<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Jun 17, 2013 at 7:59 PM, Roland Schulz <span dir="ltr"><<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</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"><div class="im">On Mon, Jun 17, 2013 at 1:10 PM, Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com">mark.j.abraham@gmail.com</a>> wrote:<br>
><br>
><br>
><br>
> On Mon, Jun 17, 2013 at 6:16 PM, Manuel Nuno Melo <<a href="mailto:m.n.melo@rug.nl">m.n.melo@rug.nl</a>> wrote:<br>
>><br>
</div><div class="im">>> Hi,<br>
>><br>
>> I have also had linking problems when making in parallel. In my case they<br>
>> could be traced back to the option to let GMX download/build its own fftw<br>
>> (-DGMX_BUILD_OWN_FFTW=ON).<br>
>><br>
>> It seems that only one of make's threads starts building fftw, while the<br>
>> others go ahead building/linking GMX. Since fftw compilation is not ready by<br>
>> the time it is needed, GMX linking is botched.<br>
><br>
><br>
</div><div class="im">> Yes, Rossen first showed this to me. I don't know if the underlying issue is<br>
> that the dependency cannot be described properly, or that we're not doing it<br>
> properly. If it's a problem, people are welcome to contribute a fix! :-)<br>
</div>It was working in <a href="https://gerrit.gromacs.org/#/c/1675/12" target="_blank">https://gerrit.gromacs.org/#/c/1675/12</a>. You then<br>
changed how the dependency works in patch set 13. You never replied to<br>
Christophs comment why this was changed (at least I can't find a<br>
reply). Do you remember?</blockquote><div><br></div><div style>I couldn't remember, but gerrit can - I never published a series of responses I made back then, sorry. Now published at <a href="https://gerrit.gromacs.org/1675">https://gerrit.gromacs.org/1675</a></div>
<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"> Otherwise I can change it back as 12 did it<br>
and it should work again.<br></blockquote><div><br></div><div style>It might do, but as I said in those secret drafts the form of patch 12 doesn't work on cmake 2.8.7 because of a bug there in add_library(...GLOBAL) (and I suspect is probably too global, anyway, but this probably does no harm?).</div>
<div style><br></div><div style>So I'm still not sure there's a convenient solution that works in all cases. Compromising the smooth running of a parallel make for someone downloading FFTW seems like the most low-impact problem of the set we could choose to have.</div>
<div style><br></div><div style>Mark</div><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">
<br>
Roland<br>
<br>
><br>
> Mark<br>
<div class=""><div class="h5">><br>
>><br>
>><br>
>> Cheers,<br>
>> Manel<br>
>><br>
>> > Hi,<br>
>> ><br>
>> > I too suspect filesystem issues or clock skews. I think I tested make -j<br>
>> > and make -j 12. The cluster is currently down for maintenance, so I can't<br>
>> > inspect the details at the moment.<br>
>> ><br>
>> > On 5 Apr 2013, at 13:14, Alexey Shvetsov <alexxy at <a href="http://omrb.pnpi.spb.ru" target="_blank">omrb.pnpi.spb.ru</a>><br>
>> > wrote:<br>
>> ><br>
>> > > Hi Erik<br>
>> > ><br>
>> > > What are underlaying filesystem on this cluster? If it slow or<br>
>> > > overloaded<br>
>> > > somehow it may lead to parallel make issues. Also it may be related to<br>
>> > > make<br>
>> > > version (some old versions may expose such behavior). How many make<br>
>> > > threads do<br>
>> > > you issued? I tryed with make -j64 and it builds fine with recent<br>
>> > > cmake<br>
>> > > (2.8.10) and make (3.82) utility.<br>
>> > ><br>
>> > ><br>
>> > > ÷ ÐÉÓØÍÅ ÏÔ 5 ÁÐÒÅÌÑ 2013 11:55:27 ÐÏÌØÚÏ×ÁÔÅÌØ Erik Marklund ÎÁÐÉÓÁÌ:<br>
>> > >> Hi,<br>
>> > >><br>
>> > >> Building gromacs 4.6.1 failed whenever I issued parallel make, i.e.<br>
>> > >> make -j.<br>
>> > >> I reported this to the cluster admins since I had never seen such<br>
>> > >> behaviour<br>
>> > >> before from gromacs' side, and here's their reply. I can't tell<br>
>> > >> whether<br>
>> > >> gromacs is at fault or the cluster.<br>
>> > >><br>
>> > >> Erik<br>
>> > >><br>
>> > >> Begin forwarded message:<br>
>> > >>> Hi,<br>
>> > >>><br>
>> > >>>> I was compiling gromacs on tintin's login node the other day and it<br>
>> > >>>><br>
>> > >>>> šseems that parallel make, i.e. make -j, doesn't work on tintin. I<br>
>> > >>>> šgot linker errors that never showed up when make was run serially.<br>
>> > >>>> šI've never encountered such behaviour before.<br>
>> > >>><br>
>> > >>> Without any more information (or being able to look for actual files<br>
>> > >>> right<br>
>> > >>> now), I'd guess this is a problem with the makefiles rather than the<br>
>> > >>> actual make. It seems somewhat unexpected that CMake would create<br>
>> > >>> makefiles that aren't safe for parallel building, but it does seem<br>
>> > >>> the<br>
>> > >>> most likely culprit (assuming it doesn't let developers add rules<br>
>> > >>> directly to the makefile to work around problems, I don't remember<br>
>> > >>> if<br>
>> > >>> that's possible).<br>
>> > >>><br>
>> > >>> That you only see the problem on tintin can likely be explained by<br>
>> > >>> timing<br>
>> > >>> or other non deterministic factors.<br>
>> > > --<br>
>> > > Best Regards,<br>
>> > > Alexey 'Alexxy' Shvetsov<br>
>><br>
</div></div><div class="im">>> --<br>
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