<div dir="ltr">Hi,<br><br>I have also had linking problems when making in parallel. In my case they could be traced back to the option to let GMX download/build its own fftw (-DGMX_BUILD_OWN_FFTW=ON).<br><br>It seems that only one of make's threads starts building fftw, while the others go ahead building/linking GMX. Since fftw compilation is not ready by the time it is needed, GMX linking is botched.<br>
<br>Cheers,<br>Manel<br><br>> Hi,<br>><br>> I too suspect filesystem issues or clock skews. I think I tested make -j and make -j 12. The cluster is currently down for maintenance, so I can't 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">omrb.pnpi.spb.ru</a>> wrote:<br>><br>> > Hi Erik<br>> ><br>> > What are underlaying filesystem on this cluster? If it slow or overloaded<br>
> > somehow it may lead to parallel make issues. Also it may be related to make<br>> > version (some old versions may expose such behavior). How many make threads do<br>> > you issued? I tryed with make -j64 and it builds fine with recent cmake<br>
> > (2.8.10) and make (3.82) utility.<br>> ><br>> ><br>> > В письме от 5 апреля 2013 11:55:27 пользователь Erik Marklund написал:<br>> >> Hi,<br>> >><br>> >> Building gromacs 4.6.1 failed whenever I issued parallel make, i.e. make -j.<br>
> >> I reported this to the cluster admins since I had never seen such behaviour<br>> >> before from gromacs' side, and here's their reply. I can't tell 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>> >>>> seems that parallel make, i.e. make -j, doesn't work on tintin. I<br>> >>>> got linker errors that never showed up when make was run serially.<br>> >>>> I've never encountered such behaviour before.<br>
> >>><br>> >>> Without any more information (or being able to look for actual files 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 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 if<br>
> >>> that's possible).<br>> >>><br>> >>> That you only see the problem on tintin can likely be explained by timing<br>> >>> or other non deterministic factors.<br>> > --<br>
> > Best Regards,<br>> > Alexey 'Alexxy' Shvetsov<br></div>