<div dir="ltr">Hi,<div><br></div><div>That's now submitted, so once you rebase on master HEAD, Jenkins should only deliver the pain that your code deserves ;-)</div><div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr">On Tue, Sep 15, 2015 at 11:44 PM Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com">mark.j.abraham@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Sorry, <a href="https://gerrit.gromacs.org/#/c/5095/" target="_blank">https://gerrit.gromacs.org/#/c/5095/</a> is the relevant merge </p>
<p dir="ltr">Mark </p>
<br><div class="gmail_quote"><div dir="ltr">On Tue, 15 Sep 2015 22:20 Szilárd Páll <<a href="mailto:pall.szilard@gmail.com" target="_blank">pall.szilard@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div><div>On Tue, Sep 15, 2015 at 10:11 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>></span> wrote:<br></div></div></div></div><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>When verified, reviewed and merged, <a href="https://gerrit.gromacs.org/#/c/5094/" target="_blank">https://gerrit.gromacs.org/#/c/5094/</a> should resolve this for master branch.</div></div></blockquote><div><br></div></div></div></div><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div>Are you referring to the TSC synchronization issue? The change you liked fixes #1823, a different issue.</div><div><br></div><div><div><div>--<br>Szilárd</div></div></div></div></div></div><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><span><font color="#888888"><div><br></div><div>Mark</div></font></span></div><div><div><br><div class="gmail_quote"><div dir="ltr">On Tue, Sep 15, 2015 at 6:18 PM Szilárd Páll <<a href="mailto:pall.szilard@gmail.com" target="_blank">pall.szilard@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Tue, Sep 15, 2015 at 5:16 PM, Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Hi,<br>
<br>
We didn't realize that modern x86 cpus no longer synchronize clocks between cores. </blockquote><div><br></div></div></div></div><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div>Actually, having read up a bit more, the _opposite_ seems to be the case: on older CPUs there could be a problem, but on newer ones the TSC should be:</div><div>- "constant", i.e. not affected by frequency scaling,</div><div>- "nonstop", i.e. unaffected by CPU ACPI states.</div><div>The "constant_tsc" and "nonstop_tsc" cpuid flags indicate whether these are supported (most AMD and Nehalem+ on Intel).</div><div><br></div><div>Intel seems to call both these cases "invariant TSC" (dev manual section 17.14.1 [1]). Apparently a number sources claim [2,3] that invariant TSC implies that TSC is synchronized (or can be if the BIOS syncs at boot) and the Intel docs seems to suggest this too by claiming that the OS can use TSC for wall clock.</div><div><br></div><div><br></div><div>Based on this the issue you observed could only be caused by something funny with your BIOS (or OS/kernel?). Thoughts?</div><div><br></div><div><br></div><div>Cheers,</div><div>--<br>Szilárd<br></div><div> </div><div><br></div><div>[1] <a href="http://www.intel.com/content/dam/www/public/us/en/documents/manuals/64-ia-32-architectures-software-developer-manual-325462.pdf" target="_blank">http://www.intel.com/content/dam/www/public/us/en/documents/manuals/64-ia-32-architectures-software-developer-manual-325462.pdf</a></div><div><br></div><div>[2] <a href="http://www.gossamer-threads.com/lists/xen/devel/185419" target="_blank">http://www.gossamer-threads.com/lists/xen/devel/185419</a></div><div><br></div><div>[3] <a href="https://software.intel.com/en-us/forums/intel-isa-extensions/topic/289368" target="_blank">https://software.intel.com/en-us/forums/intel-isa-extensions/topic/289368</a></div></div></div></div><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">We should get the fix for this merged asap:<br>
<a href="https://gerrit.gromacs.org/#/c/5091/" rel="noreferrer" target="_blank">https://gerrit.gromacs.org/#/c/5091/</a><br>
<br>
Cheers,<br>
<br>
Berk<span><br>
<br>
On 09/15/2015 05:06 PM, David van der Spoel wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Hi,<br>
<br>
my patch stumbled over this issue in Jenkins:<br>
<br>
Program: gmx mdrun, VERSION 5.2-dev-20150915-ef00eb4-local<br>
Source file: src/gromacs/timing/wallcycle.cpp (line 398)<br>
Function: void subtract_cycles(wallcc_t *, int, int)<br>
<br>
Assertion failed:<br>
Condition: wcc[ewc_main].c >= wcc[ewc_sub].c<br>
Subcounter cannot have more ticks than parent<br>
<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" rel="noreferrer" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
<br>
Any clue? Or is this assertion just overly pedantic?<br>
</blockquote>
<br>
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