<div dir="ltr">Hi Somajit,<br><div><br></div><div>Sounds like a useful tool - we've thought about adding something like this ourselves too.</div><div><br></div><div>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.</div><div><br></div><div>Cheers,</div><div><br></div><div>Erik</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Nov 30, 2020 at 4:01 PM sdphys_rs Calcutta University <<a href="mailto:sdphys_rs@caluniv.ac.in">sdphys_rs@caluniv.ac.in</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">Hello all,<br>
<br>
I have recently released a command-line utility, called 'progrep'<br>
(DOI: 10.5281/zenodo.4294762), which is intended to show % completed,<br>
wall-time remaining (ETA), wall-time elapsed, number of threads, CPU<br>
usage and speed (Frames Per Second) for any molecular dynamics (MD)<br>
simulation. 'progrep' works in client+server model. The server can be<br>
installed in the simulation source code (such as md.cpp in<br>
src/gromacs/mdrun/) with only 4 extra lines, viz.<br>
<br>
# include <cprogrep.h> // The progrep header for C++ code<br>
<br>
progrep_installer(); //Installs SIGWINCH handler<br>
<br>
progrep_tot=<total number of MD steps>; //Before entering the main loop<br>
<br>
progrep_curr=<current MD step>; //Inside the main loop<br>
<br>
When the 'progrep' command is invoked through terminal, it queries this<br>
server by sending a SIGWINCH signal at 1s intervals. The server<br>
handles this signal by writing the current simulation state (just 16<br>
bytes) atomically to a binary pipe, which the user-invoked client then<br>
reads, processes and displays. 'progrep' does not interfere with or<br>
slow down the simulation when not invoked. Even when invoked, the<br>
overhead is insignificant (only 16 bytes stream output every second).<br>
<br>
The purpose of this mail is to inquire if integration of the<br>
progrep-server or driver in the official version of GROMACS would be<br>
useful in your opinion. If GROMACS ships with 'progrep', the end-user<br>
would be able to track the above-mentioned aspects of live GROMACS<br>
simulations easily in real-time, any time, without waiting for /<br>
depending on the md.log updates that only happen once in a while. In<br>
addition, with the command: progrep list, the user would be able to<br>
list all active GROMACS simulations with their respective process id,<br>
start time and login/user name - an empty list indicating all GROMACS<br>
jobs are complete/terminated.<br>
<br>
'progrep' can be availed under GPL-v3-or-later from DOI:<br>
10.5281/zenodo.4294762 or <a href="https://sourceforge.net/projects/progrep/" rel="noreferrer" target="_blank">https://sourceforge.net/projects/progrep/</a> .<br>
Sample codes are provided therein to demonstrate how it all works.<br>
<br>
Regards,<br>
-- <br>
Somajit Dey<br>
Department of Physics, University of Calcutta<br>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>Erik Lindahl <<a href="mailto:erik.lindahl@dbb.su.se" target="_blank">erik.lindahl@dbb.su.se</a>></div><div>Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm University</div><div>Science for Life Laboratory, Box 1031, 17121 Solna, Sweden</div></div></div></div></div></div></div></div></div>