[gmx-developers] parallel make problems

Alexey Shvetsov alexxy at omrb.pnpi.spb.ru
Fri Apr 5 13:14:10 CEST 2013

Hi Erik

What are underlaying filesystem on this cluster? If it slow or overloaded 
somehow it may lead to parallel make issues. Also it may be related to make 
version (some old versions may expose such behavior). How many make threads do 
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. make -j.
> I reported this to the cluster admins since I had never seen such behaviour
> 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 right
> > 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 timing
> > or other non deterministic factors.
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, 
Gatchina, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru
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