[gmx-developers] PME tuning-related hang [was Re: Gromacs 2016.3 (and earlier) freezing up.]

Mon Sep 18 18:34:28 CEST 2017

Hi Szilárd

These runs used 2M huge pages. I will file a redmine shortly.

On a related topic, how difficult would it be to modify GROMACS to support
> 50%
PME nodes?

John

On Fri, Sep 15, 2017 at 6:37 PM, Szilárd Páll <pall.szilard at gmail.com>
wrote:

> Hi John,
>
> Thanks for diagnosing the issue!
>
> We have been aware of this behavior, but been both intentional (as we
> re-scan grids after the first pass at least once more); plus, it's
> also simply been considered a "not too big of a deal" given that in
> general mdrun has very low memory footprint. However, it seems that,
> at least on this particular machine, our assumption was wrong. What is
> the page sizes on Cori KNL?
>
> Can you please file a redmine with your observations?
>
> Thanks,
> --
> Szilárd
>
>
> On Fri, Sep 15, 2017 at 8:25 PM, John Eblen <jeblen at acm.org> wrote:
> > This issue appears to not be a GROMACS problem so much as a problem with
> > "huge pages" that is
> > triggered by PME tuning. PME tuning creates a large data structure for
> every
> > cutoff that it tries, which
> > is replicated on each PME node. These data structures are not freed
> during
> > tuning, so memory usage
> > expands. Normally it is still too small to cause problems. With huge
> pages,
> > however, I get errors from
> > "libhugetlbfs" and very slow runs if more than about five cutoffs are
> > attempted.
> >
> > Sample output on NERSC Cori KNL with 32 nodes. Input system size is
> 248,101
> > atoms.
> >
> > step 0
> > step 100, remaining wall clock time:    24 s
> > step  140: timed with pme grid 128 128 128, coulomb cutoff 1.200: 66.2
> > M-cycles
> > step  210: timed with pme grid 112 112 112, coulomb cutoff 1.336: 69.6
> > M-cycles
> > step  280: timed with pme grid 100 100 100, coulomb cutoff 1.496: 63.6
> > M-cycles
> > step  350: timed with pme grid 84 84 84, coulomb cutoff 1.781: 85.9
> M-cycles
> > step  420: timed with pme grid 96 96 96, coulomb cutoff 1.559: 68.8
> M-cycles
> > step  490: timed with pme grid 100 100 100, coulomb cutoff 1.496: 68.3
> > M-cycles
> > libhugetlbfs [nid08887:140420]: WARNING: New heap segment map at
> > 0x10001200000 failed: Cannot allocate memory
> > libhugetlbfs [nid08881:97968]: WARNING: New heap segment map at
> > 0x10001200000 failed: Cannot allocate memory
> > libhugetlbfs [nid08881:97978]: WARNING: New heap segment map at
> > 0x10001200000 failed: Cannot allocate memory
> >
> > Szilárd, to answer to your questions: This is the verlet scheme. The
> problem
> > happens during tuning, and
> > no problems occur if -notunepme is used. In fact, the best performance
> thus
> > far has been with 50% PME
> > nodes, using huge pages, and '-notunepme'.
> >
> >
> > John
> >
> > On Wed, Sep 13, 2017 at 6:20 AM, Szilárd Páll <pall.szilard at gmail.com>
> > wrote:
> >>
> >> Forking the discussion as now we've learned more about the issue Åke
> >> is reporting and it is quiterather dissimilar.
> >>
> >> On Mon, Sep 11, 2017 at 8:09 PM, John Eblen <jeblen at acm.org> wrote:
> >> > Hi Szilárd
> >> >
> >> > No, I'm not using the group scheme.
> >>
> >>  $ grep -i 'cutoff-scheme' md.log
> >>    cutoff-scheme                  = Verlet
> >>
> >> > The problem seems similar because:
> >> >
> >> > 1) Deadlocks and very slow runs can be hard to distinguish.
> >> > 2) Since Mark mentioned it, I assume he believes PME tuning is a
> >> > possible
> >> >     cause, which is also the cause in my situation.
> >>
> >> Does that mean you tested with "-notunepme" and the excessive memory
> >> usage could not be reproduced? Did the memory usage increase only
> >> during the tuning or did it keep increasing after the tuning
> >> completed?
> >>
> >> > 3) Åke may be experiencing higher-than-normal memory usage as far as I
> >> > know.
> >> >     Not sure how you know otherwise.
> >> > 4) By "successful," I assume you mean the tuning had completed. That
> >> > doesn't
> >> >     mean, though, that the tuning could not be creating conditions
> that
> >> > causes the
> >> >     problem, like an excessively high cutoff.
> >>
> >> Sure. However, it's unlikely that the tuning creates conditions under
> >> which the run proceeds after the after the initial tuning phase and
> >> keeps allocating memory (which is more prone to be the source of
> >> issues).
> >>
> >> I suggest to first rule our the bug I linked and if that's not the
> >> culprit, we can have a closer look.
> >>
> >> Cheers,
> >> --
> >> Szilárd
> >>
> >> >
> >> >
> >> > John
> >> >
> >> > On Mon, Sep 11, 2017 at 1:09 PM, Szilárd Páll <pall.szilard at gmail.com
> >
> >> > wrote:
> >> >>
> >> >> John,
> >> >>
> >> >> In what way do you think your problem is similar? Åke seems to be
> >> >> experiencing a deadlock after successful PME tuning, much later
> during
> >> >> the run, but no excessive memory usage.
> >> >>
> >> >> Do you happen to be using the group scheme with 2016.x (release
> code)?
> >> >>
> >> >> Your issue sounds more like it could be related to the the excessive
> >> >> tuning bug with group scheme fixed quite a few months ago, but it's
> >> >> yet to be released (https://redmine.gromacs.org/issues/2200).
> >> >>
> >> >> Cheers,
> >> >> --
> >> >> Szilárd
> >> >>
> >> >>
> >> >> On Mon, Sep 11, 2017 at 6:50 PM, John Eblen <jeblen at acm.org> wrote:
> >> >> > Hi
> >> >> >
> >> >> > I'm having a similar problem that is related to PME tuning. When it
> >> >> > is
> >> >> > enabled, GROMACS often, but not
> >> >> > always, slows to a crawl and uses excessive amounts of memory.
> Using
> >> >> > "huge
> >> >> > pages" and setting a high
> >> >> > number of PME processes seems to exacerbate the problem.
> >> >> >
> >> >> > Also, occurrences of this problem seem to correlate with how high
> the
> >> >> > tuning
> >> >> > raises the cutoff value.
> >> >> >
> >> >> > Mark, can you give us more information on the problems with PME
> >> >> > tuning?
> >> >> > Is
> >> >> > there a redmine?
> >> >> >
> >> >> >
> >> >> > Thanks
> >> >> > John
> >> >> >
> >> >> > On Mon, Sep 11, 2017 at 10:53 AM, Mark Abraham
> >> >> > <mark.j.abraham at gmail.com>
> >> >> > wrote:
> >> >> >>
> >> >> >> Hi,
> >> >> >>
> >> >> >> Thanks. Was PME tuning active? Does it reproduce if that is
> >> >> >> disabled?
> >> >> >> Is
> >> >> >> the PME tuning still active? How many steps have taken place (at
> >> >> >> least
> >> >> >> as
> >> >> >> reported in the log file but ideally from processes)?
> >> >> >>
> >> >> >> Mark
> >> >> >>
> >> >> >> On Mon, Sep 11, 2017 at 4:42 PM Åke Sandgren
> >> >> >> <ake.sandgren at hpc2n.umu.se>
> >> >> >> wrote:
> >> >> >>>
> >> >> >>> My debugger run finally got to the lockup.
> >> >> >>>
> >> >> >>> All processes are waiting on various MPI operations.
> >> >> >>>
> >> >> >>> Attached a stack dump of all 56 tasks.
> >> >> >>>
> >> >> >>> I'll keep the debug session running for a while in case anyone
> >> >> >>> wants
> >> >> >>> some more detailed data.
> >> >> >>> This is a RelwithDeb build though so not everything is available.
> >> >> >>>
> >> >> >>> On 09/08/2017 11:28 AM, Berk Hess wrote:
> >> >> >>> > But you should be able to get some (limited) information by
> >> >> >>> > attaching a
> >> >> >>> > debugger to an aldready running process with a release build.
> >> >> >>> >
> >> >> >>> > If you plan on compiling and running a new case, use a release
> +
> >> >> >>> > debug
> >> >> >>> > symbols build. That should run as fast as a release build.
> >> >> >>> >
> >> >> >>> > Cheers,
> >> >> >>> >
> >> >> >>> > Berk
> >> >> >>> >
> >> >> >>> > On 2017-09-08 11:23, Åke Sandgren wrote:
> >> >> >>> >> We have, at least, one case that when run over 2 nodes, or
> more,
> >> >> >>> >> quite
> >> >> >>> >> often (always) hangs, i.e. no more output in md.log or
> otherwise
> >> >> >>> >> while
> >> >> >>> >> mdrun still consumes cpu time. It takes a random time before
> it
> >> >> >>> >> happens,
> >> >> >>> >> like 1-3 days.
> >> >> >>> >>
> >> >> >>> >> The case can be shared if someone else wants to investigate.
> I'm
> >> >> >>> >> planning to run it in the debugger to be able to break and
> look
> >> >> >>> >> at
> >> >> >>> >> states when it happens, but since it takes so long with the
> >> >> >>> >> production
> >> >> >>> >> build it is not something i'm looking forward to.
> >> >> >>> >>
> >> >> >>> >> On 09/08/2017 11:13 AM, Berk Hess wrote:
> >> >> >>> >>> Hi,
> >> >> >>> >>>
> >> >> >>> >>> We are far behind schedule for the 2017 release. We are
> working
> >> >> >>> >>> hard
> >> >> >>> >>> on
> >> >> >>> >>> it, but I don't think we can promise a date yet.
> >> >> >>> >>>
> >> >> >>> >>> We have a 2016.4 release planned for this week (might slip to
> >> >> >>> >>> next
> >> >> >>> >>> week). But if you can give us enough details to track down
> your
> >> >> >>> >>> hanging
> >> >> >>> >>> issue, we might be able to fix it in 2016.4.
> >> >> >>> >
> >> >> >>>
> >> >> >>> --
> >> >> >>> Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> >> >> >>> Internet: ake at hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46
> 90-580
> >> >> >>> 14
> >> >> >>> Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
> >> >> >>> --
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