[gmx-developers] parallel make problems

Roland Schulz roland at utk.edu
Tue Jun 18 18:47:58 CEST 2013


On Tue, Jun 18, 2013 at 11:05 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
>
>
> On Mon, Jun 17, 2013 at 7:59 PM, Roland Schulz <roland at utk.edu> wrote:
>>
>> 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?
>
>
> I couldn't remember, but gerrit can - I never published a series of
> responses I made back then, sorry. Now published at
> https://gerrit.gromacs.org/1675
>
>> Otherwise I can change it back as 12 did it
>> and it should work again.
>
>
> It might do, but as I said in those secret drafts the form of patch 12
> doesn't work on cmake 2.8.7 because of a bug there in add_library(...GLOBAL)
> (and I suspect is probably too global, anyway, but this probably does no
> harm?).
>
> So I'm still not sure there's a convenient solution that works in all cases.
> Compromising the smooth running of a parallel make for someone downloading
> FFTW seems like the most low-impact problem of the set we could choose to
> have.

Probably true. Just doesn't give a good first impression of us to new users.
I think we should also consider for the future whether we really want
to support ~11 unmaintained version of cmake (including for all our
optional features). Downloading cmake is no big deal. They have
binaries to download. And cmake doesn't fix any version but for the
most recent version. So it seems odd that we try to maintain
workarounds for the last ~11 versions which are all unmaintained by
the cmake developers. That seems like it is going to stay a really
annoying maintenance task.

Roland


>
> Mark
>
>>
>> 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
>> >>
>> >> --
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>> >
>> >
>>
>>
>>
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>> 865-241-1537, ORNL PO BOX 2008 MS6309
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>
>



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



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