[gmx-developers] Gromacs 2016.3 (and earlier) freezing up.
ake.sandgren at hpc2n.umu.se
Mon Sep 11 17:24:44 CEST 2017
Command run was
srun gmx_mpi mdrun -ntomp 1 -dlb yes -s ion_channel.tpr
Not sure if PME tuning is on or off (not a use, just a sysadmin).
Starting point is step 0, last checkpoint written is step 29776020.
nstlog is 0 so no other output then checkpoint status.
(This is ion_channel from Erik L. that we used as part of the benchmark
for our system so he might know more of the details)
On 09/11/2017 04:53 PM, Mark Abraham wrote:
> 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)?
> On Mon, Sep 11, 2017 at 4:42 PM Åke Sandgren <ake.sandgren at hpc2n.umu.se
> <mailto: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,
> >> often (always) hangs, i.e. no more output in md.log or otherwise
> >> mdrun still consumes cpu time. It takes a random time before it
> >> 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
> >> 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
> >>> 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 <mailto:ake at hpc2n.umu.se> Phone: +46 90
> 7866134 <tel:090-786%2061%2034> Fax: +46 90-580 14 <tel:090-580%2014>
> Mobile: +46 70 7716134 <tel:070-771%2061%2034> WWW:
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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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