[gmx-developers] parallel make problems

Erik Marklund erikm at xray.bmc.uu.se
Fri Apr 5 13:51:24 CEST 2013


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> wrote:

> 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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