February 19th, biweekly GROMACS developer meeting - morning edition

Developers discussions
1

Dear all,

Next GROMACS developer meeting will be Wednesday, February 19, 2025 10:00 AM on zoom. Everybody is welcome.

If there are any specific topics you wish to discuss, just add to the agenda by editing this post or answer it.

Agenda:

  • Restructuring Gromacs I/O framework (planning and design) - Issue #5154, Dmitry Belyakov (4th year student)
  • Release testing
  • Open questions

We usually reserve in total 20 min for each discussion topic. We suggest to use 5-10 min to present the problem and focus on a question that you want to address.

To be able to post or edit wiki post in the developers category, you need to member of the forum and send a request to join the GROMACS developers group using the following link

3

Dear all,
Next GROMACS developer meeting will be Wednesday, February 19, 2025 10:00 AM

Agenda:

  • Restructuring Gromacs I/O framework (planning and design) - Issue #5154, Dmitry Belyakov
  • Release testing, Berk Hess
  • Planning for Quarterly Develepers Meeting in March

Everybody is welcome.

Below zoom details

See you tomorrow

When 2025-02-19 at 11:00 CET

Where: Join our Zoom Meeting (magic link)

Meeting ID: 692 7708 9234
Password: gmxdevs

Join by SIP:
69277089234@zoom.nordu.net

4

The restructuring of the I/O framework Restructuring Gromacs I/O framework (#5154) · Issues · GROMACS / GROMACS · GitLab has been linked to (incomplete) work on modularizing trjconv, where some work on an I/O framework has already been done. We need to see what is there and what is left to do in order to decide how to proceed.

5

For the release testing the agreement is that we need a set of test systems. There is already an issue for this: Develop a validation test suite (#4592) · Issues · GROMACS / GROMACS · GitLab. Then it would be nice to have one or more scripts to automate setting up, running/submission of jobs and extracting the results. Carsten told about a script they use at the MPI, maybe that can be generalized.

We also discuss a list of test targets that can be ticked off. If we have such a list, it would be nice if the results from running a script can automatically tick of boxes.

6

Summary of IO framework discussion:

  • The current implementation lacks a centralized structure, leading to scattered and inefficient handling of structural data.
  • Some tools like PDB2GMX, TRJConv, Modify, and TBR all interact with structural data in a fragmented way.
  • MDRun’s mdoutf structure can be taken for inspiration.
  • Paul Bauer has previously worked on a coordinate IO framework, some old merge requests might already include useful improvements. Note on gitlab
7

About Quarterly Planning Meeting:

  • When: every 3 months – on Wednesday 13-17 CET - next occasion 12 March
  • Aim: to provide an overview on the planned and future developement effort on GROMACS, to build synergy between developer interests and contributions and promote planning and coordination.
  • Format: oral presentations (10 min max) & discussion - hybrid format.
  • Contributions will be grouped according to topic and each topic will be followed by questions and discussions.
    Titles will be collected one week before (5 March) to allow to define the meeting agenda in advance.