[gmx-developers] Gromacs 2016.3 (and earlier) freezing up.

[Åke Sandgren]

As you wish, attached.

On 09/11/2017 05:32 PM, Szilárd Páll wrote:
> It could be helpful if you also shared the log file that the run has
> produced so far.
> --
> Szilárd
> 
> 
> On Mon, Sep 11, 2017 at 5:24 PM, Åke Sandgren <ake.sandgren at hpc2n.umu.se> wrote:
>> 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:
>>> 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
>>> <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,
>>>     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 <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:
>>>     http://www.hpc2n.umu.se
>>>     --
>>>     Gromacs Developers mailing list
>>>
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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
>> --
>> Gromacs Developers mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before posting!
>>
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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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