-later from DOI:
> 10.5281/zenodo.4294762 or https://sourceforge.net/projects/progrep/ .
> Sample codes are provided therein to demonstrate how it all works.
> Somajit Dey
> Department of Physics, University of Calcutta
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Erik Lindahl <erik.lindahl at dbb.su.se>
Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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