<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi,</div><div><br></div><div>I agree. A more thorough cleanup of the code, which is a very good idea, would take (me)longer than a week or so. That said, I'm going through the code now to figure out the source of an error so I guess I could clean up the code in the meantime. But as I said, it may take longer than a week so that means that it will not go into 4.6 then.</div><div><br></div><div>Best,</div><div><br></div><div>Erik</div><br><div><div>19 jun 2012 kl. 08.53 skrev Berk Hess:</div><br class="Apple-interchange-newline"><blockquote type="cite">
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<br><br>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.<br>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.<br><br>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.<br><br>Cheers,<br><br>Berk<br><br><div id="htc_header" style="">----- Reply message -----<br>From: "Erik Marklund" <<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>><br>To: "Discussion list for GROMACS development" <<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>Subject: [gmx-developers] help needed: gmx_hbond cleanup<br>Date: Thu, Jun 14, 2012 15:39<br><br></div><br>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.<div><br></div><div>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?<br><div><br></div><div>Erik</div><div><br><div><div>14 jun 2012 kl. 15.30 skrev Szilárd Páll:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi,<br><br>Although it's a little late, we've just realized that it would be<br>beneficial to have gmx_hbond cleaned up a bit and fixed to adhere to<br>the new OpenMP setup. Would there be anyone willing to pitch in with<br>this say within a week?<br><br>I know we don' twant to accept new features/"features", but this is an<br>essential tool which people do. Moreover, does have OpenMP<br>parallelization, so it only needs cleanup and a bit of adjustments. So<br>we thought with Berk that this can go into 4.6 without interfering<br>with anything if it gets done in time.<br><br>Contact me or Berk if you would like to help!<br><br>Cheers,<br>--<br>Szilárd<br>--<br>gmx-developers mailing list<br><a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to gmx-developers-request@gromacs.org.<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
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<br></div></div></div>-- <br>gmx-developers mailing list<br><a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>http://lists.gromacs.org/mailman/listinfo/gmx-developers<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-developers-request@gromacs.org.</blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
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