[gmx-developers] parallel make problems

[Roland Schulz]

On Mon, Jun 17, 2013 at 1:10 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
>
>
> On Mon, Jun 17, 2013 at 6:16 PM, Manuel Nuno Melo <m.n.melo at rug.nl> wrote:
>>
>> Hi,
>>
>> 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).
>>
>> 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.
>
>
> Yes, Rossen first showed this to me. I don't know if the underlying issue is
> that the dependency cannot be described properly, or that we're not doing it
> properly. If it's a problem, people are welcome to contribute a fix! :-)
It was working in https://gerrit.gromacs.org/#/c/1675/12. You then
changed how the dependency works in patch set 13. You never replied to
Christophs comment why this was changed (at least I can't find a
reply). Do you remember? Otherwise I can change it back as 12 did it
and it should work again.

Roland

>
> Mark
>
>>
>>
>> Cheers,
>> Manel
>>
>> > Hi,
>> >
>> > 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
>>
>> --
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-developers-request at gromacs.org.
>
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309