Re: [gmx-developers] help needed: gmx_hbond cleanup

Berk Hess hess at
Tue Jun 19 08:53:39 CEST 2012


g_hbond is a critical tool for Gromacs. As for any tool, all options should give correct output or be removed. I heard from Gerrit that people get different results with different compilations.
Coding wise we should try to avoid different code paths and lots of defines in the code. Ideally the OpenMP and non OpenMP versions should use the same code path and the same functions.

Mainly the code complexity should be significantly reduced. We would rather have basic functionality that works reliably than lots of functionality with unreliable compilation/output.



----- Reply message -----
From: "Erik Marklund" <erikm at>
To: "Discussion list for GROMACS development" <gmx-developers at>
Subject: [gmx-developers] help needed: gmx_hbond cleanup
Date: Thu, Jun 14, 2012 15:39
I might be able to do that. I did the OpenMP parallelization and are going through the code now anyway. I'll just have to think hard about actually having the time to do this within a week.
What is the current restrictions/framework/wrappers/macros for OpenMP in gromacs? Essentially: what do I need to know to adhere to our coding standards in this case?

14 jun 2012 kl. 15.30 skrev Szilárd Páll:Hi,

Although it's a little late, we've just realized that it would be
beneficial to have gmx_hbond cleaned up a bit and fixed to adhere to
the new OpenMP setup. Would there be anyone willing to pitch in with
this say within a week?

I know we don' twant to accept new features/"features", but this is an
essential tool which people do. Moreover, does have OpenMP
parallelization, so it only needs cleanup and a bit of adjustments. So
we thought with Berk that this can go into 4.6 without interfering
with anything if it gets done in time.

Contact me or Berk if you would like to help!

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-----------------------------------------------Erik Marklund, PhDDept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596,    75124 Uppsala, Swedenphone:    +46 18 471 6688        fax: +46 18 511 755erikm at xray.bmc.uu.se
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