[gmx-developers] parallel make problems
Manuel Nuno Melo
m.n.melo at rug.nl
Mon Jun 17 18:16:59 CEST 2013
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
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.
> 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.
> On 5 Apr 2013, at 13:14, Alexey Shvetsov <alexxy at omrb.pnpi.spb.ru>
> > Hi Erik
> > What are underlaying filesystem on this cluster? If it slow or
> > somehow it may lead to parallel make issues. Also it may be related to
> > version (some old versions may expose such behavior). How many make
> > you issued? I tryed with make -j64 and it builds fine with recent cmake
> > (2.8.10) and make (3.82) utility.
> > В письме от 5 апреля 2013 11:55:27 пользователь Erik Marklund написал:
> >> Hi,
> >> Building gromacs 4.6.1 failed whenever I issued parallel make, i.e.
> >> I reported this to the cluster admins since I had never seen such
> >> before from gromacs' side, and here's their reply. I can't tell whether
> >> gromacs is at fault or the cluster.
> >> Erik
> >> Begin forwarded message:
> >>> Hi,
> >>>> I was compiling gromacs on tintin's login node the other day and it
> >>>> seems that parallel make, i.e. make -j, doesn't work on tintin. I
> >>>> got linker errors that never showed up when make was run serially.
> >>>> I've never encountered such behaviour before.
> >>> Without any more information (or being able to look for actual files
> >>> now), I'd guess this is a problem with the makefiles rather than the
> >>> actual make. It seems somewhat unexpected that CMake would create
> >>> makefiles that aren't safe for parallel building, but it does seem the
> >>> most likely culprit (assuming it doesn't let developers add rules
> >>> directly to the makefile to work around problems, I don't remember if
> >>> that's possible).
> >>> That you only see the problem on tintin can likely be explained by
> >>> or other non deterministic factors.
> > --
> > Best Regards,
> > Alexey 'Alexxy' Shvetsov
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